LeafNodesContainer.h

/*
 * LeafNodesContainer.h
 *
 *  Created on: Feb 6, 2015
 *      Author: tchipev
 *
 *  A bare-bones secondary Linked-Cells structure to allow
 *  carrying out P2P, P2M, L2P operations when the tree is deeper
 *  than what would be allowed by the Lennard-Jones cutoff radius.
 *
 *  Assumption: there is an LJ Linked-Cells structure with cells bigger or equal than these.
 */
 
#ifndef LEAFNODESCONTAINER_H_
#define LEAFNODESCONTAINER_H_
 
#include "bhfmm/containers/ParticleCellPointers.h"
#include <vector>
 
namespace bhfmm {
 
class SimpleCellProcessor;
class VectorizedChargeP2PCellProcessor;
 
class LeafNodesContainer {
public:
    LeafNodesContainer(double bBoxMin[3],
                       double bBoxMax[3],
                       double LJCellLength[3],
                       unsigned subdivisionFactor,
                       bool periodic = true
#ifdef QUICKSCHED
                       , qsched* scheduler = nullptr
#endif
    );
 
    ~~LeafNodesContainer();
 
    double* getCellLength() {
        return _cellLength;
    }
 
    void addParticle(Molecule& particle);
    void clearParticles();
    void traverseCells(SimpleCellProcessor& cellProcessor);
    void traverseCellPairs(VectorizedChargeP2PCellProcessor& cellProcessor);
    void traverseCellPairsOrig(VectorizedChargeP2PCellProcessor& cellProcessor);
    void traverseCellPairsC08(VectorizedChargeP2PCellProcessor& cellProcessor);
 
    const int *getNumCellsPerDimension() const;
 
    std::vector<ParticleCellPointers> & getCells();
 
    long int cellIndexOf3DIndex(int xIndex, int yIndex, int zIndex) const;
 
    void c08Step(long int baseIndex, VectorizedChargeP2PCellProcessor &cellProcessor);
 
private:
    void initializeCells();
    void calculateNeighbourIndices();
    void calculateCellPairOffsets();
    unsigned long int getCellIndexOfMolecule(Molecule* molecule) const;
    void threeDIndexOfCellIndex(int ind, int r[3], int dim[3]) const;
 
    bool _periodicBC;
 
    double _boundingBoxMin[3];
    double _boundingBoxMax[3];
    double _haloBoundingBoxMin[3];
    double _haloBoundingBoxMax[3];
    double _cellLength[3];
    int _numInnerCellsPerDimension[3];
    int _numCellsPerDimension[3];
    std::vector<ParticleCellPointers> _cells;
    std::vector<unsigned long> _forwardNeighbourOffsets;
    std::vector<unsigned long> _backwardNeighbourOffsets;
    unsigned _maxNeighbourOffset;
    unsigned _minNeighbourOffset;
 
    // addition for compact SimpleMD-style traversal
    std::vector<std::pair<unsigned long, unsigned long> > _cellPairOffsets;
 
    unsigned int _numActiveColours;
    std::vector<std::vector<long int> > _cellIndicesPerColour;
 
#ifdef QUICKSCHED
    struct qsched *_scheduler;
#endif
};
 
} /* namespace bhfmm */
 
#endif /* LEAFNODESCONTAINER_H_ */