ParallelDomainBase.h 22.6 KB
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// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
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// ==  TU Dresden                                                            ==
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// ==                                                                        ==
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// ==  Institut für Wissenschaftliches Rechnen                               ==
// ==  Zellescher Weg 12-14                                                  ==
// ==  01069 Dresden                                                         ==
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// ==  germany                                                               ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
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// ==  https://gforge.zih.tu-dresden.de/projects/amdis/                      ==
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// ==                                                                        ==
// ============================================================================

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/** \file ParallelDomainBase.h */

#ifndef AMDIS_PARALLELDOMAINBASE_H
#define AMDIS_PARALLELDOMAINBASE_H
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#include <map>
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#include <set>
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#include <vector>
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#include <mpi.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 "AdaptInfo.h"
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#include "parallel/InteriorBoundary.h"
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#include "Serializer.h"
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#include "BoundaryManager.h"
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#include "AMDiS_fwd.h"

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#include "petsc.h"
#include "petscsys.h"
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#include "petscao.h"
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namespace AMDiS {

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  struct DofPtrSortFct {
    bool operator() (const DegreeOfFreedom *dof0, const DegreeOfFreedom *dof1) 
    {
      return (*dof0 < *dof1);
    }
  };
   
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  class ParMetisPartitioner;

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  class ParallelDomainBase : public ProblemIterationInterface,
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			     public ProblemTimeInterface
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  {
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  private:
    /// Defines a mapping type from DOFs to rank numbers.
    typedef std::map<const DegreeOfFreedom*, int> DofToRank;

    /// Defines a mapping type from DOFs to a set of rank numbers.
    typedef std::map<const DegreeOfFreedom*, std::set<int> > DofToPartitions;

    /// Defines a mapping type from rank numbers to sets of DOFs.
    typedef std::map<int, DofContainer> RankToDofContainer;

    /// Defines a mapping type from DOF indices to DOF indices.
    typedef std::map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;

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    /// Defines a mapping type from DOFs to boolean values.
    typedef std::map<const DegreeOfFreedom*, bool> DofToBool;

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    /// Defines a mapping type from DOF indices to boolean values.
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    typedef std::map<DegreeOfFreedom, bool> DofIndexToBool;
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    /// Defines a mapping type from rank numbers to sets of coordinates.
    typedef std::map<int, std::vector<WorldVector<double> > > RankToCoords;

    /// Forward type (it maps rank numbers to the interior boundary objects).
    typedef InteriorBoundary::RankToBoundMap RankToBoundMap;

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    typedef std::map<int, DofContainer> ElementIdxToDofs;

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    typedef std::map<const DegreeOfFreedom*, DegreeOfFreedom> DofIndexMap;

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    typedef std::map<DegreeOfFreedom, std::set<DegreeOfFreedom> > PeriodicDofMap;
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    typedef std::vector<MeshStructure> MeshCodeVec;
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  public:
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    ParallelDomainBase(ProblemVec *problemStat,
		       ProblemInstatVec *problemInstat);
		       
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    virtual ~ParallelDomainBase() {}
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    virtual void initParallelization(AdaptInfo *adaptInfo);
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    virtual void exitParallelization(AdaptInfo *adaptInfo);
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    /** \brief
     * 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.
     */
    void checkMeshChange();

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    void updateDofAdmins();    
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    /** \brief
     * 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.
     */
    void testForMacroMesh();
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    /// Set for each element on the partitioning level the number of leaf elements.
    double setElemWeights(AdaptInfo *adaptInfo);

    void partitionMesh(AdaptInfo *adaptInfo);

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    virtual void setTime(AdaptInfo *adaptInfo) 
    {
      if (timeIF) 
	timeIF->setTime(adaptInfo);      
    }
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    virtual void initTimestep(AdaptInfo *adaptInfo) 
    {
      if (timeIF) 
	timeIF->initTimestep(adaptInfo);
    }
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    virtual void closeTimestep(AdaptInfo *adaptInfo) 
    {
      if (timeIF) 
	timeIF->closeTimestep(adaptInfo);
    }
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    virtual void solveInitialProblem(AdaptInfo *adaptInfo);
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    virtual void transferInitialSolution(AdaptInfo *adaptInfo) 
    {
      if (timeIF) 
	timeIF->transferInitialSolution(adaptInfo);
    }
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    virtual void beginIteration(AdaptInfo *adaptInfo) 
    {
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      iterationIF->beginIteration(adaptInfo);
    }

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    virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);
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    virtual Flag buildAndAdapt(AdaptInfo *adaptInfo, Flag toDo);

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    virtual void endIteration(AdaptInfo *adaptInfo) 
    {
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      iterationIF->endIteration(adaptInfo);
    }
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    virtual void solve();
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    virtual int getNumProblems() 
    {
      return 0;
    }
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    inline virtual std::string getName() 
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    { 
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      return name; 
    }

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    /// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
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    int getNumberRankDofs() 
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    {
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      return nRankDofs;
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    }

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    void solvePetscMatrix(SystemVector &vec);
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    virtual ProblemStatBase *getProblem(int number = 0) 
    {
      return NULL;
    }
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    // Writes all data of this object to an output stream.
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    virtual void serialize(std::ostream &out);
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    // Reads the object data from an input stream.
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    virtual void deserialize(std::istream &in);
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  protected:
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    /** \brief
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     * Determines the interior boundaries, i.e. boundaries between ranks, and stores
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     * all information about them in \ref interiorBoundary.
     */
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    void createInteriorBoundaryInfo();
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    /** \brief
     * Deterimes the interior boundaries between ranks, that are based on the 
     * neighbourhood information of the macro elements. That means that in 2d the
     * function search for all edge based interior boundaries and in 3d for all face
     * based interior boundaries. This function cannot find boundaries of substructure
     * elements, i.e. vertex boundaries in 2d and vertex and edge boundaries in 3d.
     */
    void createMacroElementInteriorBoundaryInfo();

    /** \brief
     * Determines all interior boundaries between rank that consist of element's
     * substructures. In 2d these may be only vertices. In 3d there may be also
     * interior boundaries consisting of either a whole edge or of a single vertex.
     */
    void createSubstructureInteriorBoundaryInfo();

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    /// Removes all macro elements from the mesh that are not part of ranks partition.
    void removeMacroElements();

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    /// Creates from a macro mesh a correct local and global DOF index numbering.
    void createLocalGlobalNumbering();
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    /// Updates the local and global DOF numbering after the mesh has been changed.
    void updateLocalGlobalNumbering();
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    /** \brief
     * Creates 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 periodicDof.
     */
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    void createPeriodicMap();

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    /** \brief
     * This function create new mappings from local to global indices, 
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     * \ref mapLocalGlobalDofs, and from local to dof indices, \ref mapLocalToDofIndex.
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     * Furthermore, using the first argument the dof indices in ranks partition are
     * changed.
     * 
     * \param[in] rankDofsNewLocalIndex       Map from dof pointers of all dofs in rank
     *                                        to new dof indices.
     * \param[in] rankOwnedDofsNewLocalIndex  Map from dof pointers of dofs owned by
     *                                        the rank to the new local index.
     * \param[in] rankDofsNewGlobalIndex      Map from dof pointers of all dofs in rank
     *                                        to the new global index.
     */
    void createLocalMappings(DofIndexMap &rankDofsNewLocalIndex,
			     DofIndexMap &rankOwnedDofsNewLocalIndex,
			     DofIndexMap &rankDofsNewGlobalIndex);

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    /** \brief
     * This function traverses the whole mesh, i.e. before it is really partitioned,
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     * and collects information about which DOF corresponds to which rank. Can only
     * be used, if \ref partitionVec is set correctly. This is only the case, when
     * the macro mesh is partitioned.
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     *
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     * \param[out] partitionDOFs   Stores to each DOF pointer the set of ranks the DOF
     *                             is part of.
     * \param[out] rankDOFs        Stores all rank DOFs.
     * \param[out] boundaryDOFs    Stores all DOFs in ranks partition that are on an 
     *                             interior boundary but correspond to another rank.
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     */
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    void createDofMemberInfo(DofToPartitions& partitionDofs,
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			     DofContainer& rankOwnedDofs,
			     DofContainer& rankAllDofs,
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			     DofToRank& boundaryDofs,
			     DofToBool& vertexDof);
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    /// Creates a new non zero pattern structure for the Petsc matrix. 
    void createPetscNnzStructure(Matrix<DOFMatrix*> *mat);

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    /** \brief
     * Create a PETSc matrix and PETSc vectors. The given DOF matrices are used to
     * create the nnz structure of the PETSc matrix and the values are transfered to it.
     * The given DOF vectors are used to the the values of the PETSc rhs vector.
     *
     * \param[in] mat
     * \param[in] vec
     */
    void fillPetscMatrix(Matrix<DOFMatrix*> *mat, SystemVector *vec);

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    /// Takes a dof matrix and sends the values to the global petsc matrix.
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    void setDofMatrix(DOFMatrix* mat, int dispMult = 1, 
		      int dispAddRow = 0, int dispAddCol = 0);

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    /// Takes a dof vector and sends its values to a given petsc vector.
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    void setDofVector(Vec& petscVec, DOFVector<double>* vec, 
		      int disMult = 1, int dispAdd = 0);
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    /** \brief
     * 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.
     * If the mesh has  been changed by this function, it returns true. Otherwise, it
     * returns false, i.e., the given interior boundaries fit together on both sides.
     *
     * \param[in] allBound   Defines a map from rank to interior boundaries which 
     *                       should be checked.
     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);

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    void dbgCreateElementMap(ElementIdxToDofs &elMap);
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    void dbgTestElementMap(ElementIdxToDofs &elMap);
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    void dbgTestInteriorBoundary();
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    /** \brief
     * This function is used for debugging only. It traverses all interior boundaries
     * and compares the dof indices on them with the dof indices of the boundarys
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     * neighbours. The function fails, when dof indices on an interior boundary do
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     * not fit together.
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     *
     * \param  printCoords   If true, the coords of all common dofs are printed to
     *                       the screen.
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     */
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    void dbgTestCommonDofs(bool printCoords = false);
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    /** \brief
     * This function is used for debugging only. It prints all information from
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     * the local to global dof mapping, see \ref mapLocalGlobalDofs.
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     *
     * \param  rank  If specified, only the information from the given rank is printed.
     */
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    void printMapLocalGlobal(int rank = -1);
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    /** \brief
     * This function is used for debugging only. It prints all information about
     * the periodic mapping of dofs, that are on periodic boundaries.
     *
     * \param  rank  If specified, only the information from the given rank is printed.
     */
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    void printMapPeriodic(int rank = -1);

    /** \brief
     * This function is used for debugging only. It prints information about dofs
     * in rank's partition.
     *
     * \param  rank         If specified, only the information from the given 
     *                      rank is printed.
     * \param  rankDofs     List of all dofs in ranks partition that are owned by rank.
     * \param  rankAllDofs  List of all dofs in ranks partition.
     */
    void printRankDofs(int rank, DofContainer& rankDofs, DofContainer& rankAllDofs);
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    /** \brief
     * This functions create a Paraview file with the macro mesh where the elements
     * are colored by the partition they are part of. This function can be used for
     * debugging.
     */
    void writePartitioningMesh(std::string filename);

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    /** \brief
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     * This function must be used if the values of a DOFVector must be synchronised
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     * 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
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     * having these DOFs.
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     *
     * This function must be used, for example, after the lineary system is solved, or
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     * after the DOFVector is set by some user defined functions, e.g., initial
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     * solution functions.
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     */    
    void synchVector(DOFVector<double> &vec);

    /** \brief
     * 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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     */
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    void synchVector(SystemVector &vec);
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    // Removes all periodic boundaries from a given boundary map.
    void removeBoundaryCondition(BoundaryIndexMap& boundaryMap);

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    bool fitElementToMeshCode(MeshStructure &code, 
			      Element *el, 
			      int ithSide, 
			      int elType,
			      int &refCounter);
    
    bool fitElementToMeshCode2(MeshStructure &code, 
			       Element *el, 
			       int ithSide, 
			       int elType,
			       int &refCounter);

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    /// Writes a vector of dof pointers to an output stream.
    void serialize(std::ostream &out, DofContainer &data);

    /// Reads a vector of dof pointers from an input stream.
    void deserialize(std::istream &in, DofContainer &data,
		     std::map<int, const DegreeOfFreedom*> &dofMap);

    /// Writes a \ref RankToDofContainer to an output stream.
    void serialize(std::ostream &out, RankToDofContainer &data);

    /// Reads a \ref RankToDofContainer from an input stream.
    void deserialize(std::istream &in, RankToDofContainer &data,
		     std::map<int, const DegreeOfFreedom*> &dofMap);
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    /// Writes a periodic dof mapping to an output stream.
    void serialize(std::ostream &out, PeriodicDofMap &data);

    /// Reads a periodic dof mapping from an input stream.
    void deserialize(std::istream &in, PeriodicDofMap &data);

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    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
    void serialize(std::ostream &out, std::map<const DegreeOfFreedom*, T> &data)
    {
      int mapSize = data.size();
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      SerUtil::serialize(out, mapSize);
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      for (typename std::map<const DegreeOfFreedom*, T>::iterator it = data.begin();
	   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>
    void deserialize(std::istream &in, std::map<const DegreeOfFreedom*, T> &data,
		     std::map<int, const DegreeOfFreedom*> &dofMap)
    {
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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(dofMap.count(v1) != 0)("Cannot find DOF %d in map!\n", v1);

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	data[dofMap[v1]] = v2;
      }
    }
		        
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    inline void orderDofs(const DegreeOfFreedom* dof0,
			  const DegreeOfFreedom* dof1,
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			  const DegreeOfFreedom* dof2,
			  DofContainer &vec)
    {
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      DofPtrSortFct dofPtrSort;
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      vec.resize(3);
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      vec[0] = dof0; 
      vec[1] = dof1; 
      vec[2] = dof2;
      sort(vec.begin(), vec.end(), dofPtrSort);
    }
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    inline void orderDofs(const DegreeOfFreedom* dof0,
			  const DegreeOfFreedom* dof1,
			  const DegreeOfFreedom* dof2,
			  const DegreeOfFreedom* dof3,
			  DofContainer &vec)
    {
      DofPtrSortFct dofPtrSort;
      vec.resize(4);
      vec[0] = dof0; 
      vec[1] = dof1; 
      vec[2] = dof2;
      vec[3] = dof3;
      sort(vec.begin(), vec.end(), dofPtrSort);
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    }

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    inline void printColValues(int row,
			       std::vector<int>& cols,
			       std::vector<double>& values)
    {
      for (int i = 0; i < static_cast<int>(cols.size()); i++)
	std::cout << "Mat[" << row  << "][" << cols[i] << "] = " << values[i] << "\n";
    }

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  protected:
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    ///
    ProblemIterationInterface *iterationIF;

    ///
    ProblemTimeInterface *timeIF;

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    ///
    ProblemVec *probStat;

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

    /// Overall number of processes.
    int mpiSize;

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

    /// Name of the problem (as used in the init files)
    std::string name;

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    /// Finite element space of the problem.
    FiniteElemSpace *feSpace;

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    /// Mesh of the problem.
    Mesh *mesh;

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    /** \brief
     * 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.
     */    
    RefinementManager *refineManager;

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    /// Info level.
    int info;

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    /// Pointer to the paritioner which is used to devide a mesh into partitions.
    ParMetisPartitioner *partitioner;

    /// Weights for the elements, i.e., the number of leaf elements within this element.
    std::map<int, double> elemWeights;

    /// Is true, if the mesh was not partitioned before, otherwise it's false.
    bool initialPartitionMesh;

    /** \brief
     * Stores to every coarse element index the number of the partition it 
     * corresponds to.
     */
    std::map<int, int> partitionVec;

    /** \brief
     * Stores an old partitioning of elements. To every element index the number
     * of the parition it corresponds to is stored.
     */
    std::map<int, int> oldPartitionVec;    
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    /// Petsc's matrix structure.
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    Mat petscMatrix;

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    /** \brief
     * Petsc's vector structures for the rhs vector, the solution vector and a
     * temporary vector for calculating the final residuum.
     */
    Vec petscRhsVec, petscSolVec, petscTmpVec;
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    /// Arrays definig the non zero pattern of Petsc's matrix.
    int *d_nnz, *o_nnz;
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    /// Number of DOFs in the rank mesh.
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    int nRankDofs;
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    /** \brief 
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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.
     */
    InteriorBoundary myIntBoundary;
    
    /** \brief
     * 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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     */
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    InteriorBoundary otherIntBoundary;
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    /** \brief
     *
     */
    InteriorBoundary periodicBoundary;

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    /** \brief
     * This map contains for each rank the list of dofs the current rank must send
     * to exchange solution dofs at the interior boundaries.
     */
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    RankToDofContainer sendDofs;
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    /** \brief
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     * This map contains for 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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     */
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    RankToDofContainer recvDofs;
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    /// Maps local to global dof indices.
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    DofMapping mapLocalGlobalDofs;
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    /// Maps local dof indices to real dof indices.
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    DofMapping mapLocalToDofIndex;  
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    /** \brief
     * Maps all DOFs in ranks partition to a bool value. If it is true, the DOF is
     * owned by the rank. Otherwise, its an interior boundary DOF that is owned by
     * another rank.
     */
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    DofIndexToBool isRankDof;

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    /** \brief
     * Maps every dof pointer in ranks macro mesh to a boolean variable indicating 
     * wheather this dof is a vertex dof (true) or not (false).
     */
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    DofToBool vertexDof;
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    /** \brief
     * If periodic boundaries are used, this map stores to each dof in rank's 
     * partition, that is on periodic boundaries, the corresponding periodic dofs.
     * The mapping is defined by using global dof indices.
     */
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    PeriodicDofMap periodicDof;

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    /// Is the index of the first row of the linear system, which is owned by the rank.
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    int rstart;
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    /** \brief
     * Number of components of the equation. Is used to calculate the exact number
     * of rows in the the overall linear system.
     */
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    int nComponents;
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    /// Number of rows of the whole linear system that are stored on this rank.
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    int nRankRows;

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    /// Overall number of the rows in the lineary system.
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    int nOverallRows;
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    /** \brief
     * 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.
     */
    bool deserialized;
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    /** \brief
     * Stores the mesh change index. This is used to recognize changes in the mesh 
     * structure (e.g. through refinement or coarsening managers).
     */
    long lastMeshChangeIndex;
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  };
}

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#endif // AMDIS_PARALLELDOMAINBASE_H