CaBasedCellPopulation.hpp

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*/
 
#ifndef CABASEDCELLPOPULATION_HPP_
#define CABASEDCELLPOPULATION_HPP_
 
#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractUpdateRule.hpp"
#include "AbstractCaBasedDivisionRule.hpp"
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>
 
template<unsigned DIM> class AbstractCaBasedDivisionRule; // Circular definition thing.
 
template<unsigned DIM>
class CaBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestCaBasedCellPopulation;
 
private:
 
    unsigned mLatticeCarryingCapacity;
 
    std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > mSwitchingUpdateRuleCollection;
 
    std::vector<unsigned> mAvailableSpaces;
 
    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > mpCaBasedDivisionRule;
 
    void SetEmptySites(const std::set<unsigned>& rEmptySiteIndices);
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);
        archive & mSwitchingUpdateRuleCollection;
        archive & mLatticeCarryingCapacity;
        archive & mAvailableSpaces;
        archive & mpCaBasedDivisionRule;
    }
 
    void Validate();
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory);
 
public:
 
    CaBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                  std::vector<CellPtr>& rCells,
                                  const std::vector<unsigned> locationIndices,
                                  unsigned latticeCarryingCapacity=1u,
                                  bool deleteMesh=false,
                                  bool validate=false);
 
    CaBasedCellPopulation(PottsMesh<DIM>& rMesh);
 
    virtual ~CaBasedCellPopulation();
 
    std::vector<unsigned>& rGetAvailableSpaces();
 
    virtual bool IsSiteAvailable(unsigned index, CellPtr pCell);
 
    PottsMesh<DIM>& rGetMesh();
 
    const PottsMesh<DIM>& rGetMesh() const;
 
    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();
 
    Node<DIM>* GetNode(unsigned index);
 
    unsigned GetNumNodes();
 
    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
 
    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);
 
    void AddCellUsingLocationIndex(unsigned index, CellPtr pCell);
 
    void RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell);
 
     Node<DIM>* GetNodeCorrespondingToCell(CellPtr pCell);
 
    CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());
 
     double virtual EvaluateDivisionPropensity(unsigned currentNodeIndex,
                                               unsigned targetNodeIndex,
                                               CellPtr pCell);
    unsigned RemoveDeadCells();
 
    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
 
    void UpdateCellLocations(double dt);
 
    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);
 
    void Update(bool hasHadBirthsOrDeaths=true);
 
    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 GetVolumeOfCell(CellPtr pCell);
 
    double GetWidth(const unsigned& rDimension);
 
    void RemoveAllUpdateRules();
 
    void OutputCellPopulationParameters(out_stream& rParamsFile);
 
    bool IsRoomToDivide(CellPtr pCell);
 
    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > GetCaBasedDivisionRule();
 
    void SetCaBasedDivisionRule(boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > pCaBasedDivisionRule);
 
    virtual void AddUpdateRule(boost::shared_ptr<AbstractUpdateRule<DIM> > pUpdateRule);
 
    virtual const std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > GetUpdateRuleCollection() const;
 
    virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
                                            std::string& rVariableName,
                                            bool dirichletBoundaryConditionApplies=false,
                                            double dirichletBoundaryValue=0.0);
 
    virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex);
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CaBasedCellPopulation)
 
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const CaBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const PottsMesh<DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}
 
template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, CaBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    PottsMesh<DIM>* p_mesh;
    ar >> p_mesh;
 
    // Invoke inplace constructor to initialise instance
    ::new(t)CaBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...
 
 
#endif /*CABASEDCELLPOPULATION_HPP_*/