AbstractCentreBasedCellPopulation.hpp

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*/

#ifndef ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
#define ABSTRACTCENTREBASEDCELLPOPULATION_HPP_

#include "AbstractOffLatticeCellPopulation.hpp"
#include "AbstractCentreBasedDivisionRule.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class AbstractCentreBasedDivisionRule; // Circular definition thing.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
class AbstractCentreBasedCellPopulation : public AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>
{
private:
    friend class TestCentreBasedDivisionRules;

    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;
        archive & mpCentreBasedDivisionRule;
    }

protected:
    double mMeinekeDivisionSeparation;

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

    boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > mpCentreBasedDivisionRule;

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

    virtual void WriteVtkResultsToFile(const std::string& rDirectory)=0;

    virtual void AcceptCellWritersAcrossPopulation();

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);

    virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
                                            std::string& rVariableName,
                                            bool dirichletBoundaryConditionApplies=false,
                                            double dirichletBoundaryValue=0.0);

    CellPtr AddCell(CellPtr pNewCell, 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 std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);

    virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector<double,SPACE_DIM>& rDisplacement, double dt);

    virtual double GetDampingConstant(unsigned nodeIndex);

    virtual bool IsGhostNode(unsigned index);

    virtual bool IsParticle(unsigned index);

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

    double GetMeinekeDivisionSeparation();

    void SetMeinekeDivisionSeparation(double divisionSeparation);

    boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > GetCentreBasedDivisionRule();

    void SetCentreBasedDivisionRule(boost::shared_ptr<AbstractCentreBasedDivisionRule<ELEMENT_DIM, SPACE_DIM> > pCentreBasedDivisionRule);

    virtual void OutputCellPopulationParameters(out_stream& rParamsFile);

    virtual double GetDefaultTimeStep();
};

#endif /*ABSTRACTCENTREBASEDCELLPOPULATION_HPP_*/