CellBasedPdeHandler.hpp

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*/

#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 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_*/