PottsBasedCellPopulation.hpp

/*

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*/

#ifndef POTTSBASEDCELLPOPULATION_HPP_
#define POTTSBASEDCELLPOPULATION_HPP_

#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractUpdateRule.hpp"
#include "MutableMesh.hpp"

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>

template<unsigned DIM>
class PottsBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestPottsBasedCellPopulation;

private:

    VertexMesh<DIM,DIM>* mpElementTessellation;

    PottsMesh<DIM>* mpPottsMesh;

    MutableMesh<DIM,DIM>* mpMutableMesh;

    double mTemperature;

    unsigned mNumSweepsPerTimestep;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);

        /*
         * In its current form the code does not allow the direct serialization
         * of the PottsMesh class, so instead we delete mpVoronoiTessellation.
         */
        delete mpElementTessellation;
        mpElementTessellation = nullptr;

        archive & mTemperature;
        archive & mNumSweepsPerTimestep;
    }

    void Validate();

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

public:

    PottsBasedCellPopulation(PottsMesh<DIM>& rMesh,
                             std::vector<CellPtr>& rCells,
                             bool deleteMesh=false,
                             bool validate=true,
                             const std::vector<unsigned> locationIndices=std::vector<unsigned>());

    PottsBasedCellPopulation(PottsMesh<DIM>& rMesh);

    virtual ~PottsBasedCellPopulation();

    PottsMesh<DIM>& rGetMesh();

    const PottsMesh<DIM>& rGetMesh() const;

    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();

    PottsElement<DIM>* GetElement(unsigned elementIndex);

    unsigned GetNumElements();

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

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

    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);

    PottsElement<DIM>* GetElementCorrespondingToCell(CellPtr pCell);

    CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());

    unsigned RemoveDeadCells();

    void UpdateCellLocations(double dt);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);

    virtual void WriteResultsToFiles(const std::string& rDirectory);

    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);

    double GetVolumeOfCell(CellPtr pCell);

    double GetWidth(const unsigned& rDimension);

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    void SetTemperature(double temperature);

    double GetTemperature();

    void SetNumSweepsPerTimestep(unsigned numSweepsPerTimestep);

    unsigned GetNumSweepsPerTimestep();

    void CreateElementTessellation();

    VertexMesh<DIM,DIM>* GetElementTessellation();

    void CreateMutableMesh();

    MutableMesh<DIM,DIM>* GetMutableMesh();

    virtual void AddUpdateRule(boost::shared_ptr<AbstractUpdateRule<DIM> > pUpdateRule);

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

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PottsBasedCellPopulation)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const PottsBasedCellPopulation<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, PottsBasedCellPopulation<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)PottsBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*POTTSBASEDCELLPOPULATION_HPP_*/