DistributedBoxCollection.hpp

/*

Copyright (c) 2005-2021, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/
#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 mIsPeriodicInY=false, bool mIsPeriodicInZ=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_*/