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.
 
#ifdef DOXYGEN_CHASTE_ISSUE_199 // See https://github.com/Chaste/Chaste/issues/199
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
#else
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
#endif
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_*/