//
// 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.


#include <sstream>
#include <boost/lexical_cast.hpp>

#include "ProblemStat.h"
#include "Serializer.h"
#include "AbstractFunction.h"
#include "Operator.h"
#include "SystemVector.h"
#include "DOFMatrix.h"
#include "FiniteElemSpace.h"
#include "Marker.h"
#include "AdaptInfo.h"
#include "io/FileWriter.h"
#include "CoarseningManager.h"
#include "RefinementManager.h"
#include "DualTraverse.h"
#include "Mesh.h"
#include "OEMSolver.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "PeriodicBC.h"
#include "Lagrange.h"
#include "Flag.h"
#include "est/Estimator.h"
#include "io/VtkWriter.h"
#include "io/ValueReader.h"
#include "ProblemStatDbg.h"
#include "Debug.h"

namespace AMDiS {

  using namespace std;
  using boost::lexical_cast;

  ProblemStatSeq::ProblemStatSeq(string nameStr,
				 ProblemIterationInterface *problemIteration)
    : StandardProblemIteration(this),
      name(nameStr),
      nComponents(-1),
      nMeshes(0),
      traverseInfo(0),
      solver(NULL),
      solution(NULL),
      rhs(NULL),
      systemMatrix(NULL),
      useGetBound(true),
      refinementManager(NULL),
      coarseningManager(NULL),
      info(10),
      deserialized(false),
      computeExactError(false),
      boundaryConditionSet(false),
      writeAsmInfo(false)
  {
    Parameters::get(name + "->components", nComponents);
    TEST_EXIT(nComponents > 0)("components not set!\n");    
    estimator.resize(nComponents, NULL);
    marker.resize(nComponents, NULL);
    
    assembleMatrixOnlyOnce.resize(nComponents);
    assembledMatrix.resize(nComponents);
    for (int i = 0; i < nComponents; i++) {
      assembleMatrixOnlyOnce[i].resize(nComponents);
      assembledMatrix[i].resize(nComponents);
      for (int j = 0; j < nComponents; j++) {
	assembleMatrixOnlyOnce[i][j] = false;
	assembledMatrix[i][j] = false;
      }
    }
    
    exactSolutionFcts.resize(nComponents);


    // === Initialize name of components. ===

    componentNames.resize(nComponents, "");
    for (int i = 0; i < nComponents; i++)
      componentNames[i] = "solution[" + lexical_cast<string>(i) + "]";

    Parameters::get(name + "->name", componentNames);
    componentNames.resize(nComponents);

    for (int i = 0; i < nComponents; i++)
      Parameters::get(name + "->name[" + lexical_cast<string>(i) + "]",
		      componentNames[i]);
  }

  void ProblemStatSeq::initialize(Flag initFlag,
				  ProblemStatSeq *adoptProblem,
				  Flag adoptFlag)
  {
    FUNCNAME("ProblemStat::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;

	// 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 refinement/corasening-manager ===
    if (refinementManager != NULL && coarseningManager != NULL) { 
      WARNING("refinement-/coarseningmanager already created\n");
    } else {
      if (initFlag.isSet(CREATE_MESH) || 
          (!adoptFlag.isSet(INIT_MESH) &&
           (initFlag.isSet(INIT_SYSTEM) || initFlag.isSet(INIT_FE_SPACE))))
        createRefCoarseManager();

      if (adoptProblem && 
          (adoptFlag.isSet(INIT_MESH) ||
           adoptFlag.isSet(INIT_SYSTEM) ||
           adoptFlag.isSet(INIT_FE_SPACE))) {
        refinementManager = adoptProblem->refinementManager;
        coarseningManager = adoptProblem->coarseningManager;
      }
    }

    if (refinementManager == NULL || coarseningManager == NULL) 
      WARNING("no refinement-/coarseningmanager 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(NULL);

      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->getEstimators();

    // === create marker ===
    if (initFlag.isSet(INIT_MARKER))
      createMarker();

    if (adoptProblem && adoptFlag.isSet(INIT_MARKER))
      marker = adoptProblem->getMarkers();

    // === 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;
    string serializationFilename = "";
    Parameters::get("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;

      Parameters::get(name + "->input->read serialization", readSerialization);
      Parameters::get(name + "->input->serialization with adaptinfo",
		      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) {
	Parameters::get(name + "->input->serialization filename", 
			serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

	// If AMDiS is compiled for parallel computations, the deserialization is
	// controlled by the parallel problem object.
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
	ifstream in(serializationFilename.c_str());

	// Read the revision number of the AMDiS version which was used to create 
	// the serialization file.
	int revNumber = -1;
	SerUtil::deserialize(in, revNumber);

	deserialize(in);
	in.close();
#endif

	deserialized = true;
      } else {
	int globalRefinements = 0;

	// If AMDiS is compiled for parallel computations, the global refinements are
	// ignored here. Later, each rank will add the global refinements to its 
	// private mesh.
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
	Parameters::get(meshes[0]->getName() + "->global refinements", 
			globalRefinements);
#endif

	bool initMesh = initFlag.isSet(INIT_MESH);

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

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

	// === do global refinements ===

	for (unsigned int i = 0; i < meshes.size(); i++)
	  if (initMesh && meshes[i])
	    refinementManager->globalRefine(meshes[i], globalRefinements);	
      }
    }

    doOtherStuff();
  }


  void ProblemStatSeq::createMesh() 
  {
    FUNCNAME("ProblemStat::createMesh()");

    componentMeshes.resize(nComponents);
    map<int, Mesh*> meshForRefinementSet;

    string meshName("");
    Parameters::get(name + "->mesh", meshName);
    TEST_EXIT(meshName != "")("No mesh name specified for \"%s->mesh\"!\n", 
			      name.c_str());

    int dim = 0;
    Parameters::get(name + "->dim", dim);
    TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
		   name.c_str());

    for (int i = 0; i < nComponents; i++) {
      int refSet = -1;
      Parameters::get(name + "->refinement set[" + lexical_cast<string>(i) + "]", 
		      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];
    }
  }


  void ProblemStatSeq::createRefCoarseManager() 
  {
    FUNCNAME("ProblemStat::createRefCoarseManager()");

    int dim = 0;
    Parameters::get(name + "->dim", dim);
    TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
                   name.c_str());

    switch (dim) {
    case 1:
      refinementManager = new RefinementManager1d();
      coarseningManager = new CoarseningManager1d();
      break;
    case 2:
      refinementManager = new RefinementManager2d();
      coarseningManager = new CoarseningManager2d();
      break;
    case 3:
      refinementManager = new RefinementManager3d();
      coarseningManager = new CoarseningManager3d();
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }


  void ProblemStatSeq::createFeSpace(DOFAdmin *admin)
  {
    FUNCNAME("ProblemStat::createFeSpace()");

    map<pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
    int dim = -1;
    Parameters::get(name + "->dim", dim);
    TEST_EXIT(dim != -1)("no problem dimension specified!\n");

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

    for (int i = 0; i < nComponents; i++) {
      int degree = 1;
      Parameters::get(name + "->polynomial degree[" + 
		      boost::lexical_cast<string>(i) + "]", degree);

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

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

	FiniteElemSpace *newFeSpace = 
	  FiniteElemSpace::provideFeSpace(admin, Lagrange::getLagrange(dim, degree),
					  componentMeshes[i], s.str());
	feSpaceMap[pair<Mesh*, int>(componentMeshes[i], degree)] = newFeSpace;
	feSpaces.push_back(newFeSpace);
      }

      componentSpaces[i] = feSpaceMap[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 ProblemStatSeq::createMatricesAndVectors()
  {
    FUNCNAME("ProblemStat::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);

    for (int i = 0; i < nComponents; i++) {
      (*systemMatrix)[i][i] = new DOFMatrix(componentSpaces[i], 
					    componentSpaces[i], "A_ii");
      (*systemMatrix)[i][i]->setCoupleMatrix(false);

      rhs->setDOFVector(i, new DOFVector<double>(componentSpaces[i], 
						 "rhs[" + lexical_cast<string>(i) + "]"));

      solution->setDOFVector(i, new DOFVector<double>(componentSpaces[i],
      						      componentNames[i]));
      solution->getDOFVector(i)->setCoarsenOperation(COARSE_INTERPOL);
      solution->getDOFVector(i)->set(0.0);
    }
  }


  void ProblemStatSeq::createSolver()
  {
    FUNCNAME("ProblemStat::createSolver()");

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


  void ProblemStatSeq::createEstimator()
  {
    FUNCNAME("ProblemStat::createEstimator()");

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

    for (int i = 0; i < nComponents; i++) {
      TEST_EXIT(estimator[i] == NULL)("estimator already created\n");
      string estName = 
	name + "->estimator[" + boost::lexical_cast<string>(i) + "]";

      // === create estimator ===
      string estimatorType("0");
      Parameters::get(estName, estimatorType);
      EstimatorCreator *estimatorCreator = 
	dynamic_cast<EstimatorCreator*>(CreatorMap<Estimator>::getCreator(estimatorType, estName));
      if (estimatorCreator) {
	estimatorCreator->setName(estName);
	estimatorCreator->setRow(i);
	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 ProblemStatSeq::createMarker()
  {
    FUNCNAME("ProblemStat::createMarker()");

    int nMarkersCreated = 0;

    for (int i = 0; i < nComponents; i++) {
      marker[i] = Marker::createMarker
	(name + "->marker[" + boost::lexical_cast<string>(i) + "]", 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 ProblemStatSeq::createFileWriter()
  {
    FUNCNAME("ProblemStat::createFileWriter()");
  
    // Create one filewriter for all components of the problem
    string numberedName  = name + "->output";
    string filename = "";
    Parameters::get(numberedName + "->filename", filename);

    if (filename != "") {
      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
    for (int i = 0; i < nComponents; i++) {
      numberedName = name + "->output[" + boost::lexical_cast<string>(i) + "]";
      filename = "";
      Parameters::get(numberedName + "->filename", filename);

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

    int writeSerialization = 0;
    Parameters::get(name + "->output->write serialization", writeSerialization);
    if (writeSerialization)
      fileWriters.push_back(new Serializer<ProblemStatSeq>(this));
  }


  void ProblemStatSeq::doOtherStuff()
  {
  }


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

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

    clock_t first = clock();
    
    solver->solveSystem(solverMatrix, *solution, *rhs);

    INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
		  TIME_USED(first, clock()));

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


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

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    double first = MPI::Wtime();
#else
    clock_t first = clock();
#endif

    if (computeExactError) {
      computeError(adaptInfo);
    } else {
      for (int i = 0; i < nComponents; i++) {
	Estimator *scalEstimator = estimator[i];
	
	if (scalEstimator) {
	  traverseInfo.updateStatus();
	  scalEstimator->setTraverseInfo(traverseInfo);
	  scalEstimator->estimate(adaptInfo->getTimestep());

	  adaptInfo->setEstSum(scalEstimator->getErrorSum(), i);
	  adaptInfo->setEstMax(scalEstimator->getErrorMax(), i);

	  if (adaptInfo->getRosenbrockMode() == false) {
	    adaptInfo->setTimeEstSum(scalEstimator->getTimeEst(), i);
	    adaptInfo->setTimeEstMax(scalEstimator->getTimeEstMax(), i);
	  }
	}
      }
    }

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    MPI::COMM_WORLD.Barrier();
    INFO(info, 8)("estimation of the error needed %.5f seconds\n", 
		  MPI::Wtime() - first);
#else
    INFO(info, 8)("estimation of the error needed %.5f seconds\n",
		  TIME_USED(first, clock()));
#endif
  }


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

    TEST_EXIT_DBG(static_cast<unsigned int>(nComponents) == marker.size())
      ("Wrong number of markers!\n");

    Flag markFlag = 0;
    for (int i = 0; i < nComponents; i++)
      if (marker[i])
	markFlag |= marker[i]->markMesh(adaptInfo, componentMeshes[i]);
    
    return markFlag;
  }


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

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

    return refineFlag;
  }


  Flag ProblemStatSeq::coarsenMesh(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemStat::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]);

    return coarsenFlag;
  }


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

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

//     buildAfterCoarsen_sebastianMode(adaptInfo, flag);
//     return;

    if (dualMeshTraverseRequired()) {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
      ERROR_EXIT("Dual mesh assemble does not work in parallel code!\n");
#endif

      dualAssemble(adaptInfo, flag, asmMatrix, asmVector);
      return;
    }

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    double first = MPI::Wtime();
#endif


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


#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    MPI::COMM_WORLD.Barrier();
    INFO(info, 8)("dof compression needed %.5f seconds\n", 
		  MPI::Wtime() - first);

    first = MPI::Wtime();
#else
    clock_t first = clock();
#endif


    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;

  
    traverseInfo.updateStatus();
    // Used to calculate the overall number of non zero entries.
    int nnz = 0;

    for (int i = 0; i < nComponents; i++) {

      MSG("%d DOFs for %s\n", 
	  componentSpaces[i]->getAdmin()->getUsedDofs(), 
	  componentSpaces[i]->getName().c_str());

      rhs->getDOFVector(i)->set(0.0);

      for (int j = 0; j < nComponents; j++) {

	if (writeAsmInfo)
	  MSG("--------- %d %d -------------\n", i, 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 = (asmMatrix ? (*systemMatrix)[i][j] : NULL);

	if (writeAsmInfo && matrix) {
	  for (vector<Operator*>::iterator it = matrix->getOperatorsBegin();
	       it != matrix->getOperatorsEnd(); ++it) {
	    Assembler *assembler = (*it)->getAssembler();
	    if (assembler->getZeroOrderAssembler()) 
	      cout << "ZOA: " << assembler->getZeroOrderAssembler()->getName() << endl;
	    if (assembler->getFirstOrderAssembler(GRD_PSI)) 
	      cout << "FOA GRD_PSI: " << assembler->getFirstOrderAssembler(GRD_PSI)->getName() << endl;
	    if (assembler->getFirstOrderAssembler(GRD_PHI)) 
	      cout << "FOA GRD_PHI: " << assembler->getFirstOrderAssembler(GRD_PHI)->getName() << endl;
	    if (assembler->getSecondOrderAssembler()) 
	      cout << "SOA: " << assembler->getSecondOrderAssembler()->getName() << endl;
	  }
	}

	if (matrix) 
	  matrix->calculateNnz();
	
	// 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;
	} else if (matrix) {
	  matrix->getBaseMatrix().
	    change_dim(componentSpaces[i]->getAdmin()->getUsedSize(), 
		       componentSpaces[j]->getAdmin()->getUsedSize());

	  set_to_zero(matrix->getBaseMatrix());
	}

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
	if (!matrix || !assembleMatrix)
	  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) {
	  if (matrix)
	    nnz += matrix->getBaseMatrix().nnz();

	  continue;
	}

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

	// 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);
      
	assembledMatrix[i][j] = true;

	if (assembleMatrix)
	  matrix->finishInsertion();

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

	if (matrix)
	  nnz += matrix->getBaseMatrix().nnz();
      }
      


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

    if (asmMatrix) {
      solver->setMultipleRhs(false);
      solverMatrix.setMatrix(*systemMatrix);

      INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
    } else {
      solver->setMultipleRhs(true);
    }


#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    MPI::COMM_WORLD.Barrier();
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  MPI::Wtime() - first);
#else
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
#endif
  }


  void ProblemStatSeq::buildAfterCoarsen_sebastianMode(AdaptInfo *adaptInfo, Flag flag)
  {
    FUNCNAME("ProblemStat::buildAfterCoarsen()");

    clock_t first = clock();

    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;

    traverseInfo.updateStatus();

    // Used to calculate the overall number of non zero entries.
    int nnz = 0;  


    /// === INITIALIZE ===

    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++) {
	// 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 (matrix) 
	  matrix->calculateNnz();
	
	// 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;
	} else if (matrix) {
	  matrix->getBaseMatrix().
	    change_dim(componentSpaces[i]->getAdmin()->getUsedSize(), 
		       componentSpaces[j]->getAdmin()->getUsedSize());

	  set_to_zero(matrix->getBaseMatrix());	  
	}

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
	if (!matrix || !assembleMatrix)
	  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) {
	  if (matrix)
	    nnz += matrix->getBaseMatrix().nnz();

	  continue;
	}

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

	if (matrix && assembleMatrix) 
	  matrix->startInsertion(matrix->getNnz());
      }
    }

    // === TRAVERSE ===

    Mesh *mesh = componentMeshes[0];
    const FiniteElemSpace *feSpace = componentSpaces[0];
    const BasisFunction *basisFcts = feSpace->getBasisFcts();
    ElementMatrix elMat(basisFcts->getNumber(), basisFcts->getNumber());
    ElementMatrix tmpElMat(elMat);
    ElementVector elVec(basisFcts->getNumber());
    ElementVector tmpElVec(elVec);
    TraverseStack stack;
    BoundaryType *bound = 
      useGetBound ? new BoundaryType[basisFcts->getNumber()] : NULL;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
    while (elInfo) {
      if (useGetBound)
	basisFcts->getBound(elInfo, bound);

      for (map<Operator*, vector<OperatorPos> >::iterator opIt = operators.begin();
	   opIt != operators.end(); ++opIt) {
	if (opIt->first->getNeedDualTraverse() == true)
	  continue;

	if (opFlags[opIt->first].isSet(Operator::MATRIX_OPERATOR)) {
	  set_to_zero(elMat);
	  opIt->first->getElementMatrix(elInfo, elMat, 1.0);
	}
	if (opFlags[opIt->first].isSet(Operator::VECTOR_OPERATOR)) {
	  set_to_zero(elVec);
	  opIt->first->getElementVector(elInfo, elVec, 1.0);
	}
	
	for (vector<OperatorPos>::iterator posIt = opIt->second.begin();
	     posIt != opIt->second.end(); ++posIt) {

	  if (posIt->operatorType.isSet(Operator::MATRIX_OPERATOR)) {
	    if (!posIt->factor || *(posIt->factor) == 1.0) {
	      (*systemMatrix)[posIt->row][posIt->col]->addElementMatrix(elMat, bound, elInfo, NULL);
	    } else {
	      tmpElMat = *(posIt->factor) * elMat;
	      (*systemMatrix)[posIt->row][posIt->col]->addElementMatrix(tmpElMat, bound, elInfo, NULL);
	    }
	  }
	  
	  if (posIt->operatorType.isSet(Operator::VECTOR_OPERATOR)) {
	    if (!posIt->factor || *(posIt->factor) == 1.0) {
	      rhs->getDOFVector(posIt->row)->addElementVector(1.0, elVec, bound, elInfo);
	    } else {
	      tmpElVec = *(posIt->factor) * elVec;
	      rhs->getDOFVector(posIt->row)->addElementVector(1.0, tmpElVec, bound, elInfo);
	    }
	  }
	}
      }

      elInfo = stack.traverseNext(elInfo);
    } 
      
    if (useGetBound)
      delete [] bound;

    // === FINELIZE ===

    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	bool assembleMatrix = true;
	DOFMatrix *matrix = (*systemMatrix)[i][j];

	if (assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j])
	  assembleMatrix = false;
	if (!matrix || !assembleMatrix)
	  assembleMatrix = false;
	if (!assembleMatrix && i != j)
	  continue;

	assembledMatrix[i][j] = true;

	if (assembleMatrix) {
	  matrix->removeRowsWithDBC(matrix->getApplyDBCs());
	  matrix->finishInsertion();
	}
 	if (assembleMatrix && matrix->getBoundaryManager())
 	  matrix->getBoundaryManager()->exitMatrix(matrix);
	if (matrix)
	  nnz += matrix->getBaseMatrix().nnz();
      }

      assembleBoundaryConditions(rhs->getDOFVector(i),
				 solution->getDOFVector(i),
				 componentMeshes[i],
				 assembleFlag);     
    }

    solverMatrix.setMatrix(*systemMatrix);

    INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));
  }


  bool ProblemStatSeq::dualMeshTraverseRequired()
  {
    FUNCNAME("ProblemStat::dualMeshTraverseRequired()");

    TEST_EXIT(meshes.size() <= 2)("More than two meshes are not yet supported!\n");

    return (meshes.size() == 2);
  }
  

  void ProblemStatSeq::dualAssemble(AdaptInfo *adaptInfo, Flag flag, 
				    bool asmMatrix, bool asmVector)
  {
    FUNCNAME("ProblemStat::dualAssemble()");

    TEST_EXIT(asmVector)("Not yet implemented!\n");

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


    clock_t first = clock();
    
    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;

    traverseInfo.updateStatus();

    if (writeAsmInfo) {
      MSG("TraverseInfo:\n");
      for (int i = 0; i < nComponents; i++) {
	MSG("  component %d:   difAuxSpace = %d\n", i, traverseInfo.difAuxSpace(i));
	
	for (int j = 0; j < nComponents; j++) {
	  MSG("  component %d-%d:  difAuxSpace = %d\n", 
	      i, j, traverseInfo.difAuxSpace(i, j));
	}
      }
    }

    // Used to calculate the overall number of non zero entries.
    int nnz = 0;

    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 (writeAsmInfo)
	  cout << "-------" << i << " " << j << "----------------" << endl;

	// 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 = (asmMatrix ? (*systemMatrix)[i][j] : NULL);

	if (writeAsmInfo && matrix) {
	  for (vector<Operator*>::iterator it = matrix->getOperatorsBegin();
	       it != matrix->getOperatorsEnd(); ++it) {
	    Assembler *assembler = (*it)->getAssembler();
	    if (assembler->getZeroOrderAssembler()) 
	      cout << "ZOA: " << assembler->getZeroOrderAssembler()->getName() << endl;
	    if (assembler->getFirstOrderAssembler(GRD_PSI)) 
	      cout << "FOA GRD_PSI: " << assembler->getFirstOrderAssembler(GRD_PSI)->getName() << endl;
	    if (assembler->getFirstOrderAssembler(GRD_PHI)) 
	      cout << "FOA GRD_PHI: " << assembler->getFirstOrderAssembler(GRD_PHI)->getName() << endl;
	    if (assembler->getSecondOrderAssembler()) 
	      cout << "SOA: " << assembler->getSecondOrderAssembler()->getName() << endl;
	  }
	}

	if (matrix) 
	  matrix->calculateNnz();
	
	// 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;
	} else if (matrix) {
	  matrix->getBaseMatrix().
	    change_dim(componentSpaces[i]->getAdmin()->getUsedSize(), 
		       componentSpaces[j]->getAdmin()->getUsedSize());

	  set_to_zero(matrix->getBaseMatrix());
	  matrix->startInsertion(matrix->getNnz());

	  if (matrix->getBoundaryManager())
	    matrix->getBoundaryManager()->initMatrix(matrix);
	}

	// If there is no DOFMatrix, e.g., if it is completly 0, do not assemble.
	if (!matrix || !assembleMatrix)
	  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)
	  if (matrix)
	    nnz += matrix->getBaseMatrix().nnz();

	if (matrix && !assembleMatrix) {
	  ERROR_EXIT("Not yet implemented!\n");
	}
      }
    }

    TEST_EXIT(meshes.size() == 2)("There is something wrong!\n");

    const BasisFunction *basisFcts = componentSpaces[0]->getBasisFcts();
    BoundaryType *bound = 
      useGetBound ? new BoundaryType[basisFcts->getNumber()] : NULL;

    DualTraverse dualTraverse;
    DualElInfo dualElInfo;
    int oldElIndex0 = -1;
    int oldElIndex1 = -1;
    dualTraverse.setFillSubElemMat(true, basisFcts);
    bool cont = dualTraverse.traverseFirst(meshes[0], meshes[1], -1, -1, 
					   assembleFlag, assembleFlag, dualElInfo);

    while (cont) {     
      bool newEl0 = (dualElInfo.rowElInfo->getElement()->getIndex() != oldElIndex0);
      bool newEl1 = (dualElInfo.colElInfo->getElement()->getIndex() != oldElIndex1);
      oldElIndex0 = dualElInfo.rowElInfo->getElement()->getIndex();
      oldElIndex1 = dualElInfo.colElInfo->getElement()->getIndex();      

      for (int i = 0; i < nComponents; i++) {
	for (int j = 0; j < nComponents; j++) {
	  DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);

	  if (!matrix)
	    continue;	  

	  if (traverseInfo.eqSpaces(i, j)) {

	    ElInfo *elInfo = NULL;	    
	    if (componentMeshes[i] == meshes[0] && newEl0)
	      elInfo = dualElInfo.rowElInfo;	    
	    if (componentMeshes[i] == meshes[1] && newEl1)
	      elInfo = dualElInfo.colElInfo;
	  

	    if (elInfo != NULL) { 
	      if (useGetBound)
		basisFcts->getBound(elInfo, bound);
	      
	      if (matrix)
		matrix->assemble(1.0, elInfo, bound);
	      
	      if (i == j)
		rhs->getDOFVector(i)->assemble(1.0, elInfo, bound);
	    }

	    ElInfo *mainElInfo, *auxElInfo;
	    if (traverseInfo.getRowFeSpace(i)->getMesh() == meshes[0]) {
	      mainElInfo = dualElInfo.rowElInfo;
	      auxElInfo = dualElInfo.colElInfo;
	    } else {
	      mainElInfo = dualElInfo.colElInfo;
	      auxElInfo = dualElInfo.rowElInfo;
	    }

	    if (useGetBound && mainElInfo != elInfo)
	      basisFcts->getBound(mainElInfo, bound);
	    
 	    if (traverseInfo.difAuxSpace(i) && i == j)
 	      rhs->getDOFVector(i)->assemble2(1.0, mainElInfo, auxElInfo,
 					      dualElInfo.smallElInfo, 
					      dualElInfo.largeElInfo, bound);	    

 	    if (traverseInfo.difAuxSpace(i, j) && matrix)
 	      matrix->assemble2(1.0, mainElInfo, auxElInfo,
 				dualElInfo.smallElInfo, dualElInfo.largeElInfo, bound);	    

	    if (matrix && matrix->getBoundaryManager())
	      matrix->getBoundaryManager()->fillBoundaryConditions(mainElInfo, matrix);	

	  } else {

	    TEST_EXIT_DBG(traverseInfo.getStatus(i, j) != 
			  SingleComponentInfo::DIF_SPACES_WITH_DIF_AUX)
	      ("Not yet supported!\n");

	    ElInfo *rowElInfo, *colElInfo;
	    if (componentMeshes[i] == meshes[0]) {
	      rowElInfo = dualElInfo.rowElInfo;
	      colElInfo = dualElInfo.colElInfo;
	    } else {
	      rowElInfo = dualElInfo.colElInfo;
	      colElInfo = dualElInfo.rowElInfo;
	    }
	    
	    if (useGetBound)
	      basisFcts->getBound(rowElInfo, bound);	      
	    
	    if (matrix) {
 	      matrix->assemble(1.0, rowElInfo, colElInfo, 
 			       dualElInfo.smallElInfo, dualElInfo.largeElInfo, bound);
	      
	      if (matrix->getBoundaryManager())
		matrix->getBoundaryManager()->fillBoundaryConditions(rowElInfo, matrix);
	    }
	    
 	    if (i == j)
 	      rhs->getDOFVector(i)->assemble(1.0, rowElInfo, bound);	    
	  }	  
	}
      }

      cont = dualTraverse.traverseNext(dualElInfo);
    }


    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++) {
	DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);

	if (!matrix)
	  continue;

	matrix->removeRowsWithDBC(matrix->getApplyDBCs());      
	matrix->finishInsertion();

 	if (matrix->getBoundaryManager())
 	  matrix->getBoundaryManager()->exitMatrix(matrix);	

	nnz += matrix->getBaseMatrix().nnz();	 
      }

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

    solverMatrix.setMatrix(*systemMatrix);

    INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);

    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", 
		  TIME_USED(first, clock()));    
  }


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

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    double first = MPI::Wtime();
#else
    clock_t first = clock();
#endif

    for (int i = 0; i < static_cast<int>(fileWriters.size()); i++)
      fileWriters[i]->writeFiles(adaptInfo, force);

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
    MPI::COMM_WORLD.Barrier();
    INFO(info, 8)("writeFiles needed %.5f seconds\n",
		  MPI::Wtime() - first);
#else
    INFO(info, 8)("writeFiles needed %.5f seconds\n",
		  TIME_USED(first, clock()));
#endif
  }


  void ProblemStatSeq::writeFiles(AdaptInfo &adaptInfo, bool force) 
  {
    writeFiles(&adaptInfo, force);
  }


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

    solution->interpol(fct);
  }


  void ProblemStatSeq::addMatrixOperator(Operator *op, int i, int j,
					 double *factor, double *estFactor)
  {
    FUNCNAME("ProblemStat::addMatrixOperator()");

    TEST_EXIT(i < nComponents && j < nComponents)
      ("Cannot add matrix operator at position %d/%d. The stationary problem has only %d components!\n",
       i, j, nComponents);

    TEST_EXIT(!boundaryConditionSet)
      ("Do not add operators after boundary conditions were set!\n");
   
    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());

      if (estimator[i])
	estimator[i]->setNewMatrix(j, (*systemMatrix)[i][j]);
    }    

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

    traverseInfo.getMatrix(i, j).setAuxFeSpaces(op->getAuxFeSpaces()); 

    for (std::set<const FiniteElemSpace*>::iterator it = op->getAuxFeSpaces().begin();
	 it != op->getAuxFeSpaces().end(); ++it) {
      if ((*it)->getMesh() != componentSpaces[i]->getMesh() ||
	  (*it)->getMesh() != componentSpaces[j]->getMesh()) {
	op->setNeedDualTraverse(true);
	break;
      }          
    } 

    OperatorPos opPos = {i, j, factor, estFactor, Operator::MATRIX_OPERATOR};
    operators[op].push_back(opPos);
    opFlags[op].setFlag(Operator::MATRIX_OPERATOR);
  }


  void ProblemStatSeq::addMatrixOperator(Operator &op, int i, int j,
					 double *factor, double *estFactor)
  {
    addMatrixOperator(&op, i, j, factor, estFactor);
  }


  void ProblemStatSeq::addVectorOperator(Operator *op, int i, 
					 double *factor, double *estFactor)	
  {
    FUNCNAME("ProblemStat::addVectorOperator()");

    TEST_EXIT(i < nComponents)
      ("Cannot add vector operator at position %d. The stationary problem has only %d components!\n",
       i, nComponents);

    TEST_EXIT(!boundaryConditionSet)
      ("Do not add operators after boundary conditions were set!\n");

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

    traverseInfo.getVector(i).setAuxFeSpaces(op->getAuxFeSpaces()); 

    for (std::set<const FiniteElemSpace*>::iterator it = op->getAuxFeSpaces().begin();
	 it != op->getAuxFeSpaces().end(); ++it) {
      if ((*it)->getMesh() != componentSpaces[i]->getMesh()) {     
	op->setNeedDualTraverse(true);
	break;      
      }    
    }

    OperatorPos opPos = {i, -1, factor, estFactor, Operator::VECTOR_OPERATOR};
    operators[op].push_back(opPos);
    opFlags[op].setFlag(Operator::VECTOR_OPERATOR);
  }


  void ProblemStatSeq::addVectorOperator(Operator &op, int i, 
					 double *factor, double *estFactor)	
  {
    addVectorOperator(&op, i, factor, estFactor);
  }


  void ProblemStatSeq::addDirichletBC(BoundaryType type, int row, int col,
				      AbstractFunction<double, WorldVector<double> >* b)
  {
    FUNCNAME("ProblemStat::addDirichletBC()");

    TEST_EXIT(row >= 0 && row < nComponents)("Wrong row number: %d\n", row);
    TEST_EXIT(col >= 0 && col < nComponents)("Wrong col number: %d\n", col);

    boundaryConditionSet = true;

    DirichletBC *dirichletApply = 
      new DirichletBC(type, b, componentSpaces[row], componentSpaces[col], true);
    DirichletBC *dirichletNotApply = 
      new DirichletBC(type, b, componentSpaces[row], componentSpaces[col], false);

    for (int i = 0; i < nComponents; i++)
      if (systemMatrix && (*systemMatrix)[row][i]) {
	if (i == col)
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletApply);
	else
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletNotApply);
      }	

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


  void ProblemStatSeq::addDirichletBC(BoundaryType type, int row, int col,
				      DOFVector<double> *vec)
  {
    FUNCNAME("ProblemStat::addDirichletBC()");

    TEST_EXIT(row >= 0 && row < nComponents)("Wrong row number: %d\n", row);
    TEST_EXIT(col >= 0 && col < nComponents)("Wrong col number: %d\n", col);

    boundaryConditionSet = true;

    DirichletBC *dirichletApply = new DirichletBC(type, vec, true);
    DirichletBC *dirichletNotApply = new DirichletBC(type, vec, false);

    for (int i = 0; i < nComponents; i++)
      if (systemMatrix && (*systemMatrix)[row][i]) {
	if (i == col)
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletApply);
	else
	  (*systemMatrix)[row][i]->getBoundaryManager()->addBoundaryCondition(dirichletNotApply);
      }

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


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

    boundaryConditionSet = true;

    NeumannBC *neumann = 
      new NeumannBC(type, n, componentSpaces[row], componentSpaces[col]);

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


  void ProblemStatSeq::addNeumannBC(BoundaryType type, int row, int col, 
				    DOFVector<double> *n)
  {
    FUNCNAME("ProblemStat::addNeumannBC()");

    boundaryConditionSet = true;

    NeumannBC *neumann = 
      new NeumannBC(type, n, componentSpaces[row], componentSpaces[col]);

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


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

    boundaryConditionSet = true;

    RobinBC *robin = 
      new RobinBC(type, n, r, componentSpaces[row], componentSpaces[col]);

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


  void ProblemStatSeq::addRobinBC(BoundaryType type, int row, int col, 
				  DOFVector<double> *n,
				  DOFVector<double> *r)
  {
    FUNCNAME("ProblemStat::addRobinBC()");

    boundaryConditionSet = true;

    RobinBC *robin = 
      new RobinBC(type, n, r, componentSpaces[row], componentSpaces[col]);

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


  void ProblemStatSeq::addRobinBC(BoundaryType type, int row, int col, 
				  Operator *n,
				  Operator *r)
  {
    FUNCNAME("ProblemStat::addRobinBC()");

    boundaryConditionSet = true;

    RobinBC *robin = 
      new RobinBC(type, n, r, componentSpaces[row], componentSpaces[col]);

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


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

    boundaryConditionSet = true;

    FiniteElemSpace *feSpace = componentSpaces[row];
    PeriodicBC *periodic = new PeriodicBC(type, feSpace);

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

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


  void ProblemStatSeq::addBoundaryMatrixOperator(BoundaryType type, 
          Operator *op, int row, int col)
  {
    FUNCNAME("ProblemStat::addBoundaryOperator()");

    boundaryConditionSet = true;

    RobinBC *robin = 
      new RobinBC(type, NULL, op, componentSpaces[row], componentSpaces[col]);

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


  void ProblemStatSeq::addBoundaryVectorOperator(BoundaryType type, 
          Operator *op, int row)
  {
    FUNCNAME("ProblemStat::addBoundaryOperator()");

    boundaryConditionSet = true;

    RobinBC *robin = 
      new RobinBC(type, op, NULL, componentSpaces[row]);

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


  void ProblemStatSeq::assembleOnOneMesh(FiniteElemSpace *feSpace, 
					 Flag assembleFlag,
					 DOFMatrix *matrix, 
					 DOFVector<double> *vector)
  {
    FUNCNAME("ProblemStat::assembleOnOnMesh()");

    Mesh *mesh = feSpace->getMesh();
    const BasisFunction *basisFcts = feSpace->getBasisFcts();

    TraverseStack stack;

    BoundaryType *bound = 
      useGetBound ? new BoundaryType[basisFcts->getNumber()] : NULL;

    if (matrix)
      matrix->startInsertion(matrix->getNnz());
    
    if (vector)
      vector->set(0.0);

    // == Traverse mesh and assemble. ==
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
    while (elInfo) {
      if (useGetBound)
	basisFcts->getBound(elInfo, bound);

      if (matrix) {
	matrix->assemble(1.0, elInfo, bound);
	
	// Take the matrix boundary manager from the public matrix,
	// but assemble the boundary conditions on the thread private matrix.
	if (matrix->getBoundaryManager())
	  matrix->getBoundaryManager()->fillBoundaryConditions(elInfo, matrix);
      }
	
      if (vector)
	vector->assemble(1.0, elInfo, bound, NULL);	

      elInfo = stack.traverseNext(elInfo);
    }

    // == Finally, if we have assembled in parallel, we have to add the thread ==
    // == private matrix and vector to the global one.                         ==

    if (matrix)
      matrix->removeRowsWithDBC(matrix->getApplyDBCs());      

    if (useGetBound)
      delete [] bound;     
  }


  void ProblemStatSeq::assembleBoundaryConditions(DOFVector<double> *rhs,
						  DOFVector<double> *solution,
						  Mesh *mesh,
						  Flag assembleFlag)
  {
    FUNCNAME("ProblemStat::assembleBoundaryConditions()");


    // === Initialization of vectors ===

    if (rhs->getBoundaryManager())
      rhs->getBoundaryManager()->initVector(rhs);      
    if (solution->getBoundaryManager())
      solution->getBoundaryManager()->initVector(solution);
    
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
    while (elInfo) {
      if (rhs->getBoundaryManager())
	rhs->getBoundaryManager()->fillBoundaryConditions(elInfo, rhs);
      
      if (solution->getBoundaryManager())
	solution->getBoundaryManager()->fillBoundaryConditions(elInfo, solution);
      
      elInfo = stack.traverseNext(elInfo);
    }    


    // === Finalize vectors ===

    if (rhs->getBoundaryManager())
      rhs->getBoundaryManager()->exitVector(rhs);
    if (solution->getBoundaryManager())
      solution->getBoundaryManager()->exitVector(solution);
  }


  void ProblemStatSeq::writeResidualMesh(int comp, 
					 AdaptInfo *adaptInfo, 
					 string name)
  {
    FUNCNAME("ProblemStat::writeResidualMesh()");

    map<int, double> vec;    
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(this->getMesh(comp),  -1, 
					 Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
    
    while (elInfo) {		  
      vec[elInfo->getElement()->getIndex()] = elInfo->getElement()->getEstimation(comp);
      elInfo = stack.traverseNext(elInfo);
    }

    ElementFileWriter::writeFile(vec, this->getMesh(comp), name);
  }


  void ProblemStatSeq::serialize(ostream &out) 
  {
    FUNCNAME("ProblemStat::serialize()");
   
    for (unsigned int i = 0; i < meshes.size(); i++)
      meshes[i]->serialize(out);

    solution->serialize(out);
  }


  void ProblemStatSeq::deserialize(istream &in) 
  {
    FUNCNAME("ProblemStat::deserialize()");
    if (in.fail())
      ERROR_EXIT("File not found for deserialization!\n");

    for (unsigned int i = 0; i < meshes.size(); i++)
      meshes[i]->deserialize(in);

    solution->deserialize(in);
  }


  void ProblemStatSeq::computeError(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("ProblemStat::computeError()");

    for (int i = 0; i < nComponents; i++) {		
      TEST_EXIT(exactSolutionFcts[i])("No solution function given!\n");

      // Compute the difference between exact and computed solution
      DOFVector<double> *tmp = new DOFVector<double>(componentSpaces[i], "tmp");
      tmp->interpol(exactSolutionFcts[i]);
      double solMax = tmp->absMax();
      *tmp -= *(solution->getDOFVector(i));
      
      MSG("L2    error = %.8e\n", tmp->L2Norm());
      MSG("L-inf error = %.8e\n", tmp->absMax() / solMax);
      
      adaptInfo->setEstSum(tmp->absMax() / solMax, i);
      adaptInfo->setEstMax(tmp->absMax() / solMax, i);
      
      // To set element estimates, compute a vector with the difference
      // between exact and computed solution for each DOF.
      DOFVector<double> *sol = new DOFVector<double>(componentSpaces[i], "tmp");
      sol->interpol(exactSolutionFcts[i]);
      DOFVector<double>::Iterator it1(sol, USED_DOFS);
      DOFVector<double>::Iterator it2(tmp, USED_DOFS);
      for (it1.reset(), it2.reset(); !it1.end(); ++it1, ++it2) {
	if (abs(*it1) <= DBL_TOL || abs(*it2) <= DBL_TOL)
	  *it2 = 0.0;
	else
	  *it2 = abs(*it2 / *it1);
      }

      // Compute estimate for every mesh element
      vector<DegreeOfFreedom> locInd(componentSpaces[i]->getBasisFcts()->getNumber());
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(componentMeshes[i], -1, Mesh::CALL_LEAF_EL);
      while (elInfo) {
	componentSpaces[i]->getBasisFcts()->getLocalIndices(elInfo->getElement(),
							    componentSpaces[i]->getAdmin(),
							    locInd);
	double estimate = 0.0;
	for (int j = 0; j < componentSpaces[i]->getBasisFcts()->getNumber(); j++)
	  estimate += (*tmp)[locInd[j]];

	elInfo->getElement()->setEstimation(estimate, i);
	elInfo->getElement()->setMark(0);
								
	elInfo = stack.traverseNext(elInfo);
      }  
      
      delete tmp;	
      delete sol;
    }						           
  }
  
}