CellBasedSimulationWithPdes.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 CellBasedSimulationWITHPDES_HPP_
#define CellBasedSimulationWITHPDES_HPP_

#include <map>
#include "ChasteSerialization.hpp"

#include "CellBasedSimulation.hpp"

#include "PdeAndBoundaryConditions.hpp"
#include "TetrahedralMesh.hpp"
#include "PetscTools.hpp"

#include "OutputFileHandler.hpp"
#include "Cell.hpp"

template<unsigned DIM>
class CellBasedSimulationWithPdes : public CellBasedSimulation<DIM>
{
    // Allow tests to access private members, in order to test computation of private functions
    friend class TestCellBasedSimulationWithPdes;

private:

    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<CellBasedSimulation<DIM> >(*this);
        archive & mWriteAverageRadialPdeSolution;
        archive & mWriteDailyAverageRadialPdeSolution;
        archive & mNumRadialIntervals;
        archive & mCellPdeElementMap;
    }

    std::vector<PdeAndBoundaryConditions<DIM>*> mPdeAndBcCollection;

    out_stream mpVizPdeSolutionResultsFile;

    out_stream mpAverageRadialPdeSolutionResultsFile;

    bool mWriteAverageRadialPdeSolution;

    bool mWriteDailyAverageRadialPdeSolution;

    unsigned mNumRadialIntervals;

    TetrahedralMesh<DIM,DIM>* mpCoarsePdeMesh;

    std::map<CellPtr, unsigned> mCellPdeElementMap;

    void SetupSolve();

    void SetupWritePdeSolution();

    void WritePdeSolution(double time);

    void WriteAverageRadialPdeSolution(double time, unsigned numIntervals);

    void SolvePde();

    void SolvePdeUsingCoarseMesh();

    unsigned FindCoarseElementContainingCell(CellPtr pCell);

    void PostSolve();

    void AfterSolve();

    void CreateCoarsePdeMesh(double coarseGrainScaleFactor);

    void InitialiseCoarsePdeMesh();

    void WriteVisualizerSetupFile();

public:

     CellBasedSimulationWithPdes(AbstractCellPopulation<DIM>& rCellPopulation,
                              std::vector<PdeAndBoundaryConditions<DIM>*> pdeAndBcCollection=std::vector<PdeAndBoundaryConditions<DIM>*>(),
                              bool deleteCellPopulationAndForceCollection=false,
                              bool initialiseCells=true);

    ~CellBasedSimulationWithPdes();

    void SetPdeAndBcCollection(std::vector<PdeAndBoundaryConditions<DIM>*> pdeAndBcCollection);

    Vec GetCurrentPdeSolution(unsigned pdeIndex);

    void SetWriteAverageRadialPdeSolution(unsigned numRadialIntervals=10,
                                          bool writeDailyResults=false);

    void UseCoarsePdeMesh(double coarseGrainScaleFactor=10.0);

    void OutputSimulationParameters(out_stream& rParamsFile);
};


#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellBasedSimulationWithPdes)

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

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

    // Invoke inplace constructor to initialise instance
    ::new(t)CellBasedSimulationWithPdes<DIM>(*p_cell_population, std::vector<PdeAndBoundaryConditions<DIM>*>(), true, false);
}
}
} // namespace ...


#endif /*CellBasedSimulationWITHPDES_HPP_*/

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