VertexBasedCellPopulation.hpp

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*/

#ifndef VERTEXBASEDCELLPOPULATION_HPP_
#define VERTEXBASEDCELLPOPULATION_HPP_

#include "AbstractOffLatticeCellPopulation.hpp"
#include "MutableVertexMesh.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 VertexBasedCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
private:

    friend class TestVertexBasedDivisionRules;

    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;

     bool mThrowStepSizeException = true;

    virtual void WriteVtkResultsToFile(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);

    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);

    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 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);
};

#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;
}

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;

    // Invoke inplace constructor to initialise instance
    ::new(t)VertexBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*VERTEXBASEDCELLPOPULATION_HPP_*/