NodeBasedCellPopulation.hpp

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*/
 
#ifndef NODEBASEDCELLPOPULATION_HPP_
#define NODEBASEDCELLPOPULATION_HPP_
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
 
 
#include "ObjectCommunicator.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"
 
template<unsigned DIM>
class NodeBasedCellPopulation : public AbstractCentreBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulation;
    friend class TestNodeBasedCellPopulationParallelMethods;
    friend class TestPeriodicNodeBasedCellPopulationParallelMethods;
 
protected:
 
    NodesOnlyMesh<DIM>* mpNodesOnlyMesh;
 
private:
 
    c_vector<double, DIM> mMinSpatialPositions;
 
    c_vector<double, DIM> mMaxSpatialPositions;
 
    std::vector< std::pair<Node<DIM>*, Node<DIM>* > > mNodePairs;
 
    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:
 
    virtual void UpdateParticlesAfterReMesh(NodeMap& rMap);
 
    virtual void Validate();
 
private:
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory);
 
    unsigned CalculateMessageTag(unsigned senderI, unsigned receiverJ);
 
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;
 
    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();
 
    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 AcceptPopulationEventWriter(boost::shared_ptr<AbstractCellPopulationEventWriter<DIM, DIM> > pPopulationEventWriter);
 
    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, 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_*/