MeshBasedCellPopulation.hpp

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*/
 
#ifndef MESHBASEDCELLPOPULATION_HPP_
#define MESHBASEDCELLPOPULATION_HPP_
 
#include <map>
#include "AbstractCentreBasedCellPopulation.hpp"
#include "MutableMesh.hpp"
#include "VertexMesh.hpp"
#include "TrianglesMeshReader.hpp"
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>
 
#ifdef DOXYGEN_CHASTE_ISSUE_199 // See https://github.com/Chaste/Chaste/issues/199
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
#else
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
#endif
class MeshBasedCellPopulation : public AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestMeshBasedCellPopulation;
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM> >(*this);
 
        /*
         * In its current form the code does not allow the direct serialization
         * of the VertexMesh class, so instead we delete mpVoronoiTessellation.
         */
        delete mpVoronoiTessellation;
        mpVoronoiTessellation = nullptr;
 
        archive & mSpringRestLengths;
        archive & mUseAreaBasedDampingConstant;
        archive & mAreaBasedDampingConstantParameter;
        archive & mWriteVtkAsPoints;
        archive & mBoundVoronoiTessellation;
        archive & mScaleBoundByEdgeLength; 
        archive & mBoundedVoroniTesselationLengthCutoff;
        archive & mOffsetNewBoundaryNodes;
        archive & mHasVariableRestLength;
        this->Validate();
    }
 
protected:
    VertexMesh<ELEMENT_DIM, SPACE_DIM>* mpVoronoiTessellation;
 
    MutableMesh<ELEMENT_DIM, SPACE_DIM>* mpMutableMesh;
 
    bool mDeleteMesh;
 
    std::map<std::pair<unsigned,unsigned>, double> mSpringRestLengths;
 
    bool mUseAreaBasedDampingConstant;
 
    double mAreaBasedDampingConstantParameter;
 
    bool mWriteVtkAsPoints;
 
    bool mBoundVoronoiTessellation;
 
    bool mScaleBoundByEdgeLength;
 
    double mBoundedVoroniTesselationLengthCutoff;
 
    bool mOffsetNewBoundaryNodes;
 
    bool mHasVariableRestLength;
 
    std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > > mNodePairs;
 
    virtual void UpdateGhostNodesAfterReMesh(NodeMap& rMap);
 
    virtual void Validate();
 
public:
    MeshBasedCellPopulation(MutableMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                            std::vector<CellPtr>& rCells,
                            const std::vector<unsigned> locationIndices = {},
                            bool deleteMesh = false,
                            bool validate = true);
 
    MeshBasedCellPopulation(MutableMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);
 
    virtual ~MeshBasedCellPopulation();
 
    MutableMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh();
 
    const MutableMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh() const;
 
    virtual TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* GetTetrahedralMeshForPdeModifier();
 
    bool UseAreaBasedDampingConstant();
 
    unsigned AddNode(Node<SPACE_DIM>* pNewNode);
 
    void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM>& rNewLocation);
 
    double GetDampingConstant(unsigned nodeIndex);
 
    void SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant);
 
    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
 
    virtual unsigned RemoveDeadCells();
 
    virtual CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell);
 
    virtual void WriteResultsToFiles(const std::string& rDirectory);
 
    virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationWriter);
 
    virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationCountWriter);
 
    virtual void AcceptPopulationEventWriter(boost::shared_ptr<AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationEventWriter);
 
    virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > pCellWriter, CellPtr pCell);
 
    virtual void Update(bool hasHadBirthsOrDeaths=true);
 
    void TessellateIfNeeded();
 
    void DivideLongSprings(double springDivisionThreshold);
 
    Node<SPACE_DIM>* GetNode(unsigned index);
 
    unsigned GetNumNodes();
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory);
 
    double GetVolumeOfCell(CellPtr pCell);
 
    void CreateVoronoiTessellation();
 
    VertexMesh<ELEMENT_DIM, SPACE_DIM>* GetVoronoiTessellation();
 
    double GetVolumeOfVoronoiElement(unsigned index);
 
    double GetSurfaceAreaOfVoronoiElement(unsigned index);
 
    double GetVoronoiEdgeLength(unsigned index1, unsigned index2);
 
    double GetWidth(const unsigned& rDimension);
 
    virtual void WriteDataToVisualizerSetupFile(out_stream& pVizSetupFile);
 
    class SpringIterator
    {
    public:
 
        Node<SPACE_DIM>* GetNodeA();
 
        Node<SPACE_DIM>* GetNodeB();
 
        CellPtr GetCellA();
 
        CellPtr GetCellB();
 
        bool operator!=(const typename MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::SpringIterator& rOther);
 
        SpringIterator& operator++();
 
        SpringIterator(MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>& rCellPopulation, typename MutableMesh<ELEMENT_DIM, SPACE_DIM>::EdgeIterator edgeIter);
 
    private:
 
        std::set<std::set<unsigned> > mSpringsVisited;
 
        MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>& mrCellPopulation;
 
        typename MutableMesh<ELEMENT_DIM, SPACE_DIM>::EdgeIterator mEdgeIter;
    };
 
    SpringIterator SpringsBegin();
 
    SpringIterator SpringsEnd();
 
    void CheckCellPointers();
 
    double GetAreaBasedDampingConstantParameter();
 
    void SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter);
 
    std::vector< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& rGetNodePairs();
 
    void OutputCellPopulationParameters(out_stream& rParamsFile);
 
    void SetWriteVtkAsPoints(bool writeVtkAsPoints);
 
    bool GetWriteVtkAsPoints();
 
    void SetBoundVoronoiTessellation(bool boundVoronoiTessellation);
 
    bool GetBoundVoronoiTessellation();
 
    void SetScaleBoundByEdgeLength(bool scaleBoundByEdgeLength);
 
    bool GetScaleBoundByEdgeLength();
 
    void SetBoundedVoroniTesselationLengthCutoff(double boundedVoroniTesselationLengthCutoff);
 
    double GetBoundedVoroniTesselationLengthCutoff();
 
    void SetOffsetNewBoundaryNodes(bool offsetNewBoundaryNodes);
 
    bool GetOffsetNewBoundaryNodes();
 
    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
 
    void CalculateRestLengths();
 
    double GetRestLength(unsigned indexA, unsigned indexB);
 
    void SetRestLength(unsigned indexA, unsigned indexB, double restLength);
 
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MeshBasedCellPopulation)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const MutableMesh<ELEMENT_DIM, SPACE_DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}
 
template<class Archive,  unsigned ELEMENT_DIM, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    MutableMesh<ELEMENT_DIM, SPACE_DIM>* p_mesh;
    ar >> p_mesh;
 
    // Invoke inplace constructor to initialise instance
    ::new(t)MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>(*p_mesh);
}
}
} // namespace ...
 
#endif /*MESHBASEDCELLPOPULATION_HPP_*/