AbstractCentreBasedCellPopulation.hpp

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*/

#ifndef ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
#define ABSTRACTCENTREBASEDCELLPOPULATION_HPP_

#include "AbstractOffLatticeCellPopulation.hpp"

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"

template<unsigned ELEMENT_DIM, unsigned  SPACE_DIM=ELEMENT_DIM>
class AbstractCentreBasedCellPopulation : public AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM> >(*this);
        archive & mMeinekeDivisionSeparation;
        archive & mMarkedSprings;
    }

protected:
    double mMeinekeDivisionSeparation;

    std::set<std::pair<CellPtr,CellPtr> > mMarkedSprings;

    AbstractCentreBasedCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);

    virtual void WriteVtkResultsToFile()=0;

public:

    AbstractCentreBasedCellPopulation( AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                        std::vector<CellPtr>& rCells,
                                      const std::vector<unsigned> locationIndices=std::vector<unsigned>());

    c_vector<double, SPACE_DIM> GetLocationOfCellCentre(CellPtr pCell);

    Node<SPACE_DIM>* GetNodeCorrespondingToCell(CellPtr pCell);

    CellPtr AddCell(CellPtr pNewCell, const c_vector<double,SPACE_DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr());

    std::pair<CellPtr,CellPtr> CreateCellPair(CellPtr pCell1, CellPtr pCell2);

    bool IsMarkedSpring(const std::pair<CellPtr,CellPtr>& rCellPair);

    void MarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);

    void UnmarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    virtual void UpdateNodeLocations(const std::vector< c_vector<double, SPACE_DIM> >& rNodeForces, double dt);

    virtual double GetDampingConstant(unsigned nodeIndex);

    virtual void GenerateCellResultsAndWriteToFiles();

    virtual void WriteTimeAndNodeResultsToFiles();

    virtual bool IsGhostNode(unsigned index);

    virtual bool IsParticle(unsigned index);

    virtual std::set< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& rGetNodePairs()=0;

    double GetMeinekeDivisionSeparation();

    void SetMeinekeDivisionSeparation(double divisionSeparation);

    virtual void OutputCellPopulationParameters(out_stream& rParamsFile);
};

#endif /*ABSTRACTCENTREBASEDCELLPOPULATION_HPP_*/