VertexBasedCellPopulation.hpp

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*/
 
#ifndef VERTEXBASEDCELLPOPULATION_HPP_
#define VERTEXBASEDCELLPOPULATION_HPP_
 
#include "AbstractOffLatticeCellPopulation.hpp"
#include "MutableVertexMesh.hpp"
#include "TrapezoidEdgeVertexMeshWriter.hpp"
#include "VertexBasedPopulationSrn.hpp"
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>
 
template<unsigned DIM>
class AbstractVertexBasedDivisionRule; // Forward declaration to prevent circular include chain
template<unsigned DIM>
class VertexBasedPopulationSrn;
 
template<unsigned DIM>
class VertexBasedCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
private:
 
    friend class TestVertexBasedDivisionRules;
    friend class TestVertexBasedCellPopulation;
    friend class TestMutableVertexMeshOperationsWithPopulationSrn;
 
    bool mDeleteMesh;
 
    MutableVertexMesh<DIM, DIM>* mpMutableVertexMesh;
 
    bool mOutputCellRearrangementLocations;
 
    boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > mpVertexBasedDivisionRule;
 
    std::vector< c_vector<double, DIM> > mLocationsOfT2Swaps;
 
    std::vector< unsigned > mCellIdsOfT2Swaps;
 
    bool mRestrictVertexMovement;
 
     VertexBasedPopulationSrn<DIM> mPopulationSrn;
 
     bool mWriteCellVtkResults = true;
 
     bool mWriteEdgeVtkResults = true;
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory);
 
    virtual void WriteCellVtkResultsToFile(const std::string& rDirectory);
 
    virtual void WriteCellEdgeVtkResultsToFile(const std::string& rDirectory);
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOffLatticeCellPopulation<DIM> >(*this);
        archive & mOutputCellRearrangementLocations;
        archive & mpVertexBasedDivisionRule;
        archive & mRestrictVertexMovement;
    }
 
    void Validate();
 
public:
 
    VertexBasedCellPopulation(MutableVertexMesh<DIM, DIM>& rMesh,
                              std::vector<CellPtr>& rCells,
                              bool deleteMesh=false,
                              bool validate=true,
                              const std::vector<unsigned> locationIndices=std::vector<unsigned>());
 
    VertexBasedCellPopulation(MutableVertexMesh<DIM, DIM>& rMesh,
                              VertexBasedPopulationSrn<DIM>& rPopSrn);
 
    virtual ~VertexBasedCellPopulation();
 
    double GetDampingConstant(unsigned nodeIndex);
 
    MutableVertexMesh<DIM, DIM>& rGetMesh();
 
    const MutableVertexMesh<DIM, DIM>& rGetMesh() const;
 
    VertexElement<DIM, DIM>* GetElement(unsigned elementIndex);
 
    unsigned GetNumElements();
 
    unsigned GetNumNodes();
 
    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);
 
    Node<DIM>* GetNode(unsigned index);
 
    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
 
    std::set<std::pair<unsigned, unsigned>> GetNeighbouringEdgeIndices(CellPtr pCell, unsigned edgeLocalIndex);
 
    unsigned AddNode(Node<DIM>* pNewNode);
 
    virtual void CheckForStepSizeException(unsigned nodeIndex, c_vector<double,DIM>& rDisplacement, double dt);
 
    void SetNode(unsigned index, ChastePoint<DIM>& rNewLocation);
 
    VertexElement<DIM, DIM>* GetElementCorrespondingToCell(CellPtr pCell);
 
    CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());
 
    unsigned RemoveDeadCells();
 
    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);
 
    void Update(bool hasHadBirthsOrDeaths=true);
 
    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
 
    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);
 
    unsigned GetRosetteRankOfCell(CellPtr pCell);
 
    double GetVolumeOfCell(CellPtr pCell);
 
    std::vector< c_vector< double, DIM > > GetLocationsOfT2Swaps();
 
    std::vector< unsigned > GetCellIdsOfT2Swaps();
 
    void AddLocationOfT2Swap(c_vector< double, DIM> locationOfT2Swap);
 
    void AddCellIdOfT2Swap(unsigned idOfT2Swap);
 
    void ClearLocationsAndCellIdsOfT2Swaps();
 
    bool GetOutputCellRearrangementLocations();
 
    void SetOutputCellRearrangementLocations(bool outputCellRearrangementLocations);
 
    void OutputCellPopulationParameters(out_stream& rParamsFile);
 
    double GetWidth(const unsigned& rDimension);
 
    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
 
    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();
 
    virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex);
 
    virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
                                            std::string& rVariableName,
                                            bool dirichletBoundaryConditionApplies=false,
                                            double dirichletBoundaryValue=0.0);
 
    boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > GetVertexBasedDivisionRule();
 
    void SetVertexBasedDivisionRule(boost::shared_ptr<AbstractVertexBasedDivisionRule<DIM> > pVertexBasedDivisionRule);
 
    virtual double GetDefaultTimeStep();
 
    virtual void WriteDataToVisualizerSetupFile(out_stream& pVizSetupFile);
 
    virtual void SimulationSetupHook(AbstractCellBasedSimulation<DIM, DIM>* pSimulation);
 
    bool GetRestrictVertexMovementBoolean();
 
    void SetRestrictVertexMovementBoolean(bool restrictVertexMovement);
 
    VertexBasedPopulationSrn<DIM>& rGetVertexBasedPopulationSrn();
 
    const VertexBasedPopulationSrn<DIM>& rGetVertexBasedPopulationSrn() const;
 
    void SetWriteCellVtkResults(const bool new_val);
 
    void SetWriteEdgeVtkResults(const bool new_val);
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(VertexBasedCellPopulation)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const VertexBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const MutableVertexMesh<DIM,DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
 
    const VertexBasedPopulationSrn<DIM>& pop_srn = t->rGetVertexBasedPopulationSrn();
    ar & pop_srn;
}
 
template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, VertexBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    MutableVertexMesh<DIM,DIM>* p_mesh;
    ar >> p_mesh;
 
    VertexBasedPopulationSrn<DIM> pop_srn;
    ar & pop_srn;
    // Invoke inplace constructor to initialise instance
    ::new(t)VertexBasedCellPopulation<DIM>(*p_mesh, pop_srn);
}
}
} // namespace ...
 
#endif /*VERTEXBASEDCELLPOPULATION_HPP_*/