NodeBasedCellPopulation.hpp

/*

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*/

#ifndef NODEBASEDCELLPOPULATION_HPP_
#define NODEBASEDCELLPOPULATION_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include <boost/version.hpp>
#if BOOST_VERSION >= 103700
#include "ObjectCommunicator.hpp"
#endif

#include "AbstractCentreBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"
#include "BoxCollection.hpp"

template<unsigned DIM>
class NodeBasedCellPopulation : public AbstractCentreBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulation;
    friend class TestNodeBasedCellPopulationParallelMethods;
    friend class TestBoxCollection;

protected:

    NodesOnlyMesh<DIM>* mpNodesOnlyMesh;

private:

    c_vector<double, DIM> mMinSpatialPositions;

    c_vector<double, DIM> mMaxSpatialPositions;

    std::vector< std::pair<Node<DIM>*, Node<DIM>* > > mNodePairs;

    std::map<unsigned, std::set<unsigned> > mNodeNeighbours;

    bool mDeleteMesh;

    bool mUseVariableRadii;

    std::vector<std::pair<CellPtr, Node<DIM>* > > mCellsToSendRight;

    std::vector<std::pair<CellPtr, Node<DIM>* > > mCellsToSendLeft;

    boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > mpCellsRecvRight;

    boost::shared_ptr<std::vector<std::pair<CellPtr, Node<DIM>* > > > mpCellsRecvLeft;

    ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > mRightCommunicator;

    ObjectCommunicator<std::vector<std::pair<CellPtr, Node<DIM>* > > > mLeftCommunicator;

    static const unsigned mCellCommunicationTag = 123;

    std::vector<CellPtr> mHaloCells;

    std::map<unsigned, CellPtr> mLocationHaloCellMap;

    std::map<CellPtr, unsigned> mHaloCellLocationMap;

    bool mLoadBalanceMesh;

    unsigned mLoadBalanceFrequency;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCentreBasedCellPopulation<DIM> >(*this);
        archive & mUseVariableRadii;

        this->Validate();
    }

    unsigned AddNode(Node<DIM>* pNewNode);

    void AddMovedCell(CellPtr pCell, boost::shared_ptr<Node<DIM> > pNode);

    void DeleteMovedCell(unsigned index);

    void RefreshHaloCells();

    void AddNodeAndCellToSendRight(unsigned nodeIndex);

    void AddNodeAndCellToSendLeft(unsigned nodeIndex);

    void AddCellsToSendRight(std::vector<unsigned>& cellLocationIndices);

    void AddCellsToSendLeft(std::vector<unsigned>& cellLocationIndices);

    void AddReceivedHaloCells();

    void AddHaloCell(CellPtr pCell, boost::shared_ptr<Node<DIM> > pNode);

    void UpdateMapsAfterRemesh(NodeMap& map);

protected:

#undef COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

    virtual void UpdateParticlesAfterReMesh(NodeMap& rMap);

    virtual void Validate();

private:

    virtual void WriteVtkResultsToFile(const std::string& rDirectory);

public:

    void SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation);

    NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh,
                            std::vector<CellPtr>& rCells,
                            const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                            bool deleteMesh=false,
                            bool validate=true);

    NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh);

    virtual ~NodeBasedCellPopulation();

    NodesOnlyMesh<DIM>& rGetMesh();

    const NodesOnlyMesh<DIM>& rGetMesh() const;

    unsigned GetNumNodes();

    virtual CellPtr GetCellUsingLocationIndex(unsigned index);

    Node<DIM>* GetNode(unsigned index);

    unsigned RemoveDeadCells();

    void Clear();

    void Update(bool hasHadBirthsOrDeaths=true);

    std::vector< std::pair<Node<DIM>*, Node<DIM>* > >& rGetNodePairs();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<DIM, DIM> > pPopulationWriter);

    virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<DIM, DIM> > pPopulationCountWriter);

    virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<DIM, DIM> > pCellWriter, CellPtr pCell);

    double GetMechanicsCutOffLength();

    bool GetUseVariableRadii();

    void SetUseVariableRadii(bool useVariableRadii=true);

    void SetLoadBalanceMesh(bool loadBalanceMesh);

    void SetLoadBalanceFrequency(unsigned loadBalanceFrequency);

    double GetWidth(const unsigned& rDimension);

    c_vector<double, DIM> GetSizeOfCellPopulation();

    std::set<unsigned> GetNodesWithinNeighbourhoodRadius(unsigned index, double neighbourhoodRadius);

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);

    virtual CellPtr AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell);

    double GetVolumeOfCell(CellPtr pCell);

    // Parallel methods

    void SendCellsToNeighbourProcesses();

    void NonBlockingSendCellsToNeighbourProcesses();

    void GetReceivedCells();

    std::pair<CellPtr, Node<DIM>* > GetCellNodePair(unsigned nodeIndex);

    void AddReceivedCells();

    virtual void UpdateCellProcessLocation();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodeBasedCellPopulation)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const NodeBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const NodesOnlyMesh<DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, NodeBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    NodesOnlyMesh<DIM>* p_mesh;
    ar >> p_mesh;

    // Invoke inplace constructor to initialise instance
    ::new(t)NodeBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*NODEBASEDCELLPOPULATION_HPP_*/