NodeBasedCellPopulationWithParticles.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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   software without specific prior written permission.

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*/

#ifndef NODEBASEDCELLPOPULATIONWITHPARTICLES_HPP_
#define NODEBASEDCELLPOPULATIONWITHPARTICLES_HPP_

#include "NodeBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"

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

template<unsigned DIM>
class NodeBasedCellPopulationWithParticles : public NodeBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulationWithParticles;

protected:
    void Validate();

private:

    std::vector<bool> mIsParticle;

    void SetParticles(const std::set<unsigned>& rParticleIndices);

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

public:

    NodeBasedCellPopulationWithParticles(NodesOnlyMesh<DIM>& rMesh,
                            std::vector<CellPtr>& rCells,
                            const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                            bool deleteMesh=false);

    NodeBasedCellPopulationWithParticles(NodesOnlyMesh<DIM>& rMesh);

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

    void UpdateParticlesAfterReMesh(NodeMap& rMap);

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

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

    bool IsParticle(unsigned index);

    std::set<unsigned> GetParticleIndices();


    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(NodeBasedCellPopulationWithParticles)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const NodeBasedCellPopulationWithParticles<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const NodesOnlyMesh<DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, NodeBasedCellPopulationWithParticles<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    NodesOnlyMesh<DIM>* p_mesh;
    ar >> p_mesh;

    // Invoke inplace constructor to initialise instance
    ::new(t)NodeBasedCellPopulationWithParticles<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*NODEBASEDCELLPOPULATIONWITHPARTICLES_HPP_*/