MeshBasedCellPopulationWithGhostNodes.hpp

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*/
 
#ifndef MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_
#define MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>
 
#include "MeshBasedCellPopulation.hpp"
 
template<unsigned DIM>
class MeshBasedCellPopulationWithGhostNodes : public MeshBasedCellPopulation<DIM>
{
private:
 
    friend class TestMeshBasedCellPopulationWithGhostNodes;
 
    std::vector<bool> mIsGhostNode;
 
    double mGhostCellSpringStiffness;
 
    double mGhostGhostSpringStiffness;
 
    double mGhostSpringRestLength;
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This needs to be first so that MeshBasedCellPopulation::Validate() doesn't go mental.
        archive & mIsGhostNode;
        archive & mGhostCellSpringStiffness;
        archive & mGhostGhostSpringStiffness;
        archive & mGhostSpringRestLength;
        archive & boost::serialization::base_object<MeshBasedCellPopulation<DIM, DIM> >(*this);
    }
 
    void Validate();
 
protected:
    virtual void AcceptCellWritersAcrossPopulation();
 
public:
 
    MeshBasedCellPopulationWithGhostNodes(MutableMesh<DIM, DIM>& rMesh,
                                          std::vector<CellPtr>& rCells,
                                          const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                                          bool deleteMesh=false,
                                          double ghostCellSpringStiffness=15.0,
                                          double ghostGhostSpringStiffness=15.0,
                                          double ghostSpringRestLength=1.0);
 
    MeshBasedCellPopulationWithGhostNodes(MutableMesh<DIM, DIM>& rMesh,
                                          double ghostCellSpringStiffness=15.0,
                                          double ghostGhostSpringStiffness=15.0,
                                          double ghostSpringRestLength=1.0);
 
    virtual ~MeshBasedCellPopulationWithGhostNodes();
 
    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();
 
    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);
 
    void SetGhostNodes(const std::set<unsigned>& rGhostNodeIndices);
 
    void ApplyGhostForces();
 
    std::vector<bool>& rGetGhostNodes();
 
    bool IsGhostNode(unsigned index);
 
    std::set<unsigned> GetGhostNodeIndices();
 
    void RemoveGhostNode(unsigned nodeIndex);
 
    void UpdateGhostNodesAfterReMesh(NodeMap& rMap);
 
    c_vector<double, DIM> CalculateForceBetweenGhostNodes(const unsigned& rNodeAGlobalIndex, const unsigned& rNodeBGlobalIndex);
 
    CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell);
 
    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory);
 
    void OutputCellPopulationParameters(out_stream& rParamsFile);
};
 
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(MeshBasedCellPopulationWithGhostNodes)
 
namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const MeshBasedCellPopulationWithGhostNodes<DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const MutableMesh<DIM,DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}
 
template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, MeshBasedCellPopulationWithGhostNodes<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    MutableMesh<DIM,DIM>* p_mesh;
    ar >> p_mesh;
 
    // Invoke inplace constructor to initialise instance
    ::new(t)MeshBasedCellPopulationWithGhostNodes<DIM>(*p_mesh);
}
}
} // namespace
 
#endif /*MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_*/