ImmersedBoundaryCellPopulation.hpp

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*/
 
#ifndef IMMERSEDBOUNDARYCELLPOPULATION_HPP_
#define IMMERSEDBOUNDARYCELLPOPULATION_HPP_
 
#include "AbstractOffLatticeCellPopulation.hpp"
#include "ImmersedBoundaryMesh.hpp"
 
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>
#include "ChasteSerialization.hpp"
 
template <unsigned DIM>
class AbstractImmersedBoundaryDivisionRule;
 
template <unsigned DIM>
class ImmersedBoundaryCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
private:
    friend class TestImmersedBoundaryDivisionRules;
 
    friend class TestImmersedBoundaryCellPopulation;
 
    bool mDeleteMesh;
 
    ImmersedBoundaryMesh<DIM, DIM>* mpImmersedBoundaryMesh;
 
    boost::shared_ptr<AbstractImmersedBoundaryDivisionRule<DIM> > mpImmersedBoundaryDivisionRule;
 
    double mIntrinsicSpacing;
 
    bool mPopulationHasActiveSources;
 
    bool mOutputNodeRegionToVtk;
 
    double mInteractionDistance;
 
    unsigned mReMeshFrequency;
 
    bool mThrowStepSizeException;
 
    double mCellRearrangementThreshold;
 
    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& mpImmersedBoundaryDivisionRule;
        archive& mPopulationHasActiveSources;
        archive& mInteractionDistance;
        archive& mReMeshFrequency;
        archive& mThrowStepSizeException;
        archive& mCellRearrangementThreshold;
    }
 
    double Delta1D(double dist, double spacing);
 
    double CalculateIntrinsicCellSize();
 
    void Validate();
 
public:
    ImmersedBoundaryCellPopulation(ImmersedBoundaryMesh<DIM, DIM>& rMesh,
                                   std::vector<CellPtr>& rCells,
                                   bool deleteMesh = false,
                                   bool validate = true,
                                   const std::vector<unsigned> locationIndices = std::vector<unsigned>());
 
    ImmersedBoundaryCellPopulation(ImmersedBoundaryMesh<DIM, DIM>& rMesh);
 
    virtual ~ImmersedBoundaryCellPopulation();
 
    double GetDampingConstant(unsigned nodeIndex);
 
    ImmersedBoundaryMesh<DIM, DIM>& rGetMesh();
 
    const ImmersedBoundaryMesh<DIM, DIM>& rGetMesh() const;
 
    ImmersedBoundaryElement<DIM, DIM>* GetElement(unsigned elementIndex);
 
    ImmersedBoundaryElement<DIM - 1, DIM>* GetLamina(unsigned laminaIndex);
 
    unsigned GetNumElements();
 
    unsigned GetNumLaminas();
 
    unsigned GetNumNodes();
 
    void SetInteractionDistance(double newDistance);
 
    double GetInteractionDistance() const;
 
    void SetReMeshFrequency(unsigned newFrequency);
 
    unsigned GetReMeshFrequency() const;
 
    void SetThrowsStepSizeException(bool throws);
 
    bool ThrowsStepSizeException() const;
 
    double GetIntrinsicSpacing() const;
 
    void SetCellRearrangementThreshold(double newThreshold);
 
    double GetCellRearrangementThreshold() const;
 
    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);
 
    Node<DIM>* GetNode(unsigned index);
 
    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
 
    unsigned AddNode(Node<DIM>* pNewNode);
 
    void UpdateNodeLocations(double dt);
 
    void SetNode(unsigned index, ChastePoint<DIM>& rNewLocation);
 
    ImmersedBoundaryElement<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 AcceptPopulationEventWriter(
        boost::shared_ptr<AbstractCellPopulationEventWriter<DIM, DIM> > pPopulationEventWriter);
 
    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);
 
    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<AbstractImmersedBoundaryDivisionRule<DIM> > GetImmersedBoundaryDivisionRule();
 
    void SetImmersedBoundaryDivisionRule(
        boost::shared_ptr<AbstractImmersedBoundaryDivisionRule<DIM> > pImmersedBoundaryDivisionRule);
 
    bool DoesPopulationHaveActiveSources() const;
 
    bool IsCellOnBoundary(CellPtr pCell);
 
    void SetIfPopulationHasActiveSources(bool hasActiveSources);
 
    void SetOutputNodeRegionToVtk(bool outputNodeRegionsToVtk);
 
    virtual void CheckForStepSizeException(
        unsigned nodeIndex,
        c_vector<double, DIM>& rDisplacement,
        double dt);
 
    virtual double GetDefaultTimeStep();
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundaryCellPopulation)
 
namespace boost
{
namespace serialization
{
    template <class Archive, unsigned DIM>
    inline void save_construct_data(
        Archive& ar, const ImmersedBoundaryCellPopulation<DIM>* t, const unsigned int file_version)
    {
        // Save data required to construct instance
        const ImmersedBoundaryMesh<DIM, DIM>* p_mesh = &(t->rGetMesh());
        ar& p_mesh;
        ar& t->DoesPopulationHaveActiveSources();
        ar& t->GetInteractionDistance();
        ar& t->GetReMeshFrequency();
        ar& t->ThrowsStepSizeException();
        ar& t->GetCellRearrangementThreshold();
    }
 
    template <class Archive, unsigned DIM>
    inline void load_construct_data(
        Archive& ar, ImmersedBoundaryCellPopulation<DIM>* t, const unsigned int file_version)
    {
        // Retrieve data from archive required to construct new instance
        ImmersedBoundaryMesh<DIM, DIM>* p_mesh;
        ar >> p_mesh;
        bool hasActiveSources = false;
        ar >> hasActiveSources;
        double interactionDistance = 0.0;
        ar >> interactionDistance;
        unsigned int reMeshFrequency = 1;
        ar >> reMeshFrequency;
        bool throwStepSizeException = false;
        ar >> throwStepSizeException;
        double cellRearrangementThreshold = 0.5;
        ar >> cellRearrangementThreshold;
 
        // Invoke inplace constructor to initialise instance
        ::new (t) ImmersedBoundaryCellPopulation<DIM>(*p_mesh);
        t->SetIfPopulationHasActiveSources(hasActiveSources);
        t->SetInteractionDistance(interactionDistance);
        t->SetReMeshFrequency(reMeshFrequency);
        t->SetThrowsStepSizeException(true);
        t->SetCellRearrangementThreshold(cellRearrangementThreshold);
    }
}
} // namespace ...
 
#endif /*IMMERSEDBOUNDARYCELLPOPULATION_HPP_*/