CryptSimulation2d.hpp

/*

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*/

#ifndef CRYPTSIMULATION2D_HPP_
#define CRYPTSIMULATION2D_HPP_

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

#include "WntConcentration.hpp"
#include "OffLatticeSimulation.hpp"
#include "MeshBasedCellPopulationWithGhostNodes.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "CryptSimulationBoundaryCondition.hpp"

class CryptSimulation2d : public OffLatticeSimulation<2>
{
    // Allow tests to access private members, in order to test computation of private functions e.g. DoCellBirth()
    friend class TestCryptSimulation2dWithMeshBasedCellPopulation;
    friend class TestCryptSimulation2dWithVertexBasedCellPopulation;

protected:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<OffLatticeSimulation<2> >(*this);

        SerializableSingleton<WntConcentration<2> >* p_wnt_wrapper = WntConcentration<2>::Instance()->GetSerializationWrapper();
        archive & p_wnt_wrapper;

        archive & mWriteBetaCatenin;
    }

    bool mWriteBetaCatenin;

    out_stream mVizBetaCateninResultsFile;

    bool mUsingMeshBasedCellPopulation;

    c_vector<double, 2> CalculateCellDivisionVector(CellPtr pParentCell);

    void SetupWriteBetaCatenin();

    virtual void WriteBetaCatenin(double time);

    void SetupSolve();

    void UpdateAtEndOfTimeStep();

    void UpdateAtEndOfSolve();

public:

    CryptSimulation2d(AbstractCellPopulation<2>& rCellPopulation,
                      bool deleteCellPopulationInDestructor=false,
                      bool initialiseCells=true);

    virtual ~CryptSimulation2d();

    void UseJiggledBottomCells();

    void SetBottomCellAncestors();

    void OutputSimulationParameters(out_stream& rParamsFile);
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(CryptSimulation2d)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const CryptSimulation2d * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const AbstractCellPopulation<2>* p_cell_population = &(t->rGetCellPopulation());
    ar & p_cell_population;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, CryptSimulation2d * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    AbstractCellPopulation<2>* p_cell_population;
    ar & p_cell_population;

    // Invoke inplace constructor to initialise instance
    ::new(t)CryptSimulation2d(*p_cell_population, true, false);
}
}
} // namespace

#endif /*CRYPTSIMULATION2D_HPP_*/