AbstractPdeModifier.hpp

/*

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*/

#ifndef ABSTRACTPDEMODIFIER_HPP_
#define ABSTRACTPDEMODIFIER_HPP_

#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include <boost/shared_ptr.hpp>

#include "AbstractCellBasedSimulationModifier.hpp"
#include "TetrahedralMesh.hpp"
#include "AbstractLinearPde.hpp"
#include "AbstractBoundaryCondition.hpp"

template<unsigned DIM>
class AbstractPdeModifier : public AbstractCellBasedSimulationModifier<DIM,DIM>
{
private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellBasedSimulationModifier<DIM,DIM> >(*this);
        archive & mpPde;
        archive & mpBoundaryCondition;
        archive & mIsNeumannBoundaryCondition;
        archive & mDependentVariableName;

        // Note that archiving of mSolution is handled by the methods save/load_construct_data
        archive & mOutputDirectory;
        archive & mOutputGradient;
        archive & mOutputSolutionAtPdeNodes;
    }

protected:

    boost::shared_ptr<AbstractLinearPde<DIM,DIM> > mpPde;

    boost::shared_ptr<AbstractBoundaryCondition<DIM> > mpBoundaryCondition;

    bool mIsNeumannBoundaryCondition;

    std::string mDependentVariableName;

    Vec mSolution;

    TetrahedralMesh<DIM,DIM>* mpFeMesh;

    std::string mOutputDirectory;

    bool mOutputGradient;

    bool mOutputSolutionAtPdeNodes;

    out_stream mpVizPdeSolutionResultsFile;

    bool mDeleteFeMesh;

public:

    AbstractPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=NULL,
                        boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
                        bool isNeumannBoundaryCondition=true,
                        Vec solution=nullptr);

    virtual ~AbstractPdeModifier();

    boost::shared_ptr<AbstractLinearPde<DIM,DIM> > GetPde();

    boost::shared_ptr<AbstractBoundaryCondition<DIM> > GetBoundaryCondition();

    bool IsNeumannBoundaryCondition();

    void SetDependentVariableName(const std::string& rName);

    std::string& rGetDependentVariableName();

    bool HasAveragedSourcePde();

    void SetUpSourceTermsForAveragedSourcePde(TetrahedralMesh<DIM,DIM>* pMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap=nullptr);

    Vec GetSolution();

    Vec GetSolution() const;

    TetrahedralMesh<DIM,DIM>* GetFeMesh() const;

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

    virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)=0;

    virtual void UpdateAtEndOfOutputTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation);

    virtual void UpdateAtEndOfSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation);

    bool GetOutputGradient();

    void SetOutputGradient(bool outputGradient);

    void SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes);

    void OutputSimulationModifierParameters(out_stream& rParamsFile);
};

#include "SerializationExportWrapper.hpp"
TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractPdeModifier)

#endif /*ABSTRACTPDEMODIFIER_HPP_*/