MeshBasedCellPopulationWithGhostNodes.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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 * Redistributions in binary form must reproduce the above copyright notice,
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*/

#ifndef MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_
#define MESHBASEDCELLPOPULATIONWITHGHOSTNODES_HPP_

#include "MeshBasedCellPopulation.hpp"
#include "TrianglesMeshReader.hpp"

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>

template<unsigned DIM>
class MeshBasedCellPopulationWithGhostNodes : public MeshBasedCellPopulation<DIM>
{
private:

    friend class TestMeshBasedCellPopulationWithGhostNodes;

    std::vector<bool> mIsGhostNode;

    double mGhostSpringStiffness;

    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 & mGhostSpringStiffness;
        archive & boost::serialization::base_object<MeshBasedCellPopulation<DIM> >(*this);
    }

    void SetGhostNodes(const std::set<unsigned>& rGhostNodeIndices);

    void Validate();

public:

    MeshBasedCellPopulationWithGhostNodes(MutableMesh<DIM, DIM>& rMesh,
                                  std::vector<CellPtr>& rCells,
                                  const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                                  bool deleteMesh=false,
                                  double ghostSpringStiffness=15.0);

    MeshBasedCellPopulationWithGhostNodes(MutableMesh<DIM, DIM>& rMesh,
                                  double ghostSpringStiffness=15.0);

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

    std::vector<bool>& rGetGhostNodes();

    bool IsGhostNode(unsigned index);

    std::set<unsigned> GetGhostNodeIndices();

    void UpdateGhostPositions(double dt);

    void UpdateGhostNodesAfterReMesh(NodeMap& rMap);

    c_vector<double, DIM> CalculateForceBetweenGhostNodes(const unsigned& rNodeAGlobalIndex, const unsigned& rNodeBGlobalIndex);

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

    void WriteVtkResultsToFile();

    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 BOOST_PFTO 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_*/