CellBasedPdeHandler.hpp

/*

Copyright (c) 2005-2015, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef CELLBASEDPDEHANDLER_HPP_
#define CELLBASEDPDEHANDLER_HPP_

#include <map>
#include <memory>

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

#include "AbstractCellPopulation.hpp"
#include "PdeAndBoundaryConditions.hpp"
#include "BoundaryConditionsContainer.hpp"
#include "TetrahedralMesh.hpp"
#include "ChasteCuboid.hpp"

template<unsigned DIM>
class CellBasedPdeHandler : public Identifiable
{
    // Allow tests to access private members, in order to test computation of private functions
    friend class TestCellBasedPdeHandler;
    friend class TestOffLatticeSimulationWithPdes;
    friend class TestOnLatticeSimulationWithPdes;

private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & mPdeAndBcCollection;
        archive & mWriteAverageRadialPdeSolution;
        archive & mWriteDailyAverageRadialPdeSolution;
        archive & mSetBcsOnCoarseBoundary;
        archive & mNumRadialIntervals;
        archive & mAverageRadialSolutionVariableName;
    }

protected:

    AbstractCellPopulation<DIM>* mpCellPopulation;

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

    std::string mDirPath;

    out_stream mpVizPdeSolutionResultsFile;

    out_stream mpAverageRadialPdeSolutionResultsFile;

    bool mWriteAverageRadialPdeSolution;

    bool mWriteDailyAverageRadialPdeSolution;

    std::string mAverageRadialSolutionVariableName;

    bool mSetBcsOnCoarseBoundary;

    unsigned mNumRadialIntervals;

    TetrahedralMesh<DIM,DIM>* mpCoarsePdeMesh;

    std::map<CellPtr, unsigned> mCellPdeElementMap;

    bool mDeleteMemberPointersInDestructor;

    void InitialiseCellPdeElementMap();

    virtual void WritePdeSolution(double time);

    void WriteAverageRadialPdeSolution(double time);

    bool PdeSolveNeedsCoarseMesh();

public:

    CellBasedPdeHandler(AbstractCellPopulation<DIM>* pCellPopulation, bool deleteMemberPointersInDestructor=false);

    virtual ~CellBasedPdeHandler();

    const AbstractCellPopulation<DIM>* GetCellPopulation() const;

    TetrahedralMesh<DIM,DIM>* GetCoarsePdeMesh();

    void OpenResultsFiles(std::string outputDirectory);

    void CloseResultsFiles();

    bool GetWriteAverageRadialPdeSolution();

    bool GetWriteDailyAverageRadialPdeSolution();

    void UpdateCellPdeElementMap();

    bool GetImposeBcsOnCoarseBoundary();

    unsigned GetNumRadialIntervals();

    virtual void SolvePdeAndWriteResultsToFile(unsigned samplingTimestepMultiple);

    virtual std::auto_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ConstructBoundaryConditionsContainer(
            PdeAndBoundaryConditions<DIM>* pPdeAndBc,
            TetrahedralMesh<DIM,DIM>* pMesh);

    double GetPdeSolutionAtPoint(const c_vector<double,DIM>& rPoint, const std::string& rVariable);

    unsigned FindCoarseElementContainingCell(CellPtr pCell);

    virtual Vec GetPdeSolution(const std::string& rName = "");

    void SetWriteAverageRadialPdeSolution(const std::string& rName,
                                            unsigned numRadialIntervals=10,
                                            bool writeDailyResults=false);

    void SetImposeBcsOnCoarseBoundary(bool setBcsOnCoarseBoundary);

    virtual void UseCoarsePdeMesh(double stepSize, ChasteCuboid<DIM> meshCuboid, bool centreOnCellPopulation = false);

    void AddPdeAndBc(PdeAndBoundaryConditions<DIM>* pPdeAndBc);

    virtual void OutputParameters(out_stream& rParamsFile);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CellBasedPdeHandler)

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

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, CellBasedPdeHandler<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)CellBasedPdeHandler<DIM>(p_cell_population, true);
}
}
}

#endif /*CELLBASEDPDEHANDLER_HPP_*/