DistributedBoxCollection.hpp

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*/
#ifndef DISTRIBUTEDBOXCOLLECTION_HPP_
#define DISTRIBUTEDBOXCOLLECTION_HPP_
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/vector.hpp>
 
#include "Node.hpp"
#include "Element.hpp"
#include "Box.hpp"
#include "PetscTools.hpp"
#include "DistributedVectorFactory.hpp"
#include <map>
#include <vector>
 
 
template<unsigned DIM>
class DistributedBoxCollection
{
private:
    friend class TestDistributedBoxCollection;
 
    std::vector< Box<DIM> > mBoxes;
 
    std::vector< Box<DIM> > mHaloBoxes;
 
    std::vector<unsigned> mHalosRight;
 
    std::vector<unsigned> mHalosLeft;
 
    std::vector<unsigned> mHaloNodesRight;
 
    std::vector<unsigned> mHaloNodesLeft;
 
    std::map<unsigned, unsigned> mHaloBoxesMapping;
 
    c_vector<double, 2*DIM> mDomainSize;
 
    double mBoxWidth;
 
    unsigned mNumBoxes;
 
    c_vector<unsigned, DIM> mNumBoxesEachDirection;
 
    unsigned mNumBoxesInAFace;
 
    std::vector< std::set<unsigned> > mLocalBoxes;
 
    unsigned mMinBoxIndex;
 
    unsigned mMaxBoxIndex;
 
    bool mIsPeriodicInX;
 
    bool mIsPeriodicInY;
 
    bool mIsPeriodicInZ;
 
    bool mIsPeriodicAcrossProcs;
 
    bool mAreLocalBoxesSet;
 
    static const double msFudge;
 
    DistributedVectorFactory* mpDistributedBoxStackFactory;
 
    bool mCalculateNodeNeighbours;
 
    void SetupHaloBoxes();
 
    friend class boost::serialization::access;
 
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        //All methods over-ridden below.
    }
 
public:
 
    DistributedBoxCollection(double boxWidth, c_vector<double, 2*DIM> domainSize, bool isPeriodicInX = false, bool isPeriodicInY=false, bool isPeriodicInZ=false, int localRows = PETSC_DECIDE);
 
    ~DistributedBoxCollection();
 
    void EmptyBoxes();
 
    void UpdateHaloBoxes();
 
    unsigned GetNumLocalRows() const;
 
    bool IsBoxOwned(unsigned globalIndex);
 
    bool IsInteriorBox(unsigned globalIndex);
 
    bool IsHaloBox(unsigned globalIndex);
 
    unsigned CalculateGlobalIndex(c_vector<unsigned, DIM> gridIndices);
 
    unsigned CalculateContainingBox(Node<DIM>* pNode);
 
    unsigned CalculateContainingBox(c_vector<double, DIM>& rLocation);
 
    c_vector<unsigned, DIM> CalculateGridIndices(unsigned globalIndex);
 
    Box<DIM>& rGetBox(unsigned boxIndex);
 
    Box<DIM>& rGetHaloBox(unsigned boxIndex);
 
    unsigned GetNumBoxes();
 
    unsigned GetNumLocalBoxes();
 
    c_vector<double, 2*DIM> rGetDomainSize() const;
 
    bool GetAreLocalBoxesSet() const;
 
    double GetBoxWidth() const;
 
    bool GetIsPeriodicInX() const;
 
    bool GetIsPeriodicInY() const;
 
    bool GetIsPeriodicInZ() const;
 
    bool GetIsPeriodicAcrossProcs() const;
 
    c_vector<bool,DIM> GetIsPeriodicAllDims() const;
 
    unsigned GetNumRowsOfBoxes() const;
 
    int LoadBalance(std::vector<int> localDistribution);
 
    void SetupLocalBoxesHalfOnly();
 
    void SetupAllLocalBoxes();
 
    std::set<unsigned>& rGetLocalBoxes(unsigned boxIndex);
 
    bool IsOwned(Node<DIM>* pNode);
 
    bool IsOwned(c_vector<double, DIM>& location);
 
    unsigned GetProcessOwningNode(Node<DIM>* pNode);
 
    std::vector<unsigned>& rGetHaloNodesRight();
 
    std::vector<unsigned>& rGetHaloNodesLeft();
 
    void SetCalculateNodeNeighbours(bool calculateNodeNeighbours);
 
    void CalculateNodePairs(std::vector<Node<DIM>*>& rNodes, std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs);
 
    void CalculateInteriorNodePairs(std::vector<Node<DIM>*>& rNodes, std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs);
 
    void CalculateBoundaryNodePairs(std::vector<Node<DIM>*>& rNodes, std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs);
 
    void AddPairsFromBox(unsigned boxIndex, std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs);
 
    std::vector<int> CalculateNumberOfNodesInEachStrip();
};
 
#include "SerializationExportWrapper.hpp"
// Declare identifier for the serializer
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DistributedBoxCollection)
 
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const DistributedBoxCollection<DIM> * t, const unsigned int file_version)
{
    // Save the number of rows that each process owns, so that on loading we can resume with
    // good load balance
    int num_local_rows = (int)(t->GetNumRowsOfBoxes());
    std::vector<int> num_rows(PetscTools::GetNumProcs());
    MPI_Gather(&num_local_rows, 1, MPI_INT, &num_rows[0], 1, MPI_INT, 0, PETSC_COMM_WORLD);
 
    if (PetscTools::AmMaster())
    {
        bool are_boxes_set = t->GetAreLocalBoxesSet();
        ar << are_boxes_set;
 
        c_vector<double, 2*DIM> domain_size = t->rGetDomainSize();
        for (unsigned i=0; i<2*DIM; i++)
        {
            ar << domain_size[i];
        }
 
        double box_width = t->GetBoxWidth();
        ar << box_width;
 
        unsigned num_procs = PetscTools::GetNumProcs();
        ar << num_procs;
 
        std::vector<int> const const_num_rows = num_rows;
        ar << const_num_rows;
    }
}
template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, DistributedBoxCollection<DIM> * t, const unsigned int file_version)
{
    bool are_boxes_set;
    ar >> are_boxes_set;
 
    // Retrieve data from archive required to construct new instance of Node
    c_vector<double,2*DIM> domain_size;
    for (unsigned i=0; i<2*DIM; i++)
    {
        double coordinate;
        ar & coordinate; //resume coordinates one by one
        domain_size[i] = coordinate;
    }
 
    // Shrink the domain size slightly so we get the correct size on construction
    for (unsigned i=0; i<DIM; i++)
    {
        domain_size[2*i+1] -= 1e-14;
    }
    double cut_off;
    ar >> cut_off;
 
    unsigned num_original_procs;
    ar >> num_original_procs;
 
    int num_rows = PETSC_DECIDE;
    std::vector<int> original_rows;
    ar >> original_rows;
    if (num_original_procs == PetscTools::GetNumProcs())
    {
        num_rows = original_rows[PetscTools::GetMyRank()];
    }
 
    // Invoke inplace constructor to initialise instance. Assume non-periodic
    ::new(t)DistributedBoxCollection<DIM>(cut_off, domain_size, false, false, false, num_rows);
 
    if (are_boxes_set)
    {
        t->SetupLocalBoxesHalfOnly();
    }
}
}
} // namespace ...
 
 
#endif /*DISTRIBUTEDBOXCOLLECTION_HPP_*/