VertexBasedCellPopulation.hpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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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>

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"

template<unsigned DIM>
class VertexBasedCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
private:

    bool mDeleteMesh;

    MutableVertexMesh<DIM, DIM>* mpMutableVertexMesh;

    out_stream mpVizElementsFile;

    out_stream mpT1SwapLocationsFile;

    out_stream mpT3SwapLocationsFile;

    void WriteVtkResultsToFile();

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

    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);

    unsigned AddNode(Node<DIM>* pNewNode);

    void UpdateNodeLocations(const std::vector< c_vector<double, DIM> >& rNodeForces, double dt);

    void SetNode(unsigned index, ChastePoint<DIM>& rNewLocation);

    VertexElement<DIM, DIM>* GetElementCorrespondingToCell(CellPtr pCell);

    CellPtr AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr());

    unsigned RemoveDeadCells();

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    void CreateOutputFiles(const std::string& rDirectory, bool cleanOutputDirectory);
    void CloseOutputFiles();

    void WriteResultsToFiles();

    void WriteCellVolumeResultsToFile();

    double GetVolumeOfCell(CellPtr pCell);

    virtual void GenerateCellResultsAndWriteToFiles();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetWidth(const unsigned& rDimension);

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
};

#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 BOOST_PFTO 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_*/