MeshDistributor.h 19.8 KB
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// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
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// ==  http://www.amdis-fem.org                                              ==
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// ==                                                                        ==
// ============================================================================
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//
// 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.


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/** \file MeshDistributor.h */
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#ifndef AMDIS_MESHDISTRIBUTOR_H
#define AMDIS_MESHDISTRIBUTOR_H
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#include <mpi.h>
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#include "parallel/DofComm.h"
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#include "parallel/ElementObjectDatabase.h"
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#include "parallel/ParallelTypes.h"
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#include "parallel/MeshLevelData.h"
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#include "parallel/MeshPartitioner.h"
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#include "parallel/InteriorBoundary.h"
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#include "parallel/ParallelDofMapping.h"
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#include "parallel/PeriodicMap.h"
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#include "parallel/StdMpi.h"
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#include "AMDiS_fwd.h"
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#include "Containers.h"
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#include "Global.h"
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#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
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#include "FiniteElemSpace.h"
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#include "Serializer.h"
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#include "BoundaryManager.h"
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#include "SystemVector.h"
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namespace AMDiS {
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  using namespace std;
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  struct BoundaryDofInfo
  {
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    map<GeoIndex, DofContainerSet> geoDofs;
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  };

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  class MeshDistributor
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  {
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  private:
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    MeshDistributor();
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    virtual ~MeshDistributor() {}
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  public:
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    void initParallelization();
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    void exitParallelization();
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    /// Adds a DOFVector to the set of \ref interchangeVecs. Thus, this vector 
    /// will be automatically interchanged between ranks when mesh is 
    /// repartitioned.
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    void addInterchangeVector(DOFVector<double> *vec)
    {
      interchangeVectors.push_back(vec);
    }

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    /// Adds all DOFVectors of a SystemVector to \ref interchangeVecs.
    void addInterchangeVector(SystemVector *vec)
    {
      for (int i = 0; i < vec->getSize(); i++)
	interchangeVectors.push_back(vec->getDOFVector(i));
    }
    
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    /** \brief
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     * This function checks if the mesh has changed on at least on rank. In 
     * this case, the interior boundaries are adapted on all ranks such that 
     * they fit together on all ranks. Furthermore the function 
     * \ref updateLocalGlobalNumbering() is called to update the DOF numberings 
     * and mappings on all rank due to the new mesh structure.
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     *
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     * \param[in]  tryRepartition   If this parameter is true, repartitioning 
     *                              may be done. This depends on several other 
     *                              parameters. If the parameter is false, the 
     *                              mesh is only checked and adapted but never 
     *                              repartitioned.
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     */
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    void checkMeshChange(bool tryRepartition = true);
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    /** \brief
     * Checks if is required to repartition the mesh. If this is the case, a new
     * partition will be created and the mesh will be redistributed between the
     * ranks.
     */
    void repartitionMesh();
    
    /// Calculates the imbalancing factor and prints it to screen.
    void printImbalanceFactor();

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    /** \brief
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     * Test, if the mesh consists of macro elements only. The mesh partitioning 
     * of the parallelization works for macro meshes only and would fail, if the 
     * mesh is already refined in some way. Therefore, this function will exit
     * the program if it finds a non macro element in the mesh.
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     */
    void testForMacroMesh();
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    /// Set for each element on the partitioning level the number of 
    /// leaf elements.
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    void setInitialElementWeights();
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    inline virtual string getName() 
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    { 
      return name; 
    }
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    inline Mesh* getMesh()
    {
      return mesh;
    }

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    /// Returns an FE space from \ref feSpaces.
    inline const FiniteElemSpace* getFeSpace(unsigned int i = 0)
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    {
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      FUNCNAME("MeshDistributor::getFeSpace()");

      TEST_EXIT_DBG(i < feSpaces.size())("Should not happen!\n");

      return feSpaces[i];
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    }
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    /// Returns all FE spaces, thus \ref feSpaces.
    inline vector<const FiniteElemSpace*>& getFeSpaces()
    {
      return feSpaces;
    }

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    /// Returns the DOF mapping object, \ref dofMap.
    inline ParallelDofMapping& getDofMap()
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    {
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      return dofMap;
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    }

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    /// Returns the periodic mapping handler, \ref periodicMap.
    inline PeriodicMap& getPeriodicMap()
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    {
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      return periodicMap;
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    }
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    /// Returns for a global index the DOF index in rank's subdomain. As there
    /// is no direct data structure that stores this information, we have to
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    /// search for it in \ref dofMap. This is not very efficient and this 
    /// function should thus be used for debugging only.
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    DegreeOfFreedom mapGlobalToLocal(const FiniteElemSpace *feSpace,
				     DegreeOfFreedom dof);
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    DofComm& getSendDofs()
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    {
      return sendDofs;
    }

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    DofComm& getRecvDofs()
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    {
      return recvDofs;
    }

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    DofComm& getPeriodicDofs()
    {
      return periodicDofs;
    }

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    inline long getLastMeshChangeIndex()
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    {
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      return lastMeshChangeIndex;
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    }
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    inline int getMpiRank()
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    {
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      return mpiRank;
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    }
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    inline int getMpiSize()
    {
      return mpiSize;
    }

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    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
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    }

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    inline bool isInitialized()
    {
      return initialized;
    }

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    // Writes all data of this object to an output stream.
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    void serialize(ostream &out);
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    // Reads the object data from an input stream.
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    void deserialize(istream &in);
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    /** \brief
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     * This function must be used if the values of a DOFVector must be 
     * synchronised over all ranks. That means, that each rank sends the 
     * values of the DOFs, which are owned by the rank and lie on an interior 
     * bounday, to all other ranks also having these DOFs.
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     *
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     * This function must be used, for example, after the lineary system is 
     * solved, or after the DOFVector is set by some user defined functions, 
     * e.g., initial solution functions.
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     */    
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    template<typename T>
    void synchVector(DOFVector<T> &vec) 
    {
      StdMpi<vector<T> > stdMpi(mpiComm);

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      const FiniteElemSpace *fe = vec.getFeSpace();

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      for (DofComm::Iterator it(sendDofs, fe); !it.end(); it.nextRank()) {
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	vector<T> dofs;
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	dofs.reserve(it.getDofs().size());
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	for (; !it.endDofIter(); it.nextDof())
	  dofs.push_back(vec[it.getDofIndex()]);
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	stdMpi.send(it.getRank(), dofs);
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      }
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      for (DofComm::Iterator it(recvDofs); !it.end(); it.nextRank())
        stdMpi.recv(it.getRank());
	     
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      stdMpi.startCommunication();
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      for (DofComm::Iterator it(recvDofs, fe); !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof())
	  vec[it.getDofIndex()] = 
	     stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
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    }
    
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    /** \brief
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     * Works in the same way as the function above defined for DOFVectors. Due
     * to performance, this function does not call \ref synchVector for each 
     * DOFVector, but instead sends all values of all DOFVectors all at once.
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     */
    void synchVector(SystemVector &vec);

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    void check3dValidMesh();

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    void setBoundaryDofRequirement(Flag flag)
    {
      createBoundaryDofFlag = flag;
    }

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    BoundaryDofInfo& getBoundaryDofInfo(const FiniteElemSpace *feSpace, 
					int level = 0)
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    {
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      FUNCNAME("MeshDistributor::getBoundaryDofInfo()");

      TEST_EXIT_DBG(level < static_cast<int>(boundaryDofInfo.size()))
	("Wrong level number: %d, whereas array size is %d!\n", 
	 level, boundaryDofInfo.size());

      return boundaryDofInfo[level][feSpace];
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    }

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    void getAllBoundaryDofs(const FiniteElemSpace *feSpace, 
			    int level,
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			    DofContainer& dofs);
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    const ElementObjectDatabase& getElementObjectDb() 
    {
      return elObjDb;
    }
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    /// Adds a stationary problem to the global mesh distributor objects.
    static void addProblemStatGlobal(ProblemStatSeq *probStat);
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    MeshLevelData& getMeshLevelData() 
    {
      return levelData;
    }

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  protected:
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    void addProblemStat(ProblemStatSeq *probStat);

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    /// Determines the interior boundaries, i.e. boundaries between ranks, and
    /// stores all information about them in \ref interiorBoundary.
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    void createInteriorBoundaryInfo();
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    void updateInteriorBoundaryInfo();

    void createMeshElementData();

    void createBoundaryData();
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    void createBoundaryDofs();

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    void createBoundaryDofs(const FiniteElemSpace *feSpace, int level);
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    /// Removes all macro elements from the mesh that are not part of ranks 
    /// partition.
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    void removeMacroElements();

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    void updateLocalGlobalNumbering();

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    /// Updates the local and global DOF numbering after the mesh has been 
    /// changed.
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    void updateLocalGlobalNumbering(const FiniteElemSpace *feSpace);
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    /// Calls \ref createPeriodicMap(feSpace) for all FE spaces that are
    /// handled by the mesh distributor.
    void createPeriodicMap();

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    /** \brief
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     * Creates, for a specific FE space, to all DOFs in rank's partition that 
     * are on a periodic boundary the mapping from dof index to the other 
     * periodic dof indices. This information is stored in \ref periodicDofMap.
     */    
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    void createPeriodicMap(const FiniteElemSpace *feSpace);
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    /** \brief
     * This function is called only once during the initialization when the
     * whole macro mesh is available on all cores. It copies the pointers of all
     * macro elements to \ref allMacroElements and stores all neighbour 
     * information based on macro element indices (and not pointer based) in 
     * \ref macroElementNeighbours. These information are then used to 
     * reconstruct macro elements during mesh redistribution.
     */
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    void createMacroElementInfo();

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    void updateMacroElementInfo();

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    /** \brief
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     * Checks for all given interior boundaries if the elements fit together on
     * both sides of the boundaries. If this is not the case, the mesh is 
     * adapted. Because refinement of a certain element may forces the 
     * refinement of other elements, it is not guaranteed that all rank's meshes
     * fit together after this function terminates. Hence, it must be called 
     * until a stable mesh refinement is reached.
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     *
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     * \param[in] allBound   Defines a map from rank to interior boundaries 
     *                       which should be checked.
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     *
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     * \return    If the mesh has  been changed by this function, it returns 
     *            true. Otherwise, it returns false, i.e., the given interior 
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     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
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    /// Sets \ref isRankDof to all matrices and rhs vectors in a given 
    /// stationary problem.
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    void setRankDofs(ProblemStatSeq *probStat);
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    /// Sets \ref isRankDof to all matrices and rhs vectors in all 
    /// stationary problems.
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    void setRankDofs();

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    /// Removes all periodic boundary condition information from all matrices and
    /// vectors of all stationary problems and from the mesh itself.
    void removePeriodicBoundaryConditions();

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    /// Removes all periodic boundary condition information from all matrices and
    /// vector of a given stationary problem.
    void removePeriodicBoundaryConditions(ProblemStatSeq *probStat);

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    // Removes all periodic boundaries from a given boundary map.
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    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
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    void createMeshLevelStructure();

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    /// Writes a vector of dof pointers to an output stream.
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    void serialize(ostream &out, DofContainer &data);
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    /// Writes a \ref RankToDofContainer to an output stream.
    void serialize(ostream &out, 
		   map<int, map<const FiniteElemSpace*, DofContainer> > &data);

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    /// Reads a vector of dof pointers from an input stream.
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    void deserialize(istream &in, DofContainer &data,
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		     map<int, const DegreeOfFreedom*> &dofIndexMap);
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    /// Reads a \ref RankToDofContainer from an input stream.
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    void deserialize(istream &in, 
		     map<int, map<const FiniteElemSpace*, DofContainer> > &data,
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		     map<const FiniteElemSpace*, map<int, const DegreeOfFreedom*> > &dofIndexMap);
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    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
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    void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
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    {
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      FUNCNAME("ParallelDomainBase::serialize()");

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      int mapSize = data.size();
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      SerUtil::serialize(out, mapSize);
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      for (typename map<const DegreeOfFreedom*, T>::iterator it = data.begin();
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	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
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	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
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      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
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    void deserialize(istream &in, map<const DegreeOfFreedom*, T> &data,
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		     map<int, const DegreeOfFreedom*> &dofIndexMap)
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    {
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      FUNCNAME("ParallelDomainBase::deserialize()");

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      int mapSize = 0;
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      SerUtil::deserialize(in, mapSize);
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      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
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	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
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	TEST_EXIT_DBG(dofIndexMap.count(v1) != 0)
	  ("Cannot find DOF %d in map!\n", v1);
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	data[dofIndexMap[v1]] = v2;
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      }
    }
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  protected:
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    /// List of all stationary problems that are managed by this mesh 
    /// distributor.
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    vector<ProblemStatSeq*> problemStat;
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    /// If true, the mesh distributor is already initialized;
    bool initialized;

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    /// The rank of the current process.
    int mpiRank;

    /// Overall number of processes.
    int mpiSize;

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    /// MPI communicator collected all processes, which should be used for
    /// calculation. The Debug procces is not included in this communicator.
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    MPI::Intracomm mpiComm;

    /// Name of the problem (as used in the init files)
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    string name;
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    /// Finite element spaces of the problem.
    vector<const FiniteElemSpace*> feSpaces;
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    /// Mesh of the problem.
    Mesh *mesh;

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    /// A refinement manager that should be used on the mesh. It is used to 
    /// refine elements at interior boundaries in order to fit together with 
    /// elements on the other side of the interior boundary.    
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    RefinementManager *refineManager;

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    /// Info level.
    int info;

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    /// Pointer to a mesh partitioner that is used to partition the mesh to 
    /// the ranks.
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    MeshPartitioner *partitioner;
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    /// Weights for the elements, i.e., the number of leaf elements within 
    /// this element.
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    map<int, double> elemWeights;
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    /// Stores to every macro element index the number of the rank that owns this
    /// macro element.
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    map<int, int> partitionMap;
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    /// Mapping object to map from local DOF indices to global ones.
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    ParallelDofMapping dofMap;

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    /// Database to store and query all sub-objects of all elements of the 
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    /// macro mesh.
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    ElementObjectDatabase elObjDb;
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    /// Maps to each macro element index a pointer to the corresponding element.
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    map<int, Element*> macroElIndexMap;
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    /// Maps to each macro element index the type of this element.
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    map<int, int> macroElIndexTypeMap;
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    /// Defines the interior boundaries of the domain that result from 
    /// partitioning the whole mesh. Contains only the boundaries, which are 
    /// owned by the rank, i.e., the object gives for every neighbour rank i 
    /// the boundaries this rank owns and shares with rank i.
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    InteriorBoundary rankIntBoundary;
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    /// Defines the interior boundaries of the domain that result from 
    /// partitioning the whole mesh. Contains only the boundaries, which are 
    /// not owned by the rank, i.e., the object gives for every neighbour rank 
    /// i the boundaries that are owned by rank i and are shared with this rank.
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    InteriorBoundary otherIntBoundary;
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    /// Defines the periodic boundaries with other ranks. Periodic boundaries
    /// have no owner, as it is the case of interior boundaries.
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    InteriorBoundary periodicBoundary;

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    /// This map contains for each rank the list of DOFs the current rank must 
    /// end to exchange solution DOFs at the interior boundaries.
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    DofComm sendDofs;
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    /// This map contains on each rank the list of DOFs from which the current 
    /// rank will receive DOF values (i.e., this are all DOFs at an interior 
    /// boundary). The DOF indices are given in rank's local numbering.
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    DofComm recvDofs;
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    /// This map contains on each rank a list of DOFs along the interior bound-
    /// aries to communicate with other ranks. The DOF indices are given in rank's
    /// local numbering. Periodic boundaries within one subdomain are not 
    /// considered here. 
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    DofComm periodicDofs;

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    PeriodicMap periodicMap;
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    /// This set of values must be interchanged between ranks when the mesh is 
    /// repartitioned.
    vector<DOFVector<double>*> interchangeVectors;
		        
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    /// If the problem definition has been read from a serialization file, this 
    /// variable is true, otherwise it is false. This variable is used to stop the
    /// initialization function, if the problem definition has already been read
    /// from a serialization file.
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    bool deserialized;
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    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

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    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;

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    /// Stores the number of mesh changes that must lie in between to 
    /// repartitionings.
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    int repartitionIthChange;

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    /// Counts the number of mesh changes after the last mesh repartitioning 
    /// was done.
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    int nMeshChangesAfterLastRepartitioning;
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    /// Countes the number of mesh repartitions that were done. Till now, this 
    /// variable is used only for debug outputs.
    int repartitioningCounter;
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    /// Directory name where all debug output files should be written to.
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    string debugOutputDir;
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    /// Stores the mesh change index. This is used to recognize changes in the
    /// mesh structure (e.g. through refinement or coarsening managers).
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    long lastMeshChangeIndex;
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    /// Stores for all macro elements of the original macro mesh the
    /// neighbourhood information based on element indices. Thus, each macro
    /// element index is mapped to a vector containing all indices of 
    /// neighbouring macro elements.
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    map<int, vector<int> > macroElementNeighbours;
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    /// Store all macro elements of the overall mesh, i.e., before the
    /// mesh is redistributed for the first time.
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    vector<MacroElement*> allMacroElements;
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    Flag createBoundaryDofFlag;

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    /// Stores on each mesh level for all FE spaces the information about
    /// all boundary DOFs.
    vector<map<const FiniteElemSpace*, BoundaryDofInfo> > boundaryDofInfo;
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    MeshLevelData levelData;

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  public:
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    bool sebastianMode;

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    /// The boundary DOFs are sorted by subobject entities, i.e., first all
    /// face DOFs, edge DOFs and to the last vertex DOFs will be set to
    /// communication structure vectors, \ref sendDofs and \ref recvDofs.
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    static const Flag BOUNDARY_SUBOBJ_SORTED;

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    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will send to other ranks (thus, rank 
    /// owned DOFs.
    static const Flag BOUNDARY_FILL_INFO_SEND_DOFS;

    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will receive from other ranks (thus, DOFs
    /// that are owned by another rank).
    static const Flag BOUNDARY_FILL_INFO_RECV_DOFS;
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    static MeshDistributor *globalMeshDistributor;

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    friend class ParallelDebug;
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  };
}

607
#endif // AMDIS_MESHDISTRIBUTOR_H