CryptSimulation2d.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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 PostSolve();

    void AfterSolve();

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_*/