ProblemVec.cc

#include <sstream>

#include "ProblemVec.h"
#include "RecoveryEstimator.h"
#include "Serializer.h"
#include "AbstractFunction.h"
#include "Operator.h"
#include "SystemVector.h"
#include "DOFMatrix.h"
#include "FiniteElemSpace.h"
#include "Estimator.h"
#include "Marker.h"
#include "AdaptInfo.h"
#include "FileWriter.h"
#include "CoarseningManager.h"
#include "RefinementManager.h"
#include "DualTraverse.h"
#include "Mesh.h"
#include "OEMSolver.h"
#include "Preconditioner.h"
#include "MatVecMultiplier.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"
#include "Flag.h"
#include "TraverseParallel.h"
#include "VtkWriter.h"
#include "ValueReader.h"

namespace AMDiS {

  void ProblemVec::initialize(Flag initFlag,
			      ProblemVec *adoptProblem,
			      Flag adoptFlag)
  {
    FUNCNAME("ProblemVec::initialize()");
    
    // === create meshes ===
    if (meshes.size() != 0) { 
      WARNING("meshes already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
	  ((!adoptFlag.isSet(INIT_MESH))&&
	   (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE)))) {
	createMesh();
      } 
      if (adoptProblem && 
	  (adoptFlag.isSet(INIT_MESH) || 
	   adoptFlag.isSet(INIT_SYSTEM) ||
	   adoptFlag.isSet(INIT_FE_SPACE))) {
	meshes = adoptProblem->getMeshes();
	componentMeshes = adoptProblem->componentMeshes;
	refinementManager = adoptProblem->refinementManager;
	coarseningManager = adoptProblem->coarseningManager;

	// If the adopt problem has fewer components than this problem, but only one
	// mesh for all component, than scal up the componentMeshes array.
	if (adoptProblem->getNumComponents() < nComponents) {
	  TEST_EXIT(meshes.size() == 1)("Daran muss ich noch arbeiten!\n");
	  
	  componentMeshes.resize(nComponents);
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++) {
	    componentMeshes[i] = componentMeshes[0];
	  }
	}

      }
    }

    if (meshes.size() == 0) 
      WARNING("no mesh created\n");

    // === create fespace ===
    if (feSpaces.size() != 0) {
      WARNING("feSpaces already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
	  (initFlag.isSet(INIT_SYSTEM)&&!adoptFlag.isSet(INIT_FE_SPACE))) {
	createFESpace();
      } 
      if (adoptProblem &&
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
	feSpaces = adoptProblem->getFESpaces();
	componentSpaces = adoptProblem->componentSpaces;
	traverseInfo = adoptProblem->traverseInfo;

	// If the adopt problem has fewer components than this problem, but only one
	// fe space for all component, than scal up the componentSpaces array.
	if (adoptProblem->getNumComponents() < nComponents) {
	  TEST_EXIT(feSpaces.size() == 1)("Daran muss ich noch arbeiten!\n");
	  
	  componentSpaces.resize(nComponents);
	  for (int i = adoptProblem->getNumComponents(); i < nComponents; i++) {
	    componentSpaces[i] = componentSpaces[0];
	  }
	}

      }
    }

    if (feSpaces.size() == 0) 
      WARNING("no feSpace created\n");

    // === create system ===
    if (initFlag.isSet(INIT_SYSTEM)) {
      createMatricesAndVectors();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
      solution = adoptProblem->getSolution();
      rhs = adoptProblem->getRHS();
      systemMatrix = adoptProblem->getSystemMatrix();
    }

    // === create solver ===
    if (solver) {
      WARNING("solver already created\n");
    } else {
      if (initFlag.isSet(INIT_SOLVER)) {
	createSolver();
      } 
      if (adoptProblem && adoptFlag.isSet(INIT_SOLVER)) {
	TEST_EXIT(!solver)("solver already created\n");
	solver = adoptProblem->getSolver();
      }
    }

    if (!solver) 
      WARNING("no solver created\n");

    // === create estimator ===
    if (initFlag.isSet(INIT_ESTIMATOR)) {
      createEstimator();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR)) {
      estimator = adoptProblem->getEstimator();
    } 

    // === create marker ===
    if (initFlag.isSet(INIT_MARKER)) {
      createMarker();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_MARKER)) {
      marker = adoptProblem->getMarker();
    } 


    // === create file writer ===
    if (initFlag.isSet(INIT_FILEWRITER)) {
      createFileWriter();
    }

    
    // === read serialization and init mesh ===
    
    // There are two possiblities where the user can define a serialization
    // to be read from disk. Either by providing the parameter -rs when executing
    // the program or in the init file. The -rs parameter is always checked first,
    // because it can be added automatically when  rescheduling the program
    // before timeout of the runqueue.

    int readSerialization = 0;
    std::string serializationFilename = "";
    GET_PARAMETER(0, "argv->rs", &serializationFilename);

    // If the parameter -rs is set, we do nothing here, because the problem will be
    // deserialized in the constructor of a following AdaptInstationary initialization.
    if (!serializationFilename.compare("")) {
      int readSerializationWithAdaptInfo = 0;

      GET_PARAMETER(0, name + "->input->read serialization", "%d", 
		    &readSerialization);
      GET_PARAMETER(0, name + "->input->serialization with adaptinfo", "%d",
		    &readSerializationWithAdaptInfo);

      // The serialization file is only read, if the adaptInfo part should not be used.
      // If the adaptInfo part should be also read, the serialization file will be read
      // in the constructor of the AdaptInstationary problem, because we do not have here
      // the adaptInfo object.
      if (readSerialization && !readSerializationWithAdaptInfo) {
	GET_PARAMETER(0, name + "->input->serialization filename", 
		      &serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
	std::ifstream in(serializationFilename.c_str());
	deserialize(in);
	in.close();
      } else {
	int globalRefinements = 0;
	GET_PARAMETER(0, meshes[0]->getName() + "->global refinements", "%d", 
		      &globalRefinements);

	// Initialize the meshes if there is no serialization file.
	for (int i = 0; i < static_cast<int>(meshes.size()); i++)
	  if (initFlag.isSet(INIT_MESH) && meshes[i] && !(meshes[i]->isInitialized()))
	    meshes[i]->initialize();	    

	// === read value file and use it for the mesh values ===
	std::string valueFilename("");
	GET_PARAMETER(0, meshes[0]->getName() + "->value file name", &valueFilename); 
	if (valueFilename.length()) {     
	  ValueReader::readValue(valueFilename,
				 meshes[0],
				 solution->getDOFVector(0),
				 meshes[0]->getMacroFileInfo());
	  meshes[0]->clearMacroFileInfo();
	}

	// === do global refinements ===
	for (int i = 0; i < static_cast<int>(meshes.size()); i++)
	  if (initFlag.isSet(INIT_MESH) && meshes[i])
	    refinementManager->globalRefine(meshes[i], globalRefinements);
      }
    }

    doOtherStuff();
  }

  void ProblemVec::createMesh() 
  {
    FUNCNAME("ProblemVec::createMesh()");

    componentMeshes.resize(nComponents);
    std::map<int, Mesh*> meshForRefinementSet;
    char number[3];

    std::string meshName("");
    GET_PARAMETER(0, name + "->mesh", &meshName);
    TEST_EXIT(meshName != "")("no mesh name specified\n");
    int dim = 0;
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
    TEST_EXIT(dim)("no problem dimension specified!\n");

    for (int i = 0; i < nComponents; i++) {
      sprintf(number, "%d", i);
      int refSet = -1;
      GET_PARAMETER(0, name + "->refinement set[" + number + "]", "%d", &refSet);
      if (refSet < 0) {
	refSet = 0;
      }
      if (meshForRefinementSet[refSet] == NULL) {
	Mesh *newMesh = NEW Mesh(meshName, dim);
	meshForRefinementSet[refSet] = newMesh;
	meshes.push_back(newMesh);
	nMeshes++;
      }
      componentMeshes[i] = meshForRefinementSet[refSet];
    }
    switch(dim) {
    case 1:
      coarseningManager = NEW CoarseningManager1d();
      refinementManager = NEW RefinementManager1d();
      break;
    case 2:
      coarseningManager = NEW CoarseningManager2d();
      refinementManager = NEW RefinementManager2d();
      break;
    case 3:
      coarseningManager = NEW CoarseningManager3d();
      refinementManager = NEW RefinementManager3d();
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

  void ProblemVec::createFESpace()
  {
    FUNCNAME("ProblemVec::createFESpace()");

    std::map< std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
    int dim = -1;
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");

    componentSpaces.resize(nComponents, NULL);
    traverseInfo.resize(nComponents);

    for (int i = 0; i < nComponents; i++) {
      char number[3];
      sprintf(number, "%d", i);
      int degree = 1;
      GET_PARAMETER(0, name + "->polynomial degree[" + number + "]","%d", &degree);

      TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");

      if (feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] == NULL) {
	stringstream s;
	s << name << "->feSpace[" << i << "]";

	FiniteElemSpace *newFESpace = 
	  FiniteElemSpace::provideFESpace(NULL, Lagrange::getLagrange(dim, degree),
					  componentMeshes[i], s.str());
	feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)] = newFESpace;
	feSpaces.push_back(newFESpace);
      }
      componentSpaces[i] = feSpaceMap[std::pair<Mesh*, int>(componentMeshes[i], degree)];
    }

    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	traverseInfo.getMatrix(i, j).setFESpace(componentSpaces[i], componentSpaces[j]);
      }
      traverseInfo.getVector(i).setFESpace(componentSpaces[i]);
    }

    // create dof admin for vertex dofs if neccessary
    for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
      if (meshes[i]->getNumberOfDOFs(VERTEX) == 0) {
	DimVec<int> ln_dof(meshes[i]->getDim(), DEFAULT_VALUE, 0);
	ln_dof[VERTEX]= 1;
	meshes[i]->createDOFAdmin("vertex dofs", ln_dof);      
      }
    }
  }

  void ProblemVec::createMatricesAndVectors()
  {
    FUNCNAME("ProblemVec::createMatricesAndVectors()");

    // === create vectors and system matrix ===

    systemMatrix = NEW Matrix<DOFMatrix*>(nComponents, nComponents);
    systemMatrix->set(NULL);
    rhs = NEW SystemVector("rhs", componentSpaces, nComponents);
    solution = NEW SystemVector("solution", componentSpaces, nComponents);

    char number[10];
    std::string numberedName;
    for (int i = 0; i < nComponents; i++) {
      (*systemMatrix)[i][i] = NEW DOFMatrix(componentSpaces[i], 
					     componentSpaces[i], "A_ii");
      (*systemMatrix)[i][i]->setCoupleMatrix(false);
      sprintf(number, "[%d]", i);
      numberedName = "rhs" + std::string(number);
      rhs->setDOFVector(i, NEW DOFVector<double>(componentSpaces[i], numberedName));
      numberedName = name + std::string(number);
      solution->setDOFVector(i, NEW DOFVector<double>(componentSpaces[i], 
						       numberedName));
      solution->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution->getDOFVector(i)->set(0.0);
    }

    // === create matVec ===
    matVec = NEW StandardMatVec<Matrix<DOFMatrix*>, SystemVector>(systemMatrix);
  }

  void ProblemVec::createSolver()
  {
    FUNCNAME("ProblemVec::createSolver()");

    // === create solver ===
    std::string solverType("no");
    GET_PARAMETER(0, name + "->solver", &solverType);
    OEMSolverCreator<SystemVector> *solverCreator = 
      dynamic_cast<OEMSolverCreator<SystemVector>*>(
						    CreatorMap<OEMSolver<SystemVector> >
						    ::getCreator(solverType)
						    );
    TEST_EXIT(solverCreator)("no solver type\n");
    solverCreator->setName(name + "->solver");
    solver = solverCreator->create();
    solver->initParameters();

    // === create preconditioners ===
    std::string preconType("no");

    PreconditionerScal *scalPrecon;
    PreconditionerVec *vecPrecon = NEW PreconditionerVec(nComponents);

    GET_PARAMETER(0, name + "->solver->left precon", &preconType);
    CreatorInterface<PreconditionerScal> *preconCreator =
      CreatorMap<PreconditionerScal>::getCreator(preconType);

    if (!preconCreator->isNullCreator()) {
      dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	setName(name + "->solver->left precon");

      for (int i = 0; i < nComponents; i++) {
	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	  setSizeAndRow(nComponents, i);
    
	scalPrecon = preconCreator->create();
	for (int j = 0; j < nComponents; j++) {
	  scalPrecon->setMatrix(&(*systemMatrix)[i][j], j);
	}
	vecPrecon->setScalarPrecon(i, scalPrecon);
      }
      leftPrecon = vecPrecon;
    }


    vecPrecon = NEW PreconditionerVec(nComponents);

    GET_PARAMETER(0, name + "->solver->right precon", &preconType);
    preconCreator = 
      CreatorMap<PreconditionerScal>::getCreator(preconType);

    if (!preconCreator->isNullCreator()) {
      dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	setName(name + "->solver->left precon");


      for (int i = 0; i < nComponents; i++) {
	dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
	  setSizeAndRow(nComponents, i);
    
	scalPrecon = preconCreator->create();
	for (int j = 0; j < nComponents; j++) {
	  scalPrecon->setMatrix(&(*systemMatrix)[i][j], j);
	}
	vecPrecon->setScalarPrecon(i, scalPrecon);
      }
      rightPrecon = vecPrecon;
    }


    // === create vector creator ===
    solver->setVectorCreator(NEW SystemVector::Creator("temp",
							componentSpaces, 
							nComponents));
  }

  void ProblemVec::createEstimator()
  {
    FUNCNAME("ProblemVec::createEstimator()");

    // create and set leaf data prototype
    for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
      meshes[i]->setElementDataPrototype
	(NEW LeafDataEstimatableVec(NEW LeafDataCoarsenableVec));
    }  

    char number[3];
    std::string estName;

    for (int i = 0; i < nComponents; i++) {
      TEST_EXIT(estimator[i] == NULL)("estimator already created\n");
      sprintf(number, "%d", i);
      estName = name + "->estimator[" + std::string(number) + "]";

      // === create estimator ===
      std::string estimatorType("no");
      GET_PARAMETER(0, estName, &estimatorType);
      EstimatorCreator *estimatorCreator = 
	dynamic_cast<EstimatorCreator*>(
					CreatorMap<Estimator>::getCreator(estimatorType));
      if (estimatorCreator) {
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
	if (estimatorType == "recovery") {
	  dynamic_cast<RecoveryEstimator::Creator*>(estimatorCreator)->
	    setSolution(solution->getDOFVector(i));
	}
	estimator[i] = estimatorCreator->create();
      }


      if (estimator[i]) {
	for (int j = 0; j < nComponents; j++) {
	  estimator[i]->addSystem((*systemMatrix)[i][j], 
				   solution->getDOFVector(j), 
				   rhs->getDOFVector(j));
	}
      }
    }
  }

  void ProblemVec::createMarker()
  {
    FUNCNAME("ProblemVec::createMarker()");

    std::string numberedName;
    char number[10];
    int nMarkersCreated = 0;

    for (int i = 0; i < nComponents; i++) {
      sprintf(number, "[%d]", i);
      numberedName = name + "->marker" + std::string(number);
      marker[i] = Marker::createMarker(numberedName, i);
      if (marker[i]) {
	nMarkersCreated++;

	// If there is more than one marker, and all components are defined
	// on the same mesh, the maximum marking has to be enabled.
 	if ((nMarkersCreated > 1) && (nMeshes == 1))
 	  marker[i]->setMaximumMarking(true);
      }
    }
  }

  void ProblemVec::createFileWriter()
  {
    FUNCNAME("ProblemVec::createFileWriter()");
  

    // Create one filewriter for all components of the problem
    std::string numberedName  = name + "->output";
    std::string filename = "";
    GET_PARAMETER(0, numberedName + "->filename", &filename);

    if (filename != "") {
      std::vector< DOFVector<double>* > solutionList(nComponents);

      for (int i = 0; i < nComponents; i++) {
	TEST_EXIT(componentMeshes[0] == componentMeshes[i])
	  ("All Meshes have to be equal to write a vector file.\n");

	solutionList[i] = solution->getDOFVector(i);
      }

      fileWriters.push_back(NEW FileWriter(numberedName,
					    componentMeshes[0],
					    solutionList));
    }


    // Create own filewriters for each components of the problem
    char number[10];
    for (int i = 0; i < nComponents; i++) {
      sprintf(number, "[%d]", i);
      numberedName  = name + "->output" + std::string(number);
      filename = "";
      GET_PARAMETER(0, numberedName + "->filename", &filename);

      if (filename != "") {
	fileWriters.push_back(NEW FileWriter(numberedName, 
					      componentMeshes[i], 
					      solution->getDOFVector(i)));
      }
    }


    // Check for serializer
    int writeSerialization = 0;
    GET_PARAMETER(0, name + "->write serialization", "%d", &writeSerialization);
    if (writeSerialization) {
      MSG("Use are using the obsolete parameter: %s->write serialization\n", name.c_str());
      MSG("Please use instead the following parameter: %s->output->write serialization\n", name.c_str());
      ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
    }

    GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
    if (writeSerialization) {
      fileWriters.push_back(NEW Serializer<ProblemVec>(this));
    }
  }

  void ProblemVec::doOtherStuff()
  {
  }

  void ProblemVec::solve(AdaptInfo *adaptInfo, bool fixedMatrix)
  {
    FUNCNAME("Problem::solve()");

    if (!solver) {
      WARNING("no solver\n");
      return;
    }

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    clock_t first = clock();
    int iter = solver->solve(matVec, solution, rhs, leftPrecon, rightPrecon, fixedMatrix);
    
#ifdef _OPENMP
    INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()), omp_get_wtime() - wtime);
#else
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
#endif


    adaptInfo->setSolverIterations(iter);
    adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
    adaptInfo->setSolverTolerance(solver->getTolerance());
    adaptInfo->setSolverResidual(solver->getResidual());
  }

  void ProblemVec::estimate(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::estimate()");

    VtkWriter::writeFile(solution->getDOFVector(0), "test.vtu");

    clock_t first = clock();

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    if (computeExactError) {
      computeError(adaptInfo);
    } else {
      for (int i = 0; i < nComponents; i++) {
	Estimator *scalEstimator = estimator[i];
	
	if (scalEstimator) {
	  scalEstimator->estimate(adaptInfo->getTimestep());
	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);
	  adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
	  adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
	} else {
	  WARNING("no estimator for component %d\n" , i);
	}
      }
    }

#ifdef _OPENMP
    INFO(info, 8)("estimation of the error needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()), omp_get_wtime() - wtime);
#else
    INFO(info, 8)("estimation of the error needed %.5f seconds\n",
		  TIME_USED(first, clock()));

#endif

  }

  Flag ProblemVec::markElements(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::markElements()");

    // to enforce albert-like behavior: refinement even if space tolerance
    // here is reached already because of time adaption
    allowFirstRefinement();

    Flag markFlag = 0;
    for (int i = 0; i < nComponents; i++) {
      if (marker[i]) {
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
      } else {
	WARNING("no marker for component %d\n", i);
      }
    }
    
    return markFlag;
  }

  Flag ProblemVec::refineMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::refineMesh()");

    int nMeshes = static_cast<int>(meshes.size());
    Flag refineFlag = 0;
    for (int i = 0; i < nMeshes; i++) {
      refineFlag |= refinementManager->refineMesh(meshes[i]);
    }
    return refineFlag;
  }

  Flag ProblemVec::coarsenMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemVec::coarsenMesh()");

    int nMeshes = static_cast<int>(meshes.size());
    Flag coarsenFlag = 0;
    for (int i = 0; i < nMeshes; i++) {
      if (adaptInfo->isCoarseningAllowed(i)) {
	coarsenFlag |= coarseningManager->coarsenMesh(meshes[i]);

	WARNING("coarsening for component %d no allowed\n", i);
      }
    }
    return coarsenFlag;
  }

  Flag ProblemVec::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
  {
    FUNCNAME("ProblemVec::oneIteration()");

    if (allowFirstRef) {
      for (int i = 0; i < nComponents; i++) {
	adaptInfo->allowRefinement(true, i);
      }
      allowFirstRef = false;
    } else {
      for (int i = 0; i < nComponents; i++) {
	if (adaptInfo->spaceToleranceReached(i)) {
	  adaptInfo->allowRefinement(false, i);
	} else {
	  adaptInfo->allowRefinement(true, i);	
	}
      }
    }

    return StandardProblemIteration::oneIteration(adaptInfo, toDo);
  }

  void ProblemVec::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
				     bool asmMatrix, bool asmVector)
  {
    FUNCNAME("ProblemVec::buildAfterCoarsen()");

    clock_t first = clock();

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    for (int i = 0; i < static_cast<int>(meshes.size()); i++) {
      meshes[i]->dofCompress();
    }

    Flag assembleFlag = 
      flag | 
      (*systemMatrix)[0][0]->getAssembleFlag() | 
      rhs->getDOFVector(0)->getAssembleFlag()  |
      Mesh::CALL_LEAF_EL                        | 
      Mesh::FILL_COORDS                         |
      Mesh::FILL_DET                            |
      Mesh::FILL_GRD_LAMBDA |
      Mesh::FILL_NEIGH;

    if (useGetBound) {
      assembleFlag |= Mesh::FILL_BOUND;
    }


    for (int i = 0; i < nComponents; i++) {
      MSG("%d DOFs for %s\n", 
	  componentSpaces[i]->getAdmin()->getUsedSize(), 
	  componentSpaces[i]->getName().c_str());

      rhs->getDOFVector(i)->set(0.0);
      for (int j = 0; j < nComponents; j++) {
	if ((*systemMatrix)[i][j]) {
	  // The matrix should not be deleted, if it was assembled before
	  // and it is marked to be assembled only once.
	  if (!(assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) && asmMatrix) {
	    (*systemMatrix)[i][j]->clear();
	  }
	}
      }
    }

    traverseInfo.updateStatus();

    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	// Only if this variable is true, the current matrix will be assembled.	
	bool assembleMatrix = true;
	// The DOFMatrix which should be assembled (or not, if assembleMatrix
	// will be set to false).
	DOFMatrix *matrix = (*systemMatrix)[i][j];

	// If the matrix was assembled before and it is marked to be assembled
	// only once, it will not be assembled.
	if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) {
	  assembleMatrix = false;
	}

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
	if (!matrix) {
	  assembleMatrix = false;
	}

	if (!asmMatrix) {
	  assembleMatrix = false;
	}

	// If the matrix should not be assembled, the rhs vector has to be considered.
	// This will be only done, if i == j. So, if both is not true, we can jump
	// to the next matrix.
	if (!assembleMatrix && i != j) {
	  continue;
	}

	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->initMatrix(matrix);

	if (traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_NO_AUX ||
	    traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_WITH_AUX) {

	  // Row fe space and col fe space are both equal

	  if (traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_NO_AUX ||
	      traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_WITH_AUX) {

	    // The simplest case: either the right hand side has no operaters, no aux
	    // fe spaces, or all aux fe spaces are equal to the row and col fe space.

	    assembleOnOneMesh(componentSpaces[i],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
			      ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);

	  } else if (traverseInfo.getStatus(i) == SingleComponentInfo::EQ_SPACES_WITH_DIF_AUX) {

	    // Row fe space and col fe space are both equal, but right hand side has at
	    // least one another aux fe space. 

	    assembleOnOneMesh(componentSpaces[i],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
			      ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);

	    assembleOnDifMeshes2(componentSpaces[i], 
				 traverseInfo.getAuxFESpace(i, j),
				 assembleFlag,
				 NULL,
				 ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);

	  } else {
	    ERROR_EXIT("Possible? If yes, not yet implemented!\n");
	  }

	} else if (traverseInfo.getStatus(i, j) == SingleComponentInfo::EQ_SPACES_WITH_DIF_AUX) {
	  
	  assembleOnOneMesh(componentSpaces[i],
			    assembleFlag,
			    assembleMatrix ? matrix : NULL,
			    ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);
	  
	  assembleOnDifMeshes2(componentSpaces[i],
			       traverseInfo.getAuxFESpace(i, j),
			       assembleFlag,
			       assembleMatrix ? matrix : NULL,
			       ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);

	} else if (traverseInfo.getStatus(i, j) ==  SingleComponentInfo::DIF_SPACES_NO_AUX ||
		   traverseInfo.getStatus(i, j) ==  SingleComponentInfo::DIF_SPACES_WITH_AUX) {

	  assembleOnDifMeshes(componentSpaces[i], componentSpaces[j],
			      assembleFlag,
			      assembleMatrix ? matrix : NULL,
			      ((i == j) && asmVector) ? rhs->getDOFVector(i) : NULL);	  

	  TEST_EXIT_DBG(matrix->getUsedSize() == componentSpaces[i]->getAdmin()->getUsedSize())
	    ("Assembled matrix has wrong dimension!\n");
	  TEST_EXIT_DBG(matrix->getNumCols() == componentSpaces[j]->getAdmin()->getUsedSize())
	    ("Assembled matrix has wrong dimension!\n");	  

	} else {
	  ERROR_EXIT("Not yet implemented!\n");
	}

	if (assembleMatrix && matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->exitMatrix(matrix);	  
	
	assembledMatrix[i][j] = true;
      }

      // And now assemble boundary conditions on the vectors
      assembleBoundaryConditions(rhs->getDOFVector(i),
				 solution->getDOFVector(i),
				 componentMeshes[i],
				 assembleFlag);
    }

#ifdef _OPENMP
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()), omp_get_wtime() - wtime);
#else
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
#endif
  }

  void ProblemVec::writeFiles(AdaptInfo *adaptInfo, bool force) 
  {
    FUNCNAME("ProblemVec::writeFiles()");

    clock_t first = clock();

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    int i;
    int size = static_cast<int>(fileWriters.size());
#ifdef _OPENMP
#pragma omp parallel for schedule(static, 1)
#endif
    for (i = 0; i < size; i++) {
      fileWriters[i]->writeFiles(adaptInfo, force);
    }
    
#ifdef _OPENMP
    INFO(info, 8)("writeFiles needed %.5f seconds system time / %.5f seconds wallclock time\n",
		  TIME_USED(first, clock()),
		  omp_get_wtime() - wtime);
#else
    INFO(info, 8)("writeFiles needed %.5f seconds\n",
		  TIME_USED(first, clock()));
#endif
  }

  void ProblemVec::interpolInitialSolution(std::vector<AbstractFunction<double, WorldVector<double> >*> *fct) 
  {
    FUNCNAME("ProblemVec::interpolInitialSolution()");

    solution->interpol(fct);
  }

  void ProblemVec::addMatrixOperator(Operator *op, 
				     int i, int j,
				     double *factor,
				     double *estFactor,
				     bool fake)
  {
    FUNCNAME("ProblemVec::addMatrixOperator()");
   
    if (!(*systemMatrix)[i][j]) {
      TEST_EXIT(i != j)("should have been created already\n");
      (*systemMatrix)[i][j] = NEW DOFMatrix(componentSpaces[i], componentSpaces[j], "");
      (*systemMatrix)[i][j]->setCoupleMatrix(true);
      (*systemMatrix)[i][j]->getBoundaryManager()->
	setBoundaryConditionMap((*systemMatrix)[i][i]->getBoundaryManager()->
				getBoundaryConditionMap());
    }    

    (*systemMatrix)[i][j]->addOperator(op, factor, estFactor);

    if (!fake) {    
      traverseInfo.getMatrix(i, j).setAuxFESpaces(op->getAuxFESpaces()); 
      
      for (int k = 0; k < static_cast<int>(op->getAuxFESpaces().size()); k++) {
	if ((op->getAuxFESpaces())[k]->getMesh() != componentSpaces[i]->getMesh() ||
	    (op->getAuxFESpaces())[k]->getMesh() != componentSpaces[j]->getMesh()) {
	  op->setNeedDualTraverse(true);
	  break;
	}
      }    
    } 
  }

  void ProblemVec::addVectorOperator(Operator *op, int i,
				     double *factor,
				     double *estFactor,
				     bool fake)
  {
    FUNCNAME("ProblemVec::addVectorOperator()");

    rhs->getDOFVector(i)->addOperator(op, factor, estFactor);

    if (!fake) {
      traverseInfo.getVector(i).setAuxFESpaces(op->getAuxFESpaces()); 
      
      for (int j = 0; j < static_cast<int>(op->getAuxFESpaces().size()); j++) {
	if ((op->getAuxFESpaces())[j]->getMesh() != componentSpaces[i]->getMesh()) {
	  op->setNeedDualTraverse(true);
	  break;
	}
      }    
    }
  }

  void ProblemVec::addDirichletBC(BoundaryType type, int system,
				  AbstractFunction<double, WorldVector<double> >* b)
  {
    FUNCNAME("ProblemVec::addDirichletBC()");

    DirichletBC *dirichlet = new DirichletBC(type, 
					     b, 
					     componentSpaces[system]);
    for (int i = 0; i < nComponents; i++) {
      if (systemMatrix && (*systemMatrix)[system][i]) {
	(*systemMatrix)[system][i]->getBoundaryManager()->addBoundaryCondition(dirichlet);
      }
    }

    if (rhs)
      rhs->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);

    if (solution)
      solution->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
  }

  void ProblemVec::addNeumannBC(BoundaryType type, int row, int col, 
				AbstractFunction<double, WorldVector<double> > *n)
  {
    FUNCNAME("ProblemVec::addNeumannBC()");

    NeumannBC *neumann = 
      new NeumannBC(type, n, 
		    componentSpaces[row], 
		    componentSpaces[col]);
    if (rhs)
      rhs->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(neumann);
  }

  void ProblemVec::addRobinBC(BoundaryType type, int row, int col, 
			      AbstractFunction<double, WorldVector<double> > *n,
			      AbstractFunction<double, WorldVector<double> > *r)
  {
    FUNCNAME("ProblemVec::addRobinBC()");

    RobinBC *robin = 
      new RobinBC(type, n, r, 
		  componentSpaces[row], 
		  componentSpaces[col]);
    if (rhs)
      rhs->getDOFVector(row)->getBoundaryManager()->addBoundaryCondition(robin);

    if (systemMatrix && (*systemMatrix)[row][col]) {
      (*systemMatrix)[row][col]->getBoundaryManager()->addBoundaryCondition(robin);
    }
  }

  void ProblemVec::addPeriodicBC(BoundaryType type, int row, int col) 
  {
    FUNCNAME("ProblemVec::addPeriodicBC()");

    FiniteElemSpace *feSpace = componentSpaces[row];

    PeriodicBC *periodic = new PeriodicBC(type, feSpace);

    if (systemMatrix && (*systemMatrix)[row][col]) 
      (*systemMatrix)[row][col]->getBoundaryManager()->addBoundaryCondition(periodic);

    if (rhs) 
      rhs->getDOFVector(row)->getBoundaryManager()->
	addBoundaryCondition(periodic);
  }

  void ProblemVec::assembleOnOneMesh(FiniteElemSpace *feSpace, 
				     Flag assembleFlag,
				     DOFMatrix *matrix, DOFVector<double> *vector)
  {
    Mesh *mesh = feSpace->getMesh();
    const BasisFunction *basisFcts = feSpace->getBasisFcts();

#ifdef _OPENMP
    TraverseParallelStack stack;
#else
    TraverseStack stack;
#endif   

#ifdef _OPENMP
#pragma omp parallel
#endif
    {
      BoundaryType *bound = useGetBound ? GET_MEMORY(BoundaryType, basisFcts->getNumber()) : NULL;

      // Create for every thread its private matrix and vector, on that
      // the thread will assemble its part of the mesh.
      DOFMatrix *tmpMatrix = NULL;
      DOFVector<double> *tmpVector = NULL; 

      if (matrix) {
	tmpMatrix = NEW DOFMatrix(matrix->getRowFESpace(), matrix->getColFESpace(), "tmp");

	// Copy the global matrix to the private matrix, because we need the
	// operators defined on the global matrix in the private one. Only the
	// values have to be set to zero.
	*tmpMatrix = *matrix;
	tmpMatrix->clear();
      }

      if (vector) {
	tmpVector = NEW DOFVector<double>(vector->getFESpace(), "tmp");

	// Copy the global vector to the private vector, because we need the
	// operatirs defined on the global vector in the private one. But set
	// the values to zero of the private vector after copying.
	*tmpVector = *vector;
	tmpVector->set(0.0);
      }

      // Because we are using the parallel traverse stack, each thread will
      // traverse only a part of the mesh.
      ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);