AbstractBoxDomainPdeModifier.hpp

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*/

#ifndef ABSTRACTBOXDOMAINPDEMODIFIER_HPP_
#define ABSTRACTBOXDOMAINPDEMODIFIER_HPP_

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

#include "AbstractPdeModifier.hpp"

template<unsigned DIM>
class AbstractBoxDomainPdeModifier : public AbstractPdeModifier<DIM>
{
    friend class TestEllipticBoxDomainPdeModifier;
    friend class TestParabolicBoxDomainPdeModifier;
    friend class TestOffLatticeSimulationWithPdes;

private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractPdeModifier<DIM> >(*this);
        archive & mpMeshCuboid;
        archive & mStepSize;
        archive & mSetBcsOnBoxBoundary;
    }

protected:

    std::map<CellPtr, unsigned> mCellPdeElementMap;

    boost::shared_ptr<ChasteCuboid<DIM> > mpMeshCuboid;

    double mStepSize;

    bool mSetBcsOnBoxBoundary;

public:

    AbstractBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=boost::shared_ptr<AbstractLinearPde<DIM,DIM> >(),
                                 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
                                 bool isNeumannBoundaryCondition=true,
                                 boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid=boost::shared_ptr<ChasteCuboid<DIM> >(),
                                 double stepSize=1.0,
                                 Vec solution=nullptr);

    virtual ~AbstractBoxDomainPdeModifier();

    double GetStepSize();

    void SetBcsOnBoxBoundary(bool setBcsOnBoxBoundary);

    bool AreBcsSetOnBoxBoundary();

    virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);

    void GenerateFeMesh(boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid, double stepSize);

    void UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation);

    void InitialiseCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation);

    void UpdateCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation);

    void OutputSimulationModifierParameters(out_stream& rParamsFile);
};

#include "SerializationExportWrapper.hpp"
TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractBoxDomainPdeModifier)

#endif /*ABSTRACTBOXDOMAINPDEMODIFIER_HPP_*/