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 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 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_*/