DistributedTetrahedralMesh.hpp

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*/
 
#ifndef DISTRIBUTEDTETRAHEDRALMESH_HPP_
#define DISTRIBUTEDTETRAHEDRALMESH_HPP_
 
#include <map>
#include <vector>
#include <set>
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
 
#include "AbstractTetrahedralMesh.hpp"
#include "Node.hpp"
#include "AbstractMeshReader.hpp"
#include "DistributedTetrahedralMeshPartitionType.hpp"
#include <parmetis.h>
 
#ifdef PARMETIS_MAJOR_VERSION
#if PARMETIS_MAJOR_VERSION != 4
#error "ParMETIS version is not supported. Please use version 4."
#endif
#else //ndef PARMETIS_MAJOR_VERSION
// If there's no PARMETIS then assume we have Scotch
#include <scotch/ptscotch.h>
#define idx_t SCOTCH_Num
#define real_t float
#define CHASTE_SCOTCH_PARMETIS
// Conditionally turn off the interface to ParMETIS_V3_Mesh2Dual which should be added into PTScotch at 7.0.9 
#if ((SCOTCH_VERSION < 7) || (SCOTCH_RELEASE < 0) || (SCOTCH_PATCHLEVEL < 9))
#define CHASTE_HOMEMADE_MESH_TO_DUAL
#endif
#endif
 
#define UNASSIGNED_NODE UINT_MAX
 
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DistributedTetrahedralMesh : public AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM>
{
    friend class TestDistributedTetrahedralMesh;
    friend class TestDistributedQuadraticMesh;
private:
 
    unsigned mTotalNumElements;
 
    unsigned mTotalNumBoundaryElements;
 
    unsigned mTotalNumNodes;
 
    std::vector<Node<SPACE_DIM>* > mHaloNodes;
 
    std::map<unsigned, unsigned> mNodesMapping;
 
    std::map<unsigned, unsigned> mHaloNodesMapping;
 
    std::map<unsigned, unsigned> mElementsMapping;
 
    std::map<unsigned, unsigned> mBoundaryElementsMapping;
 
    ChasteCuboid<SPACE_DIM>* mpSpaceRegion;
 
    DistributedTetrahedralMeshPartitionType::type mPartitioning;
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }
 
 
    void SetElementOwnerships();
 
 
public:
 
    DistributedTetrahedralMesh(DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY);
 
    virtual ~DistributedTetrahedralMesh();
 
    void SetDistributedVectorFactory(DistributedVectorFactory* pFactory);
 
    virtual void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>& rMeshReader);
 
    unsigned GetNumLocalNodes() const;
 
    unsigned GetNumHaloNodes() const;
 
    unsigned GetNumLocalElements() const;
 
    unsigned GetNumLocalBoundaryElements() const;
 
    unsigned GetNumNodes() const;
 
    unsigned GetNumAllNodes() const;
 
    unsigned GetNumElements() const;
 
    DistributedTetrahedralMeshPartitionType::type GetPartitionType() const;
 
    unsigned GetNumBoundaryElements() const;
 
    void GetHaloNodeIndices(std::vector<unsigned>& rHaloIndices) const;
 
    void SetProcessRegion(ChasteCuboid<SPACE_DIM>* pRegion);
 
    ChasteCuboid<SPACE_DIM>* GetProcessRegion();
 
    bool CalculateDesignatedOwnershipOfElement( unsigned elementIndex );
 
    bool CalculateDesignatedOwnershipOfBoundaryElement( unsigned faceIndex );
 
     void ConstructLinearMesh(unsigned width);
 
    void ConstructRectangularMesh(unsigned width, unsigned height, bool stagger=true);
 
    void ConstructCuboid(unsigned width, unsigned height, unsigned depth);
    virtual void Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0);
 
    Node<SPACE_DIM>* GetNodeOrHaloNode(unsigned index) const;
 
    virtual ChasteCuboid<SPACE_DIM> CalculateBoundingBox() const;
 
    virtual unsigned GetNearestNodeIndex(const ChastePoint<SPACE_DIM>& rTestPoint);
 
    virtual c_vector<double, 2> CalculateMinMaxEdgeLengths();
 
    void Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotationMatrix);
 
    void Translate(const c_vector<double, SPACE_DIM>& rDisplacement);
 
 
protected:
    unsigned SolveNodeMapping(unsigned index) const;
 
    unsigned SolveElementMapping(unsigned index) const;
 
    unsigned SolveBoundaryElementMapping(unsigned index) const;
private:
 
    void RegisterNode(unsigned index);
 
    void RegisterHaloNode(unsigned index);
 
    void RegisterElement(unsigned index);
 
    void RegisterBoundaryElement(unsigned index);
 
 
    void ComputeMeshPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                 std::set<unsigned>& rNodesOwned,
                                 std::set<unsigned>& rHaloNodesOwned,
                                 std::set<unsigned>& rElementsOwned,
                                 std::vector<unsigned>& rProcessorsOffset);
 
     void ParMetisLibraryNodeAndElementPartitioning(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                          std::set<unsigned>& rElementsOwned,
                                          std::set<unsigned>& rNodesOwned,
                                          std::set<unsigned>& rHaloNodesOwned,
                                          std::vector<unsigned>& rProcessorsOffset);
 
    void ReorderNodes();
 
    //                            Iterators                             //
 
public:
    // The other iterators aren't (so only need to be dereferenced once). Consistency would be good...
 
    typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator HaloNodeIterator;
 
    HaloNodeIterator GetHaloNodeIteratorBegin() const;
 
    HaloNodeIterator GetHaloNodeIteratorEnd() const;
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(DistributedTetrahedralMesh)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    unsigned num_procs = PetscTools::GetNumProcs();
    const DistributedTetrahedralMeshPartitionType::type partition_type = t->GetPartitionType();
    ar << num_procs;
    ar << partition_type;
}
 
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    unsigned num_procs;
    DistributedTetrahedralMeshPartitionType::type partition_type;
 
    ar >> num_procs;
    ar >> partition_type;
 
    // Invoke inplace constructor to initialise instance
    //::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(partition_type);
    ::new(t)DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(DistributedTetrahedralMeshPartitionType::DUMB);
 
    /*
     * The exception needs to be thrown after the call to ::new(t), or Boost will try
     * to free non-allocated memory when the exception is thrown.
     */
    if (DistributedVectorFactory::CheckNumberOfProcessesOnLoad() &&
        num_procs != PetscTools::GetNumProcs())
    {
        EXCEPTION("This archive was written for a different number of processors");
    }
 
}
}
} // namespace ...
 
#endif /*DISTRIBUTEDTETRAHEDRALMESH_HPP_*/