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"

#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 mMetisPartitioning;

    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_*/