CryptSimulation2d.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 "TissueSimulation.hpp"
#include "SimpleDataWriter.hpp"
#include "MeshBasedTissueWithGhostNodes.hpp"

class CryptSimulation2d : public TissueSimulation<2>
{
    // Allow tests to access private members, in order to test computation of
    // private functions eg. DoCellBirth
    friend class TestCryptSimulation2d;

protected:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // If Archive is an output archive, then & resolves to <<
        // If Archive is an input archive, then & resolves to >>
        archive & boost::serialization::base_object<TissueSimulation<2> >(*this);
        archive & mUseJiggledBottomCells;
    }

    bool mUseJiggledBottomCells;

    out_stream mBetaCatResultsFile;

    MeshBasedTissueWithGhostNodes<2>* mpStaticCastTissue;

    c_vector<double, 2> CalculateCellDivisionVector(TissueCell& rParentCell);

    void WriteVisualizerSetupFile();

    void SetupWriteBetaCatenin();

    void WriteBetaCatenin(double time);

    void SetupSolve();

    void OutputParameters();

    void PostSolve();

    void AfterSolve();

public :

    CryptSimulation2d(AbstractTissue<2>& rTissue,
                      std::vector<AbstractForce<2>*> forceCollection,
                      bool deleteTissueAndForceCollection=false,
                      bool initialiseCells=true);

    void UseJiggledBottomCells();

    void ApplyTissueBoundaryConditions(const std::vector<c_vector<double,2> >& rOldLocations);

    void SetBottomCellAncestors();
};


#include "SerializationExportWrapper.hpp"
// Declare identifier for the serializer
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 AbstractTissue<2>* p_tissue = &(t->rGetTissue());
    ar & p_tissue;
    const std::vector<AbstractForce<2>*> force_collection = t->rGetForceCollection();
    ar & force_collection;
}

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
    AbstractTissue<2>*p_tissue;
    ar >> p_tissue;
    std::vector<AbstractForce<2>*> force_collection;
    ar >> force_collection;

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

#endif /*CRYPTSIMULATION2D_HPP_*/