//
// 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 <algorithm>
#include <iostream>
#include <fstream>
#include <limits>
#include <stdint.h>
#include <boost/lexical_cast.hpp>
#include <boost/filesystem.hpp>

#include "parallel/MeshDistributor.h"
#include "parallel/MeshManipulation.h"
#include "parallel/ParallelDebug.h"
#include "parallel/StdMpi.h"
#include "parallel/MeshPartitioner.h"
#include "parallel/ParMetisPartitioner.h"
#include "parallel/ZoltanPartitioner.h"
#include "parallel/SimplePartitioner.h"
#include "parallel/CheckerPartitioner.h"
#include "parallel/MpiHelper.h"
#include "parallel/DofComm.h"
#include "io/ElementFileWriter.h"
#include "io/MacroInfo.h"
#include "io/MacroWriter.h"
#include "io/VtkWriter.h"
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "MacroElement.h"
#include "DOFMatrix.h"
#include "DOFVector.h"
#include "SystemVector.h"
#include "ElementDofIterator.h"
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
#include "VertexVector.h"
#include "MeshStructure.h"
#include "ProblemStat.h"
#include "ProblemInstat.h"
#include "RefinementManager3d.h"
#include "Debug.h"

namespace AMDiS {

  using boost::lexical_cast;
  using namespace boost::filesystem;
  using namespace std;

  MeshDistributor* MeshDistributor::globalMeshDistributor = NULL;

  const Flag MeshDistributor::BOUNDARY_SUBOBJ_SORTED              = 0X01L;
  const Flag MeshDistributor::BOUNDARY_FILL_INFO_SEND_DOFS        = 0X02L;
  const Flag MeshDistributor::BOUNDARY_FILL_INFO_RECV_DOFS        = 0X04L;

  inline bool cmpDofsByValue(const DegreeOfFreedom* dof1, const DegreeOfFreedom* dof2)
  {
    return (*dof1 < *dof2);
  }


  MeshDistributor::MeshDistributor()
    : problemStat(0),
      initialized(false),
      name("parallel"),
      feSpaces(0),
      mesh(NULL),
      refineManager(NULL),
      info(10),
      partitioner(NULL),
      deserialized(false),
      writeSerializationFile(false),
      repartitioningAllowed(false),
      repartitionIthChange(20),
      nMeshChangesAfterLastRepartitioning(0),
      repartitioningCounter(0),
      debugOutputDir(""),
      lastMeshChangeIndex(0),
      createBoundaryDofFlag(0),
      sebastianMode(false),
      boundaryDofInfo(1)
  {
    FUNCNAME("MeshDistributor::ParalleDomainBase()");

    mpiComm = MPI::COMM_WORLD;
    mpiRank = mpiComm.Get_rank();
    mpiSize = mpiComm.Get_size();

    Parameters::get(name + "->repartitioning", repartitioningAllowed);
    Parameters::get(name + "->debug output dir", debugOutputDir);
    Parameters::get(name + "->repartition ith change", repartitionIthChange);
    Parameters::get(name + "->log main rank", Msg::outputMainRank);

    string partStr = "parmetis";
    Parameters::get(name + "->partitioner", partStr);

    if (partStr == "parmetis") 
      partitioner = new ParMetisPartitioner(&mpiComm);

    if (partStr == "zoltan") {
#ifdef HAVE_ZOLTAN
      partitioner = new ZoltanPartitioner(&mpiComm);
#else
      ERROR_EXIT("AMDiS was compiled without Zoltan support. Therefore you cannot make use of it!\n");
#endif
    }

    if (partStr == "checker")
      partitioner = new CheckerPartitioner(&mpiComm);

    if (partStr == "simple")
      partitioner = new SimplePartitioner(&mpiComm);

    int tmp = 0;
    Parameters::get(name + "->box partitioning", tmp);
    partitioner->setBoxPartitioning(static_cast<bool>(tmp));

    TEST_EXIT(partitioner)("Could not create partitioner \"%s\"!\n", partStr.c_str());
  }


  void MeshDistributor::initParallelization()
  {
    FUNCNAME("MeshDistributor::initParallelization()");

    if (initialized)
      return;

    TEST_EXIT(mpiSize > 1)
      ("Parallelization does not work with only one process!\n");

    TEST_EXIT(feSpaces.size() > 0)
      ("No FE space has been defined for the mesh distributor!\n");
    TEST_EXIT(mesh)("No mesh has been defined for the mesh distributor!\n");

    // === Sort FE spaces with respect to the degree of the basis ===
    // === functions. Use stuiped bubble sort for this.           ===

    bool doNext = false;
    do {
      doNext = false;
      for (unsigned int i = 0; i < feSpaces.size() - 1; i++) {
	if (feSpaces[i]->getBasisFcts()->getDegree() >
	    feSpaces[i + 1]->getBasisFcts()->getDegree()) {
	  const FiniteElemSpace *tmp = feSpaces[i + 1];
	  feSpaces[i + 1] = feSpaces[i];
	  feSpaces[i] = tmp;
	  doNext = true;
	}
      }
    } while (doNext);

    elObjDb.setMesh(feSpaces[0]->getMesh());

    // If the problem has been already read from a file, we need only to set
    // isRankDofs to all matrices and rhs vector and to remove periodic 
    // boundary conditions (if there are some).
    if (deserialized) {
      updateMacroElementInfo();

      setRankDofs();

      removePeriodicBoundaryConditions();

      macroElIndexMap.clear();
      macroElIndexTypeMap.clear();

      for (vector<MacroElement*>::iterator it = allMacroElements.begin();
	   it != allMacroElements.end(); ++it) {
	macroElIndexMap.insert(make_pair((*it)->getIndex(), (*it)->getElement()));
	macroElIndexTypeMap.insert(make_pair((*it)->getIndex(), (*it)->getElType()));
      }

      createBoundaryDofs();

#if (DEBUG != 0)
      ParallelDebug::writeDebugFile(*this, debugOutputDir + "mpi-dbg", "dat");
#endif    

      initialized = true;
      return;
    }


    // Test, if the mesh is the macro mesh only! Paritioning of the mesh is supported
    // only for macro meshes, so it will not work yet if the mesh is already refined
    // in some way.
    testForMacroMesh();

    // For later mesh repartitioning, we need to store some information about the
    // macro mesh.
    createMacroElementInfo();

    // create an initial partitioning of the mesh
    partitioner->createInitialPartitioning();

    // set the element weights, which are 1 at the very first begin
    setInitialElementWeights();

    // and now partition the mesh    
    bool partitioningSucceed = partitioner->partition(elemWeights, INITIAL);
    TEST_EXIT(partitioningSucceed)("Initial partitioning does not work!\n");
    partitioner->createPartitionMap(partitionMap);


#if (DEBUG != 0)    
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);
#endif

    if (mpiRank == 0) {
#if (DEBUG != 0)    
      int writePartMesh = 1;
#else
      int writePartMesh = 0;
#endif
      Parameters::get("dbg->write part mesh", writePartMesh);

      if (writePartMesh > 0) {
	debug::writeElementIndexMesh(mesh, debugOutputDir + "elementIndex.vtu");
	ParallelDebug::writePartitioning(*this, debugOutputDir + "part.vtu");
      }
    }

    // If required, create hierarchical mesh level structure.
    createMeshLevelStructure();

    // Create interior boundary information.
    createInteriorBoundaryInfo();

#if (DEBUG != 0)    
    ParallelDebug::printBoundaryInfo(*this);
#endif
    
    // === Remove neighbourhood relations due to periodic bounday conditions. ===

    for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements(); ++it) {
      for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
	if ((*it)->getNeighbour(i) && 
	    mesh->isPeriodicAssociation((*it)->getBoundary(i))) {

	  int neighIndex = (*it)->getNeighbour(i)->getIndex();

	  (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
	  (*it)->setNeighbour(i, NULL);
	  (*it)->setBoundary(i, 0);

	  macroElementNeighbours[(*it)->getIndex()][i] = -1;
	  macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
	}
      }
    }

    for (vector<MacroElement*>::iterator it = allMacroElements.begin();
	 it != allMacroElements.end(); ++it) {
      for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
	if ((*it)->getNeighbour(i) && 
	    mesh->isPeriodicAssociation((*it)->getBoundary(i))) {

	  int neighIndex = (*it)->getNeighbour(i)->getIndex();

	  (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
	  (*it)->setNeighbour(i, NULL);
	  (*it)->setBoundary(i, 0);

	  macroElementNeighbours[(*it)->getIndex()][i] = -1;
	  macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;

	}
      }
    }

    // === Remove all macro elements that are not part of the rank partition. ===

    removeMacroElements();

    // === Create new global and local DOF numbering. ===


    // We have to remove the VertexVectors, which contain periodic assoiciations, 
    // because they are not valid anymore after some macro elements have been
    // removed and the corresponding DOFs were deleted.
    for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
	 it != mesh->getPeriodicAssociations().end(); ++it)
      const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));

    updateLocalGlobalNumbering();

    // === In 3D we have to make some test, if the resulting mesh is valid.  ===
    // === If it is not valid, there is no possiblity yet to fix this        ===
    // === problem, just exit with an error message.                         ===
    
    check3dValidMesh();

    // === If in debug mode, make some tests. ===

#if (DEBUG != 0)
    MSG("AMDiS runs in debug mode, so make some test ...\n");

    ParallelDebug::testAllElements(*this);
    debug::testSortedDofs(mesh, elMap);
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::followBoundary(*this);

    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "macro_mesh");   

    MSG("Debug mode tests finished!\n");
#endif

    // Create periodic DOF mapping, if there are periodic boundaries.
    createPeriodicMap();

    // Remove periodic boundary conditions in sequential problem definition. 
    removePeriodicBoundaryConditions();

#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif

    // === Global refinements. ===
    
    int globalRefinement = 0;
    Parameters::get(mesh->getName() + "->global refinements", globalRefinement);
    
    if (globalRefinement > 0) {
      refineManager->globalRefine(mesh, globalRefinement);

      updateLocalGlobalNumbering();

      // === Update periodic mapping, if there are periodic boundaries. ===     

      createPeriodicMap();
#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif
    }

    // Set DOF rank information to all matrices and vectors.
    setRankDofs();

    initialized = true;
  }


  void MeshDistributor::addProblemStat(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::addProblemStat()");

    TEST_EXIT_DBG(probStat->getFeSpaces().size())
      ("No FE spaces in stationary problem!\n");

    // === Add FE spaces from stationary problem to mesh distributor. ===

    for (unsigned int i = 0; i < probStat->getFeSpaces().size(); i++) {
      bool foundFeSpace = false;
      for (unsigned int j = 0; j < feSpaces.size(); j++) {
	if (feSpaces[j] == probStat->getFeSpaces()[i])
	  foundFeSpace = true;

	TEST_EXIT(feSpaces[j]->getMesh() == probStat->getFeSpaces()[i]->getMesh())
	  ("MeshDistributor does not yet support usage of different meshes!\n");
      }

      if (!foundFeSpace)
	feSpaces.push_back(probStat->getFeSpaces()[i]);
    }

    TEST_EXIT(feSpaces.size() > 0)("Should not happen!\n");

    mesh = feSpaces[0]->getMesh();
    info = probStat->getInfo();
    
    switch (mesh->getDim()) {
    case 2:
      refineManager = new RefinementManager2d();
      break;
    case 3:
      refineManager = new RefinementManager3d();
      break;
    default:
      ERROR_EXIT("This should not happen for dim = %d!\n", mesh->getDim());
    }
    
    partitioner->setMesh(mesh);
    

    // Create parallel serialization file writer, if needed.
    int writeSerialization = 0;
    Parameters::get(probStat->getName() + "->output->write serialization",  
		    writeSerialization);
    if (writeSerialization && !writeSerializationFile) {
      string filename = "";
      Parameters::get(name + "->output->serialization filename", filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel serialization file!\n");

      int tsModulo = -1;
      Parameters::get(probStat->getName() + "->output->write every i-th timestep", 
		      tsModulo);
      
      probStat->getFileWriterList().push_back(new Serializer<MeshDistributor>(this, filename, tsModulo));
      writeSerializationFile = true;
    }    

    int readSerialization = 0;
    Parameters::get(probStat->getName() + "->input->read serialization", 
		    readSerialization);
    if (readSerialization) {
      string filename = "";
      Parameters::get(probStat->getName() + "->input->serialization filename", 
		      filename);
      filename += ".p" + lexical_cast<string>(mpiRank);
      MSG("Start deserialization with %s\n", filename.c_str());
      ifstream in(filename.c_str());

      TEST_EXIT(!in.fail())("Could not open deserialization file: %s\n",
			    filename.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);

      probStat->deserialize(in);
      in.close();
      MSG("Deserialization from file: %s\n", filename.c_str());

      filename = "";
      Parameters::get(name + "->input->serialization filename", filename);
      
      TEST_EXIT(filename != "")
	("No filename defined for parallel deserialization file!\n");
      
      string rankFilename = filename + ".p" + lexical_cast<string>(mpiRank);
      in.open(rankFilename.c_str());
      
      TEST_EXIT(!in.fail())("Could not open parallel deserialization file: %s\n",
			    filename.c_str());

      // Read the revision number of the AMDiS version which was used to create 
      // the serialization file.
      revNumber = -1;
      SerUtil::deserialize(in, revNumber);
      
      deserialize(in);
      in.close();
      MSG("Deserializtion of mesh distributor from file: %s\n", rankFilename.c_str());
      deserialized = true;
    }

    problemStat.push_back(probStat);

    // If the mesh distributor is already initialized, don't forget to set rank
    // DOFs object to the matrices and vectors of the added stationary problem,
    // and to remove the periodic boundary conditions on these objects.

    if (initialized) {
      setRankDofs(probStat);
      removePeriodicBoundaryConditions(probStat);
    }
  }


  void MeshDistributor::addProblemStatGlobal(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::addProblemStatGlobal()");

    if (globalMeshDistributor == NULL)
      globalMeshDistributor = new MeshDistributor();

    globalMeshDistributor->addProblemStat(probStat);
  }


  void MeshDistributor::exitParallelization()
  {}

  
  void MeshDistributor::testForMacroMesh()
  {
    FUNCNAME("MeshDistributor::testForMacroMesh()");

    int nMacroElements = 0;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
    while (elInfo) {
      TEST_EXIT(elInfo->getLevel() == 0)
	("Mesh is already refined! This does not work with parallelization!\n");

      TEST_EXIT(elInfo->getType() == 0)
	("Only macro elements with level 0 are supported!\n");
      
      nMacroElements++;

      elInfo = stack.traverseNext(elInfo);
    }

    TEST_EXIT(nMacroElements >= mpiSize)
      ("The mesh has less macro elements than number of mpi processes!\n");
  }


  void MeshDistributor::synchVector(SystemVector &vec)
  {
    FUNCNAME("MeshDistributor::synchVector()");

    StdMpi<vector<double> > stdMpi(mpiComm);

    for (DofComm::Iterator it(sendDofs); !it.end(); it.nextRank()) {
      vector<double> dofs;

      for (int i = 0; i < vec.getSize(); i++) {
	DOFVector<double> &dofVec = *(vec.getDOFVector(i));

	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
	  dofs.push_back(dofVec[it.getDofIndex()]);
      }

      stdMpi.send(it.getRank(), dofs);
    }
	   
    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank())
      stdMpi.recv(it.getRank());

    stdMpi.startCommunication();

    for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank()) {
      int counter = 0;

      for (int i = 0; i < vec.getSize(); i++) {
	DOFVector<double> &dofVec = *(vec.getDOFVector(i));

	for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
	  dofVec[it.getDofIndex()] = stdMpi.getRecvData(it.getRank())[counter++];
      }
    }
  }


  void MeshDistributor::check3dValidMesh()
  {
    FUNCNAME("MeshDistributor::check3dValidMesh()");

    if (mesh->getDim() != 3)
      return;

    std::set<DofEdge> allEdges;
    std::set<int> rankMacroEls;

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
    while (elInfo) {
      for (int i = 0; i < 4; i++) {
	ElementObjectData elData(elInfo->getElement()->getIndex(), i);
	allEdges.insert(elObjDb.getEdgeLocalMap(elData));
      }

      rankMacroEls.insert(elInfo->getElement()->getIndex());

      elInfo = stack.traverseNext(elInfo);
    }


    FixRefinementPatch::connectedEdges.clear();
    bool valid3dMesh = true;

    for (std::set<DofEdge>::iterator it = allEdges.begin(); it != allEdges.end(); ++it) {
      vector<ElementObjectData>& edgeEls = elObjDb.getElements(*it);

      TEST_EXIT_DBG(edgeEls.size() > 0)
	("No edge %d/%d in elObjDB!\n", it->first, it->second);

      std::set<int> el0, el1;
      map<int, int> edgeNoInEl;

      for (unsigned int i = 0; i < edgeEls.size(); i++) {
	if (rankMacroEls.count(edgeEls[i].elIndex)) {
	  if (el0.empty())
	    el0.insert(edgeEls[i].elIndex);
	  else
	    el1.insert(edgeEls[i].elIndex);

	  edgeNoInEl[edgeEls[i].elIndex] = edgeEls[i].ithObject;
	}
      }
            
      TEST_EXIT_DBG(!el0.empty())("Should not happen!\n");

      if (el1.empty())
	continue;
      
      bool found = false;      
      do {
	found = false;
	for (std::set<int>::iterator elIt = el0.begin(); elIt != el0.end(); ++elIt) {
	  for (int i = 0; i < 4; i++) {
	    int neighEl = macroElementNeighbours[*elIt][i];
	    if (neighEl != -1 && el1.count(neighEl)) {
	      el0.insert(neighEl);
	      el1.erase(neighEl);
	      found = true;
	    }
	  }
	  
	  if (found)
	    break;
	}
      } while (found);
      
      if (!el1.empty()) {
	valid3dMesh = false;

	MSG_DBG("Unvalid 3D mesh with %d (%d - %d) elements on this edge!\n", 
		edgeEls.size(), el0.size(), el1.size());

	for (std::set<int>::iterator elIt0 = el0.begin(); elIt0 != el0.end(); ++elIt0) {
	  for (std::set<int>::iterator elIt1 = el1.begin(); elIt1 != el1.end(); ++elIt1) {
	    pair<Element*, int> edge0 = 
	      make_pair(macroElIndexMap[*elIt0], edgeNoInEl[*elIt0]);
	    pair<Element*, int> edge1 = 
	      make_pair(macroElIndexMap[*elIt1], edgeNoInEl[*elIt1]);

	    DofEdge dofEdge0 = edge0.first->getEdge(edge0.second);
	    DofEdge dofEdge1 = edge1.first->getEdge(edge1.second);

	    WorldVector<double> c0, c1;
	    mesh->getDofIndexCoords(dofEdge0.first, feSpaces[0], c0);
	    mesh->getDofIndexCoords(dofEdge0.second, feSpaces[0], c1);

	    /*
	    MSG_DBG("FOUND EDGE: %d %d with coords %f %f %f   %f %f %f\n",
		    dofEdge0.first, dofEdge0.second, 
		    c0[0], c0[1], c0[2],
		    c1[0], c1[1], c1[2]);
	    */

	    TEST_EXIT_DBG(dofEdge0 == dofEdge1)("Should noth happen!\n");

	    FixRefinementPatch::connectedEdges.push_back(make_pair(edge0, edge1));
	    FixRefinementPatch::connectedEdges.push_back(make_pair(edge1, edge0));
	  }
	}
      }
    }

    MSG_DBG("Mesh is 3d valid mesh: %d\n", valid3dMesh);
  }


  void MeshDistributor::getAllBoundaryDofs(const FiniteElemSpace *feSpace,
					   int level,
					   DofContainer& dofs)
  {
    FUNCNAME("MeshDistributor::getAllBoundaryDofs()");

    DofContainerSet dofSet;
    for (DofComm::Iterator it(sendDofs, level, feSpace); !it.end(); it.nextRank())
      dofSet.insert(it.getDofs().begin(), it.getDofs().end());
    for (DofComm::Iterator it(recvDofs, level, feSpace); !it.end(); it.nextRank())
      dofSet.insert(it.getDofs().begin(), it.getDofs().end());

    dofs.clear();
    dofs.insert(dofs.begin(), dofSet.begin(), dofSet.end());
  }


  void MeshDistributor::setRankDofs(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::setRankDofs()");

    int nComponents = probStat->getNumComponents();
    for (int i = 0; i < nComponents; i++) {
      for (int j = 0; j < nComponents; j++)
	if (probStat->getSystemMatrix(i, j)) {
	  const FiniteElemSpace *rowFeSpace = 
	    probStat->getSystemMatrix(i, j)->getRowFeSpace();

	  TEST_EXIT(find(feSpaces.begin(), feSpaces.end(), rowFeSpace) != feSpaces.end())
	    ("Should not happen!\n");

	  probStat->getSystemMatrix(i, j)->setDofMap(dofMap[rowFeSpace]);
	}
    

      TEST_EXIT_DBG(probStat->getRhs()->getDOFVector(i))("No RHS vector!\n");
      TEST_EXIT_DBG(probStat->getSolution()->getDOFVector(i))
	("No solution vector!\n");
      TEST_EXIT_DBG(probStat->getRhsVector(i)->getFeSpace() ==
		    probStat->getSolution(i)->getFeSpace())
	("Should not happen!\n");
      
      const FiniteElemSpace *feSpace = probStat->getRhsVector(i)->getFeSpace();
      TEST_EXIT(find(feSpaces.begin(), feSpaces.end(), feSpace) != feSpaces.end())
	("Should not happen!\n");

      probStat->getRhsVector(i)->setDofMap(dofMap[feSpace]);
      probStat->getSolution(i)->setDofMap(dofMap[feSpace]);
    }    
  }


  void MeshDistributor::setRankDofs()
  {
    for (unsigned int i = 0; i < problemStat.size(); i++) 
      setRankDofs(problemStat[i]);
  }


  void MeshDistributor::removePeriodicBoundaryConditions()
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    // Remove periodic boundaries in boundary manager on matrices and vectors.
    for (unsigned int i = 0; i < problemStat.size(); i++)
      removePeriodicBoundaryConditions(problemStat[i]);

    // Remove periodic boundaries on elements in mesh.
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh,  -1, Mesh::CALL_EVERY_EL_PREORDER);
    while (elInfo) {
      elInfo->getElement()->deleteElementData(PERIODIC);
      elInfo = stack.traverseNext(elInfo);
    }    

    // Remove periodic vertex associations
    mesh->getPeriodicAssociations().clear();
  }


  void MeshDistributor::removePeriodicBoundaryConditions(ProblemStatSeq *probStat)
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    int nComponents = probStat->getNumComponents();

    for (int j = 0; j < nComponents; j++) {
      for (int k = 0; k < nComponents; k++) {
	DOFMatrix* mat = probStat->getSystemMatrix(j, k);
	if (mat && mat->getBoundaryManager())
	  removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(mat->getBoundaryManager()->getBoundaryConditionMap()));
      }
      
      if (probStat->getSolution()->getDOFVector(j)->getBoundaryManager())
	removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat->getSolution()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
      
      if (probStat->getRhs()->getDOFVector(j)->getBoundaryManager())
	removePeriodicBoundaryConditions(const_cast<BoundaryIndexMap&>(probStat->getRhs()->getDOFVector(j)->getBoundaryManager()->getBoundaryConditionMap()));
    }
  }


  void MeshDistributor::removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap)
  {
    FUNCNAME("MeshDistributor::removePeriodicBoundaryConditions()");

    BoundaryIndexMap::iterator it = boundaryMap.begin();
    while (it != boundaryMap.end()) {
      if (it->second->isPeriodic())
	boundaryMap.erase(it++);
      else
	++it;      
    }    
  }


  void MeshDistributor::createMeshLevelStructure()
  {
    FUNCNAME("MeshDistributor::createMeshLevelStructure()");

    if (mpiSize != 16)
      return;

    std::set<int> neighbours;
    switch (mpiRank) {
    case 0:
      neighbours.insert(1); neighbours.insert(4); neighbours.insert(5);
      break;
    case 1:
      neighbours.insert(0); neighbours.insert(2); neighbours.insert(4); neighbours.insert(5); neighbours.insert(6);
      break;
    case 2:
      neighbours.insert(1); neighbours.insert(3); neighbours.insert(5); neighbours.insert(6); neighbours.insert(7);
      break;
    case 3:
      neighbours.insert(2); neighbours.insert(6); neighbours.insert(7);
      break;
    case 4:
      neighbours.insert(0); neighbours.insert(1); neighbours.insert(5); neighbours.insert(8); neighbours.insert(9);
      break;
    case 5:
      neighbours.insert(0); neighbours.insert(1); neighbours.insert(2); 
      neighbours.insert(4); neighbours.insert(6);
      neighbours.insert(8); neighbours.insert(9); neighbours.insert(10); 
      break;
    case 6:
      neighbours.insert(1); neighbours.insert(2); neighbours.insert(3); 
      neighbours.insert(5); neighbours.insert(7);
      neighbours.insert(9); neighbours.insert(10); neighbours.insert(11); 
      break;
    case 7:
      neighbours.insert(2); neighbours.insert(3); neighbours.insert(6);  neighbours.insert(10); neighbours.insert(11);
      break;
    case 8:
      neighbours.insert(4); neighbours.insert(5); neighbours.insert(9);  neighbours.insert(12); neighbours.insert(13);
      break;
    case 9:
      neighbours.insert(4); neighbours.insert(5); neighbours.insert(6); 
      neighbours.insert(8); neighbours.insert(10);
      neighbours.insert(12); neighbours.insert(13); neighbours.insert(14); 
      break;
    case 10:
      neighbours.insert(5); neighbours.insert(6); neighbours.insert(7); 
      neighbours.insert(9); neighbours.insert(11);
      neighbours.insert(13); neighbours.insert(14); neighbours.insert(15); 
      break;
    case 11:
      neighbours.insert(6); neighbours.insert(7); neighbours.insert(10);  neighbours.insert(14); neighbours.insert(15);
      break;
    case 12:
      neighbours.insert(8); neighbours.insert(9); neighbours.insert(13);
      break;
    case 13:
      neighbours.insert(8); neighbours.insert(9); neighbours.insert(10);  neighbours.insert(12); neighbours.insert(14);
      break;
    case 14:
      neighbours.insert(9); neighbours.insert(10); neighbours.insert(11);  neighbours.insert(13); neighbours.insert(15);
      break;
    case 15:
      neighbours.insert(10); neighbours.insert(11); neighbours.insert(14);
      break;
    }    

    TEST_EXIT(neighbours.size() > 0)("Should not happen!\n");

    levelData.init(neighbours);

    MSG("INIT MESH LEVEL %d\n", levelData.getLevelNumber());

    bool multiLevelTest = false;
    Parameters::get("parallel->multi level test", multiLevelTest);
    if (multiLevelTest) {
      switch (mpiRank) {
      case 0: case 1: case 4: case 5:
	{
	  std::set<int> m;
	  m.insert(0); m.insert(1); m.insert(4); m.insert(5);
	  levelData.addLevel(m, 0);
	}
	break;
      case 2: case 3: case 6: case 7:
	{
	  std::set<int> m;
	  m.insert(2); m.insert(3); m.insert(6); m.insert(7);
	  levelData.addLevel(m, 1);
	}
	break;
      case 8: case 9: case 12: case 13:
	{
	  std::set<int> m;
	  m.insert(8); m.insert(9); m.insert(12); m.insert(13);
	  levelData.addLevel(m, 2);
	}
	break;
      case 10: case 11: case 14: case 15:
	{
	  std::set<int> m;
	  m.insert(10); m.insert(11); m.insert(14); m.insert(15);
	  levelData.addLevel(m, 3);
	}
	break;
      }
    }
  }


  void MeshDistributor::checkMeshChange(bool tryRepartition)
  {
    FUNCNAME("MeshDistributor::checkMeshChange()");

    double first = MPI::Wtime();

    int skip = 0;
    Parameters::get("parallel->debug->skip check mesh change", skip);

    // === If mesh has not been changed on all ranks, return. ===

    int recvAllValues = 0;
    int sendValue = static_cast<int>(mesh->getChangeIndex() != lastMeshChangeIndex);
    mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

    if (recvAllValues == 0)
      return;

    // === At least one rank mesh has been changed, so the boundaries must be ===
    // === adapted to the new mesh structure.                                 ===

    if (skip == 0)
    do {
      bool meshChanged = false;

      // To check the interior boundaries, the ownership of the boundaries is not 
      // important. Therefore, we add all boundaries to one boundary container.
      RankToBoundMap allBound;

      for (InteriorBoundary::iterator it(rankIntBoundary); !it.end(); ++it)
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
 	  allBound[it.getRank()].push_back(*it);

      for (InteriorBoundary::iterator it(otherIntBoundary); !it.end(); ++it)
	if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	    (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
	  allBound[it.getRank()].push_back(*it);

      for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it) {
	if (it.getRank() == mpiRank) {
	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE)) {
	    MeshStructure elCode;
	    elCode.init(it->rankObj);
	    
	    MeshManipulation mm(mesh);
	    meshChanged |= mm.fitElementToMeshCode(elCode, it->neighObj);
	  }
	} else {
	  if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) || 
	      (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
	    allBound[it.getRank()].push_back(*it);	
	}
      }


      // === Check the boundaries and adapt mesh if necessary. ===
      MSG_DBG("Run checkAndAdaptBoundary ...\n");

      meshChanged |= checkAndAdaptBoundary(allBound);

      // === Check on all ranks if at least one rank's mesh has changed. ===

      int sendValue = static_cast<int>(meshChanged);
      recvAllValues = 0;
      mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);

      MSG("Mesh changed on %d ranks!\n", recvAllValues);
    } while (recvAllValues != 0);

#if (DEBUG != 0)
    debug::writeMesh(feSpaces[0], -1, debugOutputDir + "mesh");
#endif


    // Because the mesh has been changed, update the DOF numbering and mappings.
    updateLocalGlobalNumbering();

    // Update periodic mapping, if there are periodic boundaries.
    createPeriodicMap();


#if (DEBUG != 0)
    ParallelDebug::testPeriodicBoundary(*this);
#endif


    // === The mesh has changed, so check if it is required to repartition ===
    // === the mesh.                                                       ===

    nMeshChangesAfterLastRepartitioning++;


    INFO(info, 8)("Parallel mesh adaption needed %.5f seconds\n", 
		  MPI::Wtime() - first);

    if (tryRepartition &&
	repartitioningAllowed && 
	nMeshChangesAfterLastRepartitioning >= repartitionIthChange) {
      repartitionMesh();
      nMeshChangesAfterLastRepartitioning = 0;
    } else {
      MSG_DBG("Repartitioning not tried because tryRepartitioning = %d   repartitioningAllowed = %d   nMeshChange = %d   repartitionIthChange = %d\n",
	      tryRepartition, repartitioningAllowed, 
	      nMeshChangesAfterLastRepartitioning, repartitionIthChange);
    }

    // === Print imbalance factor. ===

    printImbalanceFactor();
  }

  
  void MeshDistributor::printImbalanceFactor()
  {
    FUNCNAME("MeshDistributor::printImbalanceFactor()");

    vector<int> nDofsInRank(mpiSize);
    int nDofs = mesh->getDofAdmin(0).getUsedDofs();
    mpiComm.Gather(&nDofs, 1, MPI_INT, &(nDofsInRank[0]), 1, MPI_INT, 0);

    if (mpiRank == 0) {
      int nOverallDofs = 0;
      int maxDofs = numeric_limits<int>::min();
      int minDofs = numeric_limits<int>::max();
      for (int i = 0; i < mpiSize; i++) {
	nOverallDofs += nDofsInRank[i];
	maxDofs = std::max(maxDofs, nDofsInRank[i]);
	minDofs = std::min(minDofs, nDofsInRank[i]);
      }      
//       int avrgDofs = nOverallDofs / mpiSize;
//       double imbalance0 = 
// 	(static_cast<double>(maxDofs - avrgDofs) /  avrgDofs) * 100.0;
      double imbalance1 = (static_cast<double>(maxDofs) / minDofs - 1.0) * 100.0;

      MSG("Imbalancing factor: %.1f\n", imbalance1);
    }
  }

  
  bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
  {
    FUNCNAME("MeshDistributor::checkAndAdaptBoundary()");

    // === Create mesh structure codes for all ranks boundary elements. ===
       
    map<int, MeshCodeVec> sendCodes;
   
    for (RankToBoundMap::iterator it = allBound.begin(); 
	 it != allBound.end(); ++it) {
      for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	MeshStructure elCode;
	elCode.init(boundIt->rankObj);
	sendCodes[it->first].push_back(elCode);
      }
    }

    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
    stdMpi.send(sendCodes);
    for (RankToBoundMap::iterator it = allBound.begin(); 
	 it != allBound.end(); ++it)
      stdMpi.recv(it->first);

    stdMpi.startCommunication();

    // === Compare received mesh structure codes. ===
    
    bool meshChanged = false;

    for (RankToBoundMap::iterator it = allBound.begin(); 
	 it != allBound.end(); ++it) {
     
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;
      
      for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt, i++) {

	MeshStructure elCode;	
	elCode.init(boundIt->rankObj);

#if (DEBUG != 0)
	ParallelDebug::followBoundary(mesh, *boundIt, elCode);
#endif

	if (elCode.getCode() != recvCodes[i].getCode()) {
// 	  MSG("MACRO EL %d %d %d DOES NOT FIT WITH MACRO EL %d %d %d ON RANK %d\n",
// 	      boundIt->rankObj.elIndex, boundIt->rankObj.subObj, boundIt->rankObj.ithObj,
// 	      boundIt->neighObj.elIndex, boundIt->neighObj.subObj, boundIt->neighObj.ithObj,
// 	      it->first);
	  TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");

	  MeshManipulation mm(mesh);
	  meshChanged |= mm.fitElementToMeshCode(recvCodes[i], boundIt->rankObj);
 	}
      }
    }

    return meshChanged;
  }


  void MeshDistributor::serialize(ostream &out, DofContainer &data)
  {    
    int vecSize = data.size();
    SerUtil::serialize(out, vecSize);
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = *(data[i]);
      SerUtil::serialize(out, dofIndex);
    }
  }


  void MeshDistributor::serialize(ostream &out, 
				  map<int, map<const FiniteElemSpace*, DofContainer> > &data)
  {
    int mapSize = data.size();
    SerUtil::serialize(out, mapSize);
    for (map<int, map<const FiniteElemSpace*, DofContainer> >::iterator it = data.begin(); it != data.end(); ++it) {
      int rank = it->first;
      SerUtil::serialize(out, rank);

      for (map<const FiniteElemSpace*, DofContainer>::iterator dcIt = it->second.begin();
	   dcIt != it->second.end(); ++dcIt)
	serialize(out, dcIt->second);
    }
  }

  
  void MeshDistributor::deserialize(istream &in, DofContainer &data,
				    map<int, const DegreeOfFreedom*> &dofIndexMap)
  {
    FUNCNAME("MeshDistributor::deserialize()");

    int vecSize = 0;
    SerUtil::deserialize(in, vecSize);
    data.clear();
    data.resize(vecSize);
    for (int i = 0; i < vecSize; i++) {
      int dofIndex = 0;
      SerUtil::deserialize(in, dofIndex);

      TEST_EXIT_DBG(dofIndexMap.count(dofIndex) != 0)
	("Dof index could not be deserialized correctly!\n");

      data[i] = dofIndexMap[dofIndex];
    }
  }


  void MeshDistributor::deserialize(istream &in, 
				    map<int, map<const FiniteElemSpace*, DofContainer> > &data,
				    map<const FiniteElemSpace*, map<int, const DegreeOfFreedom*> > &dofIndexMap)
  {
    data.clear();

    int mapSize = 0;
    SerUtil::deserialize(in, mapSize);
    for (int i = 0; i < mapSize; i++) {
      int rank = 0;
      SerUtil::deserialize(in, rank);

      for (unsigned int j = 0; j < feSpaces.size(); j++)
	deserialize(in, data[rank][feSpaces[j]], dofIndexMap[feSpaces[j]]);
    }
  }


  void MeshDistributor::setInitialElementWeights() 
  {
    FUNCNAME("MeshDistributor::setInitialElementWeights()");

    elemWeights.clear();
      
    string filename = "";
    Parameters::get(mesh->getName() + "->macro weights", filename);
    if (filename != "") {
      MSG("Read macro weights from %s\n", filename.c_str());

      ifstream infile;
      infile.open(filename.c_str(), ifstream::in);
      while (!infile.eof()) {
	int elNum, elWeight;
	infile >> elNum;
	if (infile.eof())
	  break;
	infile >> elWeight;

	elemWeights[elNum] = elWeight;
      }

      infile.close();
    } else {           
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
      while (elInfo) {
	elemWeights[elInfo->getElement()->getIndex()] = 1.0;
	elInfo = stack.traverseNext(elInfo);
      }
    }
  }


  void MeshDistributor::repartitionMesh()
  {
    FUNCNAME("MeshDistributor::repartitionMesh()");

    // === First we check if the rank with the maximum number of DOFs has at  ===
    // === least 20% more DOFs than the rank with the minimum number of DOFs. ===
    // === In this case, the mesh will be repartition.                        ===

    int repartitioning = 0;
    vector<int> nDofsInRank(mpiSize);
    int nDofs = mesh->getDofAdmin(0).getUsedDofs();
    mpiComm.Gather(&nDofs, 1, MPI_INT, &(nDofsInRank[0]), 1, MPI_INT, 0);

    if (mpiRank == 0) {
      int nOverallDofs = 0;
      int minDofs = numeric_limits<int>::max();
      int maxDofs = numeric_limits<int>::min();
      for (int i = 0; i < mpiSize; i++) {
	nOverallDofs += nDofsInRank[i];
	minDofs = std::min(minDofs, nDofsInRank[i]);
	maxDofs = std::max(maxDofs, nDofsInRank[i]);
      }      
     
      MSG("Overall DOFs: %d    Min DOFs: %d    Max DOFs: %d\n", 
	  nOverallDofs, minDofs, maxDofs);

      if (static_cast<double>(maxDofs) / static_cast<double>(minDofs) > 1.2) 
	repartitioning = 1;

      mpiComm.Bcast(&repartitioning, 1, MPI_INT, 0);
    } else {
      mpiComm.Bcast(&repartitioning, 1, MPI_INT, 0);
    }

    if (repartitioning == 0)
      return;

    double timePoint = MPI::Wtime();

#if (DEBUG != 0)
    ParallelDebug::testDoubleDofs(mesh);

    if (repartitioningCounter == 0)
      ParallelDebug::writePartitioningFile(debugOutputDir + "partitioning", 
					   repartitioningCounter, feSpaces[0]);
#endif
    repartitioningCounter++;

    // === Create new element weights. ===

    elemWeights.clear();
    {
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
      while (elInfo) {
	elemWeights[elInfo->getMacroElement()->getIndex()]++;      
	elInfo = stack.traverseNext(elInfo);
      }
    }

    // === Run mesh partitioner to calculate a new mesh partitioning.  ===

    partitioner->setLocalGlobalDofMap(&(dofMap[feSpaces[0]].getMap(0)));

    bool partitioningSucceed = 
      partitioner->partition(elemWeights, ADAPTIVE_REPART);
    if (!partitioningSucceed) {
      MSG("Mesh partitioner created empty partition!\n");
      return;
    }

    // In the case the partitioner does not create a new mesh partition, return
    // without and changes.
    if (!partitioner->meshChanged()) {
      MSG("Mesh partition does not create a new partition!\n");
      return;
    }

    // === Create map that maps macro element indices to pointers to the ===
    // === macro elements.                                               ===

    map<int, MacroElement*> elIndexMap;
    for (vector<MacroElement*>::iterator it = allMacroElements.begin();
	 it != allMacroElements.end(); ++it)
      elIndexMap[(*it)->getIndex()] = *it;


    // === Create set of all new macro elements this rank will receive from ===
    // === other ranks.                                                     ===

    std::set<MacroElement*> newMacroEl;
    for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
	 it != partitioner->getRecvElements().end(); ++it) {
      for (vector<int>::iterator elIt = it->second.begin();
	   elIt != it->second.end(); ++elIt) {
	TEST_EXIT_DBG(elIndexMap.count(*elIt) == 1)
	  ("Could not find macro element %d\n", *elIt);

	newMacroEl.insert(elIndexMap[*elIt]);
      }
    }

    std::set<MacroElement*> allMacroEl;
    for (std::set<MacroElement*>::iterator it = newMacroEl.begin(); 
	 it != newMacroEl.end(); ++it)
      allMacroEl.insert(*it);

    for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements(); ++it)
      allMacroEl.insert(*it);


    // === Add new macro elements to mesh. ===
    TEST_EXIT(mesh->getGeo(FACE) || mesh->getGeo(CENTER))
      ("Mh, dass macht dann doch noch etwas Arbeit für den Thomas!\n");

    for (std::set<MacroElement*>::iterator it = newMacroEl.begin();
	 it != newMacroEl.end(); ++it) {
      MacroElement *mel = *it;

      // First, reset all neighbour relations. The correct neighbours will be 
      // set later.
      for (int i = 0; i < mesh->getGeo(NEIGH); i++)
	mel->setNeighbour(i, NULL);

      // Create new DOFs for the macro element.
      mel->getElement()->createNewDofPtrs();

      for (int i = 0; i < mesh->getGeo(VERTEX); i++)
	mel->getElement()->setDof(i, mesh->getDof(VERTEX));

      for (int i = 0; i < mesh->getGeo(EDGE); i++)
	mel->getElement()->setDof(mesh->getGeo(VERTEX) + i, mesh->getDof(EDGE));

      // Push the macro element to all macro elements in mesh.
      mesh->getMacroElements().push_back(mel);
    }


    // === Send and receive mesh structure codes. ===

    map<int, MeshCodeVec> sendCodes;
    map<int, vector<vector<double> > > sendValues;

    for (map<int, vector<int> >::iterator it = partitioner->getSendElements().begin();
	 it != partitioner->getSendElements().end(); ++it) {
      for (vector<int>::iterator elIt = it->second.begin();
	   elIt != it->second.end(); ++elIt) {
	MeshStructure elCode;
	elCode.init(mesh, *elIt);
	sendCodes[it->first].push_back(elCode);

	for (unsigned int i = 0; i < interchangeVectors.size(); i++) {
	  vector<double> valVec;
	  elCode.getMeshStructureValues(*elIt, interchangeVectors[i], valVec);
	  sendValues[it->first].push_back(valVec);
	}
      }
    }

    StdMpi<MeshCodeVec> stdMpi(mpiComm, true);
    stdMpi.send(sendCodes);
    for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
	 it != partitioner->getRecvElements().end(); ++it)
      stdMpi.recv(it->first);
    stdMpi.startCommunication();

    if (interchangeVectors.size() == 0)
      WARNING("There are no interchange vectors defined!\n");

    StdMpi<vector<vector<double> > > stdMpi2(mpiComm, true);
    stdMpi2.send(sendValues);
    for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
	 it != partitioner->getRecvElements().end(); ++it)
      stdMpi2.recv(it->first);
    stdMpi2.startCommunication();


    // === Adapte the new macro elements due to the received mesh   ===
    // === structure codes.                                         ===

    for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
	 it != partitioner->getRecvElements().end(); ++it) {
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      int i = 0;

      TEST_EXIT_DBG(recvCodes.size() == it->second.size())
	("Should not happen!\n");

      for (vector<int>::iterator elIt = it->second.begin();
	   elIt != it->second.end(); ++elIt)
	recvCodes[i++].fitMeshToStructure(mesh, refineManager, false, *elIt);
    }


    // === Set correct neighbour information on macro elements. ===

    for (std::set<MacroElement* , bool(*)(MacroElement*, MacroElement*)>::iterator it = allMacroEl.begin();
	 it != allMacroEl.end(); ++it) {
      int elIndex = (*it)->getIndex();
      for (int i = 0; i < mesh->getGeo(NEIGH); i++) {

	TEST_EXIT_DBG(macroElementNeighbours.count(elIndex) == 1)
	  ("Should not happen!\n");
	TEST_EXIT_DBG(static_cast<int>(macroElementNeighbours[elIndex].size()) == 
		      mesh->getGeo(NEIGH))
	  ("Should not happen!\n");

	int neighIndex = macroElementNeighbours[elIndex][i];

	if (neighIndex == -1 || 
	    partitioner->getElementInRank()[neighIndex] == false) {
	  (*it)->setNeighbour(i, NULL);
	} else {
	  TEST_EXIT_DBG(elIndexMap.count(neighIndex) == 1)
	    ("Should not happen!\n");

	  (*it)->setNeighbour(i, elIndexMap[neighIndex]);
	}
      }
    }


    // === Delete macros from mesh. ===

    std::set<MacroElement*> deleteMacroElements;

    for (map<int, vector<int> >::iterator it = partitioner->getSendElements().begin();
	 it != partitioner->getSendElements().end(); ++it) {
      for (vector<int>::iterator elIt = it->second.begin();
	   elIt != it->second.end(); ++elIt) {
	TEST_EXIT_DBG(elIndexMap.count(*elIt) == 1)
	  ("Could not find macro element %d\n", *elIt);

	deleteMacroElements.insert(elIndexMap[*elIt]);
      }
    }


    // Note that also if there are no macros to be deleted, this function will
    // update the number of elements, vertices, etc. of the mesh.
    mesh->removeMacroElements(deleteMacroElements, feSpaces);

    // === Remove double DOFs. ===
    MeshManipulation meshManipulation(mesh);
    meshManipulation.deleteDoubleDofs(feSpaces, newMacroEl, elObjDb);

    mesh->dofCompress();
    partitioner->createPartitionMap(partitionMap);

    updateInteriorBoundaryInfo();
    updateLocalGlobalNumbering();

    
    // === After mesh adaption, set values of interchange vectors. ===
    
    for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
	 it != partitioner->getRecvElements().end(); ++it) {
      MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
      vector<vector<double> > &recvValues = stdMpi2.getRecvData()[it->first];
      int i = 0, j = 0;
      for (vector<int>::iterator elIt = it->second.begin();
	   elIt != it->second.end(); ++elIt) {
	for (unsigned int k = 0; k < interchangeVectors.size(); k++)
	  recvCodes[i].setMeshStructureValues(*elIt, 
					      interchangeVectors[k], 
					      recvValues[j++]);	
	i++;
      }
    }


    // === Update periodic mapping, if there are periodic boundaries. ===

    createPeriodicMap();


#if (DEBUG != 0)
    MSG("AMDiS runs in debug mode, so make some test ...\n");

    ParallelDebug::writePartitioningFile(debugOutputDir + "partitioning", 
					 repartitioningCounter, feSpaces[0]);
    ParallelDebug::testAllElements(*this);
    ParallelDebug::testDoubleDofs(mesh);
    ParallelDebug::testInteriorBoundary(*this);
    ParallelDebug::testPeriodicBoundary(*this);
    ParallelDebug::printBoundaryInfo(*this);

    MSG("Debug mode tests finished!\n");
#endif

    // === In 3D we have to make some test, if the resulting mesh is valid.  ===
    // === If it is not valid, there is no possiblity yet to fix this        ===
    // === problem, just exit with an error message.                         ===
    
    check3dValidMesh();

    MSG("Mesh repartitioning needed %.5f seconds\n", MPI::Wtime() - timePoint);

    
    // === Print DOF information to screen. ===

    nDofs = mesh->getDofAdmin(0).getUsedDofs();
    mpiComm.Gather(&nDofs, 1, MPI_INT, &(nDofsInRank[0]), 1, MPI_INT, 0);

    if (mpiRank == 0) {
      int nOverallDofs = 0;
      int minDofs = numeric_limits<int>::max();
      int maxDofs = numeric_limits<int>::min();
      for (int i = 0; i < mpiSize; i++) {
	nOverallDofs += nDofsInRank[i];
	minDofs = std::min(minDofs, nDofsInRank[i]);
	maxDofs = std::max(maxDofs, nDofsInRank[i]);
      }      
     
      MSG("Overall DOFs: %d    Min DOFs: %d    Max DOFs: %d\n", 
	  nOverallDofs, minDofs, maxDofs);
    }
  }


  void MeshDistributor::createInteriorBoundaryInfo()
  {
    FUNCNAME("MeshDistributor::createInteriorBoundaryInfo()");

    createMeshElementData();
    createBoundaryData();
  }


  void MeshDistributor::updateInteriorBoundaryInfo()
  {
    FUNCNAME("MeshDistributor::updateInteriorBoundaryInfo()");

    elObjDb.createRankData(partitionMap, levelData);
    createBoundaryData();

#if (DEBUG != 0)
    ParallelDebug::printBoundaryInfo(*this);
#endif
  }


  void MeshDistributor::createMeshElementData()
  {
    FUNCNAME("MeshDistributor::createMeshElementData()");


   // === Fills macro element data structures. ===

    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, 
					 Mesh::CALL_LEAF_EL | 
					 Mesh::FILL_NEIGH | 
					 Mesh::FILL_BOUND);
    while (elInfo) {
      TEST_EXIT_DBG(elInfo->getLevel() == 0)("Should not happen!\n");

      Element *el = elInfo->getElement();
      macroElIndexMap.insert(make_pair(el->getIndex(), el));
      macroElIndexTypeMap.insert(make_pair(el->getIndex(), elInfo->getType()));
     
      // Add all sub object of the element to the variable elObjDb.
      elObjDb.addElement(elInfo);

      elInfo = stack.traverseNext(elInfo);
    }


    // Create periodic data, if there are periodic boundary conditions.
    elObjDb.createPeriodicData(feSpaces[0]);

    // Create data about the reverse modes of neighbouring elements.
    elObjDb.createReverseModeData(feSpaces[0], macroElIndexMap, 
				  macroElIndexTypeMap);

    // Create mesh element data for this rank.
    elObjDb.createRankData(partitionMap, levelData);
  }


  void MeshDistributor::createBoundaryData()
  {
    FUNCNAME("MeshDistributor::createBoundaryData()");

    // === Clear all relevant data structures. ===

    rankIntBoundary.clear();
    otherIntBoundary.clear();
    periodicBoundary.clear();

    // === Create interior boundary data structure. ===

    for (int geoPos = 0; geoPos < mesh->getDim(); geoPos++) {
      GeoIndex geoIndex = INDEX_OF_DIM(geoPos, mesh->getDim());

      while (elObjDb.iterate(geoIndex)) {
	map<int, ElementObjectData>& objData = elObjDb.getIterateData();
	if (!(objData.count(mpiRank) && objData.size() > 1))
	  continue;

	int owner = elObjDb.getIterateOwner();
	ElementObjectData& rankBoundEl = objData[mpiRank];
	
	AtomicBoundary bound;
	bound.maxLevel = elObjDb.getIterateMaxLevel();

	bound.rankObj.el = macroElIndexMap[rankBoundEl.elIndex];
	bound.rankObj.elIndex = rankBoundEl.elIndex;
	bound.rankObj.elType = macroElIndexTypeMap[rankBoundEl.elIndex];
	bound.rankObj.subObj = geoIndex;
	bound.rankObj.ithObj = rankBoundEl.ithObject;
	
	if (geoIndex == FACE) {
	  for (int edgeNo = 0; edgeNo < 3; edgeNo++) {
	    int edgeOfFace = 
	      bound.rankObj.el->getEdgeOfFace(bound.rankObj.ithObj, edgeNo);
	    
	    bound.rankObj.excludedSubstructures.push_back(make_pair(EDGE, edgeOfFace));
	  }
	}
	
	
	if (owner == mpiRank) {
	  for (map<int, ElementObjectData>::iterator it2 = objData.begin();
	       it2 != objData.end(); ++it2) {
	    if (it2->first == mpiRank)
	      continue;
	    
	    bound.neighObj.el = macroElIndexMap[it2->second.elIndex];
	    bound.neighObj.elIndex = it2->second.elIndex;
	    bound.neighObj.elType = macroElIndexTypeMap[it2->second.elIndex];
	    bound.neighObj.subObj = geoIndex;
	    bound.neighObj.ithObj = it2->second.ithObject;
	    
	    bound.type = INTERIOR;
	    
	    AtomicBoundary& b = rankIntBoundary.getNewAtomic(it2->first);
	    b = bound;
	    if (geoIndex == EDGE)
	      b.neighObj.reverseMode = 
		elObjDb.getEdgeReverseMode(rankBoundEl, it2->second);
	    if (geoIndex == FACE)
	      b.neighObj.reverseMode = 
		elObjDb.getFaceReverseMode(rankBoundEl, it2->second);
	  }
	  
	} else {
	  TEST_EXIT_DBG(objData.count(owner) == 1)
	    ("Should not happen!\n");
	  
	  ElementObjectData& ownerBoundEl = objData[owner];
	  
	  bound.neighObj.el = macroElIndexMap[ownerBoundEl.elIndex];
	  bound.neighObj.elIndex = ownerBoundEl.elIndex;
	  bound.neighObj.elType = -1;
	  bound.neighObj.subObj = geoIndex;
	  bound.neighObj.ithObj = ownerBoundEl.ithObject;
	  
	  bound.type = INTERIOR;
	  
	  AtomicBoundary& b = otherIntBoundary.getNewAtomic(owner);
	  b = bound;	    
	  if (geoIndex == EDGE)
	    b.rankObj.reverseMode =
	      elObjDb.getEdgeReverseMode(rankBoundEl, ownerBoundEl);
	  if (geoIndex == FACE)
	    b.rankObj.reverseMode = 
	      elObjDb.getFaceReverseMode(rankBoundEl, ownerBoundEl);
	}
      }
    }


    // === Create periodic boundary data structure. ===

    for (PerBoundMap<DegreeOfFreedom>::iterator it = elObjDb.getPeriodicVertices().begin();
	 it != elObjDb.getPeriodicVertices().end(); ++it) {
      if (elObjDb.isInRank(it->first.first, mpiRank) == false)
	continue;

      ElementObjectData& perDofEl0 = 
	elObjDb.getElementsInRank(it->first.first)[mpiRank];

      for (map<int, ElementObjectData>::iterator elIt = elObjDb.getElementsInRank(it->first.second).begin();
	   elIt != elObjDb.getElementsInRank(it->first.second).end(); ++elIt) {

	int otherElementRank = elIt->first;
	ElementObjectData& perDofEl1 = elIt->second;

	AtomicBoundary bound;
	bound.rankObj.el = macroElIndexMap[perDofEl0.elIndex];
	bound.rankObj.elIndex = perDofEl0.elIndex;
	bound.rankObj.elType = macroElIndexTypeMap[perDofEl0.elIndex];
	bound.rankObj.subObj = VERTEX;
	bound.rankObj.ithObj = perDofEl0.ithObject;

	bound.neighObj.el = macroElIndexMap[perDofEl1.elIndex];
	bound.neighObj.elIndex = perDofEl1.elIndex;
	bound.neighObj.elType = macroElIndexTypeMap[perDofEl1.elIndex];
	bound.neighObj.subObj = VERTEX;
	bound.neighObj.ithObj = perDofEl1.ithObject;

	bound.type = it->second;

	if (sebastianMode) {
	  if (bound.rankObj.elIndex == 3 &&
	      bound.rankObj.ithObj == 1 ||
	      bound.rankObj.elIndex == 78 &&
	      bound.rankObj.ithObj == 2) {
	    AtomicBoundary& b = periodicBoundary.getNewAtomic(otherElementRank);
	    b = bound;
	  }
	} else {
	  AtomicBoundary& b = periodicBoundary.getNewAtomic(otherElementRank);
	  b = bound;	    
	}
      }
    }


    for (PerBoundMap<DofEdge>::iterator it = elObjDb.getPeriodicEdges().begin();
	 it != elObjDb.getPeriodicEdges().end(); ++it) {
      if (elObjDb.isInRank(it->first.first, mpiRank) == false)
	continue;

      ElementObjectData& perEdgeEl0 = elObjDb.getElementsInRank(it->first.first)[mpiRank];

      for (map<int, ElementObjectData>::iterator elIt = elObjDb.getElementsInRank(it->first.second).begin();
 	   elIt != elObjDb.getElementsInRank(it->first.second).end(); ++elIt) {
      
	int otherElementRank = elIt->first;
	ElementObjectData& perEdgeEl1 = elIt->second;

	AtomicBoundary bound;	    	    
	bound.rankObj.el = macroElIndexMap[perEdgeEl0.elIndex];
	bound.rankObj.elIndex = perEdgeEl0.elIndex;
	bound.rankObj.elType = macroElIndexTypeMap[perEdgeEl0.elIndex];
	bound.rankObj.subObj = EDGE;
	bound.rankObj.ithObj = perEdgeEl0.ithObject;
	
	bound.neighObj.el = macroElIndexMap[perEdgeEl1.elIndex];
	bound.neighObj.elIndex = perEdgeEl1.elIndex;
	bound.neighObj.elType = macroElIndexTypeMap[perEdgeEl1.elIndex];
	bound.neighObj.subObj = EDGE;
	bound.neighObj.ithObj = perEdgeEl1.ithObject;
	
	bound.type = it->second;
	
	AtomicBoundary& b = periodicBoundary.getNewAtomic(otherElementRank);
	b = bound;
     
	if (mpiRank > otherElementRank)
	  b.neighObj.reverseMode = 
	    elObjDb.getEdgeReverseMode(perEdgeEl0, perEdgeEl1);
	else
	  b.rankObj.reverseMode = 
	    elObjDb.getEdgeReverseMode(perEdgeEl0, perEdgeEl1);
      }
    }


    for (PerBoundMap<DofFace>::iterator it = elObjDb.getPeriodicFaces().begin();
	 it != elObjDb.getPeriodicFaces().end(); ++it) {
      if (elObjDb.isInRank(it->first.first, mpiRank) == false)
	continue;

      TEST_EXIT_DBG(elObjDb.getElements(it->first.first).size() == 1)
 	("Should not happen!\n");
      TEST_EXIT_DBG(elObjDb.getElements(it->first.second).size() == 1)
 	("Should not happen!\n");

      ElementObjectData& perFaceEl0 = elObjDb.getElementsInRank(it->first.first)[mpiRank];

      for (map<int, ElementObjectData>::iterator elIt = elObjDb.getElementsInRank(it->first.second).begin();
 	   elIt != elObjDb.getElementsInRank(it->first.second).end(); ++elIt) {
      
	int otherElementRank = elIt->first;
	ElementObjectData& perFaceEl1 = elIt->second;

	AtomicBoundary bound;	    	    
	bound.rankObj.el = macroElIndexMap[perFaceEl0.elIndex];
	bound.rankObj.elIndex = perFaceEl0.elIndex;
	bound.rankObj.elType = macroElIndexTypeMap[perFaceEl0.elIndex];
	bound.rankObj.subObj = FACE;
	bound.rankObj.ithObj = perFaceEl0.ithObject;
	
	bound.neighObj.el = macroElIndexMap[perFaceEl1.elIndex];
	bound.neighObj.elIndex = perFaceEl1.elIndex;
	bound.neighObj.elType = macroElIndexTypeMap[perFaceEl1.elIndex];
	bound.neighObj.subObj = FACE;
	bound.neighObj.ithObj = perFaceEl1.ithObject;
	
	bound.type = it->second;
	
	AtomicBoundary& b = periodicBoundary.getNewAtomic(otherElementRank);
	b = bound;
     
	if (mpiRank > otherElementRank)
	  b.neighObj.reverseMode = 
	    elObjDb.getFaceReverseMode(perFaceEl0, perFaceEl1);
	else
	  b.rankObj.reverseMode = 
	    elObjDb.getFaceReverseMode(perFaceEl0, perFaceEl1);
      }
    }
    

    // === Once we have this information, we must care about the order of the ===
    // === atomic bounds in the three boundary handling object. Eventually    ===
    // === all the boundaries have to be in the same order on both ranks that ===
    // === share the bounday.                                                 ===

    StdMpi<vector<AtomicBoundary> > stdMpi(mpiComm);
    stdMpi.send(rankIntBoundary.boundary);
    stdMpi.recv(otherIntBoundary.boundary);
    stdMpi.startCommunication();


    // === The information about all neighbouring boundaries has been         ===
    // === received. So the rank tests if its own atomic boundaries are in    ===
    // === the same order. If not, the atomic boundaries are swaped to the    ===
    // === correct order.                                                     ===

    for (RankToBoundMap::iterator rankIt = otherIntBoundary.boundary.begin();
	 rankIt != otherIntBoundary.boundary.end(); ++rankIt) {

      // === We have received from rank "rankIt->first" the ordered list of   ===
      // === element indices. Now, we have to sort the corresponding list in  ===
      // === this rank to get the same order.                                 ===
     
      for (unsigned int j = 0; j < rankIt->second.size(); j++) {

	// If the expected object is not at place, search for it.

	BoundaryObject &recvedBound = stdMpi.getRecvData()[rankIt->first][j].rankObj;

	if ((rankIt->second)[j].neighObj != recvedBound) {
	  unsigned int k = j + 1;

	  for (; k < rankIt->second.size(); k++)
 	    if ((rankIt->second)[k].neighObj == recvedBound)
	      break;

	  // The element must always be found, because the list is just in
	  // another order.
	  TEST_EXIT_DBG(k < rankIt->second.size())("Should never happen!\n");

	  // Swap the current with the found element.
	  AtomicBoundary tmpBound = (rankIt->second)[k];
	  (rankIt->second)[k] = (rankIt->second)[j];
	  (rankIt->second)[j] = tmpBound;	
	}
      }
    }


    // === Do the same for the periodic boundaries. ===

    if (periodicBoundary.boundary.size() > 0) {
      stdMpi.clear();

      InteriorBoundary sendBounds, recvBounds;
      for (RankToBoundMap::iterator rankIt = periodicBoundary.boundary.begin();
	   rankIt != periodicBoundary.boundary.end(); ++rankIt) {

	if (rankIt->first == mpiRank)
	  continue;

	if (rankIt->first < mpiRank)
	  sendBounds.boundary[rankIt->first] = rankIt->second;
	else
	  recvBounds.boundary[rankIt->first] = rankIt->second;	
      }

      stdMpi.send(sendBounds.boundary);
      stdMpi.recv(recvBounds.boundary);
      stdMpi.startCommunication();

      for (RankToBoundMap::iterator rankIt = periodicBoundary.boundary.begin();
	   rankIt != periodicBoundary.boundary.end(); ++rankIt) {

 	if (rankIt->first <= mpiRank)
 	  continue;
  
	for (unsigned int j = 0; j < rankIt->second.size(); j++) {
	  BoundaryObject &recvRankObj = 
	    stdMpi.getRecvData()[rankIt->first][j].rankObj;
	  BoundaryObject &recvNeighObj = 
	    stdMpi.getRecvData()[rankIt->first][j].neighObj;

	  if (periodicBoundary.boundary[rankIt->first][j].neighObj != recvRankObj ||
	      periodicBoundary.boundary[rankIt->first][j].rankObj != recvNeighObj) {
	    unsigned int k = j + 1;	    
	    for (; k < rankIt->second.size(); k++)
	      if (periodicBoundary.boundary[rankIt->first][k].neighObj == recvRankObj &&
		  periodicBoundary.boundary[rankIt->first][k].rankObj == recvNeighObj)
		break;
	    
	    // The element must always be found, because the list is just in 
	    // another order.
	    TEST_EXIT_DBG(k < rankIt->second.size())("Should never happen!\n");

	    // Swap the current with the found element.
	    AtomicBoundary tmpBound = (rankIt->second)[k];
	    (rankIt->second)[k] = (rankIt->second)[j];
	    (rankIt->second)[j] = tmpBound;	
	  } 
	}
      }     
    } // periodicBoundary.boundary.size() > 0
  }


  void MeshDistributor::createBoundaryDofs()
  {
    FUNCNAME("MeshDistributor::createBoundaryDofs()");

    int nLevels = levelData.getLevelNumber();
    TEST_EXIT_DBG(nLevels >= 1)("Should not happen!\n");

    sendDofs.init(nLevels);
    recvDofs.init(nLevels);

    boundaryDofInfo.resize(nLevels);

    for (unsigned int i = 0; i < feSpaces.size(); i++)
      for (int j = 0; j < nLevels; j++)
	createBoundaryDofs(feSpaces[i], j);
  }


  void MeshDistributor::createBoundaryDofs(const FiniteElemSpace *feSpace, 
					   int level)
  {
    FUNCNAME("MeshDistributor::createBoundaryDofs()");

    if (createBoundaryDofFlag.isSet(BOUNDARY_SUBOBJ_SORTED)) {

      TEST_EXIT(level < boundaryDofInfo.size())("Should not happen!\n");

      // === Clear data. ===
      for (int geo = FACE; geo >= VERTEX; geo--)
	boundaryDofInfo[level][feSpace].geoDofs[static_cast<GeoIndex>(geo)].clear();

      // === Create send DOFs. ===
      for (int geo = FACE; geo >= VERTEX; geo--) {
	for (InteriorBoundary::iterator it(rankIntBoundary, level); 
	     !it.end(); ++it) {
	  if (it->rankObj.subObj == geo) {
	    DofContainer dofs;
	    it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);

	    DofContainer& tmp = 
	      sendDofs.getDofContainer(it.getRank(), feSpace, level);
	    tmp.insert(tmp.end(), dofs.begin(), dofs.end());

	    if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_SEND_DOFS))
	      boundaryDofInfo[level][feSpace].geoDofs[static_cast<GeoIndex>(geo)].insert(dofs.begin(), dofs.end());
	  }
	}
      }

      // === Create recv DOFs. ===
      for (int geo = FACE; geo >= VERTEX; geo--) {
	for (InteriorBoundary::iterator it(otherIntBoundary, level); 
	     !it.end(); ++it) {
	  if (it->rankObj.subObj == geo) {
	    DofContainer dofs;
	    it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);

	    DofContainer& tmp = 
	      recvDofs.getDofContainer(it.getRank(), feSpace, level);
	    tmp.insert(tmp.end(), dofs.begin(), dofs.end());

	    if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_RECV_DOFS))
	      boundaryDofInfo[level][feSpace].geoDofs[static_cast<GeoIndex>(geo)].insert(dofs.begin(), dofs.end());
	  }
	}
      }
    } else {
      for (InteriorBoundary::iterator it(rankIntBoundary, level);
	   !it.end(); ++it)
	it->rankObj.el->getAllDofs(feSpace, it->rankObj, 
				   sendDofs.getDofContainer(it.getRank(), feSpace, level));
      
      for (InteriorBoundary::iterator it(otherIntBoundary, level); 
	   !it.end(); ++it)
	it->rankObj.el->getAllDofs(feSpace, it->rankObj, 
				   recvDofs.getDofContainer(it.getRank(), feSpace, level));
    }

    // === Delete all empty DOF send and recv positions ===

    sendDofs.removeEmpty();
    recvDofs.removeEmpty();
  }


  void MeshDistributor::removeMacroElements()
  {
    FUNCNAME("MeshDistributor::removeMacroElements()");
    
    std::set<MacroElement*> macrosToRemove;
    for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements(); ++it)
      if (partitioner->getElementInRank()[(*it)->getIndex()] == false)
	macrosToRemove.insert(*it);    

    mesh->removeMacroElements(macrosToRemove, feSpaces);
  }


  void MeshDistributor::updateLocalGlobalNumbering()
  {
    FUNCNAME("MeshDistributor::updateLocalGlobalNumbering()");

#if (DEBUG != 0)
    debug::ElementIdxToDofs elMap;
    debug::createSortedDofs(mesh, elMap);   
#endif

    int nLevels = levelData.getLevelNumber();
    TEST_EXIT_DBG(nLevels >= 1)("Should not happen!\n");

    dofMap.init(levelData, feSpaces, feSpaces, true, true);
    dofMap.setDofComm(sendDofs, recvDofs);
    dofMap.clear();

    createBoundaryDofs();

    for (unsigned int i = 0; i < feSpaces.size(); i++)
      updateLocalGlobalNumbering(feSpaces[i]);

    dofMap.update();

#if (DEBUG != 0)
    MSG("------------- Debug information -------------\n");
    MSG("|  number of levels:         %d\n", nLevels);
    MSG("|  number of FE spaces:      %d\n", feSpaces.size());

    for (int level = 0; level < nLevels; level++) {
      for (unsigned int i = 0; i < feSpaces.size(); i++) {
	MSG("|  level = %d   FE space = %d:\n", level, i);
	MSG("|      nRankDofs    = %d\n", dofMap[feSpaces[i]].nRankDofs[level]);
	MSG("|      nOverallDofs = %d\n", dofMap[feSpaces[i]].nOverallDofs[level]);
	MSG("|      rStartDofs   = %d\n", dofMap[feSpaces[i]].rStartDofs[level]);
      }
    }

    stringstream oss;
    oss << debugOutputDir << "elementIndex-" << mpiRank << ".vtu";
    debug::writeElementIndexMesh(mesh, oss.str());
    ParallelDebug::writeDebugFile(*this, debugOutputDir + "mpi-dbg", "dat");
    debug::testSortedDofs(mesh, elMap);
    ParallelDebug::testCommonDofs(*this, true);
    ParallelDebug::testGlobalIndexByCoords(*this);   
#else
    int tmp = 0;
    Parameters::get(name + "->write parallel debug file", tmp);
    if (tmp)
      ParallelDebug::writeDebugFile(*this, debugOutputDir + "mpi-dbg", "dat");
#endif
  }


  void MeshDistributor::updateLocalGlobalNumbering(const FiniteElemSpace *feSpace)
  {
    FUNCNAME("MeshDistributor::updateLocalGlobalNumbering()");

    mesh->dofCompress();

    // === Get all DOFs in ranks partition. ===

    std::set<const DegreeOfFreedom*> rankDofSet;
    mesh->getAllDofs(feSpace, rankDofSet);

    DofContainer rankDofs(rankDofSet.begin(), rankDofSet.end());
    sort(rankDofs.begin(), rankDofs.end(), cmpDofsByValue);

    // === Traverse interior boundaries and get all DOFs on them. ===

    int nLevels = levelData.getLevelNumber();
    for (int level = 0; level < nLevels; level++) {
      DofContainerSet nonRankDofs;
      for (DofComm::Iterator it(recvDofs, level, feSpace); !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof())
	  nonRankDofs.insert(it.getDof());
      
      for (unsigned int i = 0; i < rankDofs.size(); i++)
	if (nonRankDofs.count(rankDofs[i]) == 0)
	  dofMap[feSpace].insertRankDof(level, *(rankDofs[i]));
      
      for (DofComm::Iterator it(recvDofs, level, feSpace); !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof())
	  dofMap[feSpace].insertNonRankDof(level, it.getDofIndex());
    }

    // === Update DOF admins due to new number of DOFs. ===
  
    lastMeshChangeIndex = mesh->getChangeIndex();

#if (DEBUG != 0)
    ParallelDebug::testDofContainerCommunication(*this, 
						 sendDofs.getData(), 
						 recvDofs.getData());
#endif
  }


  void MeshDistributor::createPeriodicMap()
  {
    FUNCNAME("MeshDistributor::createPeriodicMap()");

    // Clear all periodic DOF mappings calculated before. We do it from scratch.
    periodicDofs.init(levelData.getLevelNumber());
    periodicMap.clear();

    // If there are no periodic boundaries, return. Note that periodicDofs and
    // periodicMap must be still cleared before: if we do repartitioning and
    // there were periodic boundaries in subdomain before and after repartitioning
    // there are no more periodic boundaries.
    if (periodicBoundary.boundary.size() == 0)
      return;

    for (unsigned int i = 0; i < feSpaces.size(); i++)
      createPeriodicMap(feSpaces[i]);
  }


  void MeshDistributor::createPeriodicMap(const FiniteElemSpace *feSpace)
  {
    FUNCNAME("MeshDistributor::createPeriodicMap()");

    StdMpi<vector<int> > stdMpi(mpiComm, false);

    // === Each rank traverse its periodic boundaries and sends the DOF      ===
    // === indices to the rank "on the other side" of the periodic boundary. ===

    map<int, vector<int> > rankToDofType;

    for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
	 it != periodicBoundary.boundary.end(); ++it) {

      if (it->first == mpiRank) {
	// Here we have a periodic boundary within rank's subdomain. So we can
	// compute the periodic mappings without communication.

	TEST_EXIT_DBG(it->second.size() % 2 == 0)("Should not happen!\n");

	for (unsigned int i = 0; i < it->second.size(); i++) {
	  AtomicBoundary &bound = it->second[i];

	  TEST_EXIT_DBG(bound.rankObj.el)("No rank object!\n");
	  TEST_EXIT_DBG(bound.neighObj.el)("No neigh object!\n");

	  DofContainer dofs0, dofs1;
	  bound.rankObj.el->getAllDofs(feSpace, bound.rankObj, dofs0);
	  bound.neighObj.el->getAllDofs(feSpace, bound.neighObj, dofs1);

	  TEST_EXIT_DBG(dofs0.size() == dofs1.size())
	    ("Number of DOFs does not fit together: %d %d\n", 
	     dofs0.size(), dofs1.size());	  

	  BoundaryType type = bound.type;

	  for (unsigned int j = 0; j < dofs0.size(); j++) {
	    DegreeOfFreedom globalDof0 = dofMap[feSpace][0][*(dofs0[j])].global;
	    DegreeOfFreedom globalDof1 = dofMap[feSpace][0][*(dofs1[j])].global;

	    if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDof0))
	      periodicMap.add(feSpace, type, globalDof0, globalDof1);
	  }
	}

      } else {
	// Here we have a periodic boundary between two ranks.

	// Create DOF indices on the boundary. 
	DofContainer& dofs = periodicDofs.getDofContainer(it->first, feSpace);
	for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	     boundIt != it->second.end(); ++boundIt) {

	  int nDofs = dofs.size();
	  boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);

	  for (unsigned int i = 0; i < (dofs.size() - nDofs); i++)
	    rankToDofType[it->first].push_back(boundIt->type);
	}
	
	// Send the global indices to the rank on the other side.
	stdMpi.getSendData(it->first).reserve(dofs.size());
	for (unsigned int i = 0; i < dofs.size(); i++)
	  stdMpi.getSendData(it->first).push_back(dofMap[feSpace][0][*(dofs[i])].global);
	
	// Receive from this rank the same number of dofs.
	stdMpi.recv(it->first, dofs.size());
      }
    }

    stdMpi.updateSendDataSize();
    stdMpi.startCommunication();


    // === The rank has received the DOFs from the rank on the other side of ===
    // === the boundary. Now it can use them to create the mapping between   ===
    // === the periodic DOFs in this rank and the corresponding periodic     ===
    // === DOFs from the other ranks.                                        ===


    for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
	 it != periodicBoundary.boundary.end(); ++it) {
      DofContainer& dofs = periodicDofs.getDofContainer(it->first, feSpace);
      vector<int>& types = rankToDofType[it->first];

      TEST_EXIT_DBG(dofs.size() == types.size())("Should not happen!\n");

      // Added the received DOFs to the mapping.
      for (unsigned int i = 0; i < dofs.size(); i++) {
	int globalDofIndex = dofMap[feSpace][0][*(dofs[i])].global;
	int mapGlobalDofIndex = stdMpi.getRecvData(it->first)[i];
	BoundaryType type = types[i];

	// Check if this global DOF with the corresponding boundary type was
	// not added before by another periodic boundary from other rank.
	if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDofIndex))
	  periodicMap.add(feSpace, type, globalDofIndex, mapGlobalDofIndex);
      }
    }


    StdMpi<PeriodicDofMap> stdMpi2(mpiComm);


    for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
	 it != periodicBoundary.boundary.end(); ++it) {
      if (it->first == mpiRank)
	continue;

      PeriodicDofMap perObjMap;

      for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
	   boundIt != it->second.end(); ++boundIt) {
	// If the boundary type is a normal periodic BC, continue. We just
	// operate on indirectly connected periodic boundaries.
	if (elObjDb.isValidPeriodicType(boundIt->type))
	  continue;
	
	DofContainer dofs;
	boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);

	for (unsigned int i = 0; i < dofs.size(); i++) {
	  DegreeOfFreedom globalDof = dofMap[feSpace][0][*dofs[i]].global;

	  std::set<BoundaryType>& assoc = 
	    periodicMap.getAssociations(feSpace, globalDof);
	  TEST_EXIT_DBG(assoc.size() > 0)("Should not happen!\n");

	  for (std::set<BoundaryType>::iterator perAscIt = assoc.begin();
	       perAscIt != assoc.end(); ++perAscIt)
	    if (elObjDb.isValidPeriodicType(*perAscIt))
	      perObjMap[*perAscIt][globalDof] = 
		periodicMap.map(feSpace, *perAscIt, globalDof);	    
	}
      }

      stdMpi2.send(it->first, perObjMap);
      stdMpi2.recv(it->first);
    }

    stdMpi2.startCommunication();

    // NOTE: Before changing the data structure of periodic boundary DOFS,
    //       at this place no periodicDofAssociations are set for the received
    //       DOFs. I'm note sure what is correct here.
    for (map<int, PeriodicDofMap>::iterator it = stdMpi2.getRecvData().begin();
	 it != stdMpi2.getRecvData().end(); ++it)
      periodicMap.add(feSpace, it->second);
  }


  void MeshDistributor::createMacroElementInfo()
  {
    FUNCNAME("MeshDistributor::createMacroElementInfo()");

    for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
	 it != mesh->endOfMacroElements(); ++it) {

      allMacroElements.push_back(*it);

      int elIndex = (*it)->getIndex();

      macroElementNeighbours[elIndex].resize(mesh->getGeo(NEIGH));
      for (int i = 0; i < mesh->getGeo(NEIGH); i++)
	macroElementNeighbours[elIndex][i] = 
	  (*it)->getNeighbour(i) ? (*it)->getNeighbour(i)->getIndex() : -1;
    }     
  }


  void MeshDistributor::updateMacroElementInfo()
  {
    deque<MacroElement*>& meshMacros = mesh->getMacroElements();

    for (unsigned int i = 0; i < allMacroElements.size(); i++) {
      for (deque<MacroElement*>::iterator it = meshMacros.begin();
	   it != meshMacros.end(); ++it) {
	if ((*it)->getIndex() == allMacroElements[i]->getIndex() &&
	    *it != allMacroElements[i]) {
	  delete allMacroElements[i];
	  allMacroElements[i] = *it;
	}
      }
    }
  }


  void MeshDistributor::serialize(ostream &out)
  {
    FUNCNAME("MeshDistributor::serialize()");

    checkMeshChange(false);
    
    partitioner->serialize(out);

    SerUtil::serialize(out, elemWeights);
    SerUtil::serialize(out, partitionMap);

    elObjDb.serialize(out);

    rankIntBoundary.serialize(out);
    otherIntBoundary.serialize(out);
    periodicBoundary.serialize(out);

    serialize(out, sendDofs.getData());
    serialize(out, recvDofs.getData());

    // === Serialieze FE space dependent data ===

    dofMap.serialize(out);

    periodicMap.serialize(out, feSpaces);

    SerUtil::serialize(out, macroElementNeighbours);

    int nSize = allMacroElements.size();
    SerUtil::serialize(out, nSize);
    for (int i = 0; i < nSize; i++)
      allMacroElements[i]->serialize(out);

    SerUtil::serialize(out, nMeshChangesAfterLastRepartitioning);
    SerUtil::serialize(out, repartitioningCounter);

    levelData.serialize(out);
  }


  void MeshDistributor::deserialize(istream &in)
  {
    FUNCNAME("MeshDistributor::deserialize()");

    partitioner->deserialize(in);

    SerUtil::deserialize(in, elemWeights);
    SerUtil::deserialize(in, partitionMap);

    // Create two maps: one from from element indices to the corresponding element 
    // pointers, and one map from Dof indices to the corresponding dof pointers.
    map<int, Element*> elIndexMap;
    map<const FiniteElemSpace*, map<int, const DegreeOfFreedom*> > dofIndexMap;
    for (unsigned int i = 0; i < feSpaces.size(); i++) {
      ElementDofIterator elDofIter(feSpaces[i]);
      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
      while (elInfo) {
	Element *el = elInfo->getElement();
	elIndexMap[el->getIndex()] = el;
	
	if (el->isLeaf()) {
	  elDofIter.reset(el);
	  do {
	    dofIndexMap[feSpaces[i]][elDofIter.getDof()] = elDofIter.getDofPtr();
	  } while (elDofIter.next());      
	}
	
	elInfo = stack.traverseNext(elInfo);
      }
    }

    elObjDb.deserialize(in);
   
    rankIntBoundary.deserialize(in, elIndexMap);
    otherIntBoundary.deserialize(in, elIndexMap);
    periodicBoundary.deserialize(in, elIndexMap);

    deserialize(in, sendDofs.getData(), dofIndexMap);
    deserialize(in, recvDofs.getData(), dofIndexMap);

    // === Deerialieze FE space dependent data ===
    
    dofMap.deserialize(in);

    periodicMap.deserialize(in, feSpaces);

    SerUtil::deserialize(in, macroElementNeighbours);

    int nSize = 0;
    SerUtil::deserialize(in, nSize);
    allMacroElements.resize(nSize);
    for (int i = 0; i < nSize; i++) {
      // We do not need the neighbour indices, but must still read them.
      vector<int> indices;
      allMacroElements[i] = new MacroElement(mesh->getDim());
      allMacroElements[i]->writeNeighboursTo(&indices);
      allMacroElements[i]->deserialize(in);
      allMacroElements[i]->getElement()->setMesh(mesh);
    }

    SerUtil::deserialize(in, nMeshChangesAfterLastRepartitioning);
    SerUtil::deserialize(in, repartitioningCounter);

    levelData.deserialize(in);

    deserialized = true;
  }

}