AbstractBoxDomainPdeModifier.hpp

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*/
 
#ifndef ABSTRACTBOXDOMAINPDEMODIFIER_HPP_
#define ABSTRACTBOXDOMAINPDEMODIFIER_HPP_
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
 
#include "AbstractPdeModifier.hpp"
#include "BoundaryConditionsContainer.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;
        archive & mSetBcsOnBoundingSphere;
        archive & mUseVoronoiCellsForInterpolation;
        archive & mTypicalCellRadius;
    }
 
protected:
 
    std::map<CellPtr, unsigned> mCellPdeElementMap;
 
    boost::shared_ptr<ChasteCuboid<DIM> > mpMeshCuboid;
 
    double mStepSize;
 
    bool mSetBcsOnBoxBoundary;
 
    bool mSetBcsOnBoundingSphere;
 
    bool mUseVoronoiCellsForInterpolation;
 
    double mTypicalCellRadius;
 
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);
 
    ~AbstractBoxDomainPdeModifier() override = default;
 
    double GetStepSize() const;
 
    void SetBcsOnBoxBoundary(bool setBcsOnBoxBoundary);
 
    bool AreBcsSetOnBoxBoundary() const;
 
    void SetBcsOnBoundingSphere(bool setBcsOnBoundingSphere);
 
    bool AreBcsSetOnBoundingSphere() const;
 
    void SetUseVoronoiCellsForInterpolation(bool useVoronoiCellsForInterpolation);
 
    bool GetUseVoronoiCellsForInterpolation() const;
 
    void SetTypicalCellRadius(double typicalCellRadius);
 
    double GetTypicalCellRadius() const;
 
 
    void ConstructBoundaryConditionsContainerHelper(AbstractCellPopulation<DIM,DIM>& rCellPopulation,
                                                    std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > pBcc);
 
    void SetupSolve(AbstractCellPopulation<DIM, DIM>& rCellPopulation, std::string outputDirectory) override;
 
    void GenerateFeMesh(boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid, double stepSize);
 
    void GenerateAndReturnFeMesh(boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid, double stepSize, TetrahedralMesh<DIM,DIM>* pMesh);
 
    void UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    void InitialiseCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    void UpdateCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    void OutputSimulationModifierParameters(out_stream& rParamsFile) override;
};
 
#include "SerializationExportWrapper.hpp"
TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractBoxDomainPdeModifier)
 
#endif /*ABSTRACTBOXDOMAINPDEMODIFIER_HPP_*/