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 = nullptr;
 
    TetrahedralMesh<DIM,DIM>* mpFeMesh = nullptr;
 
    std::string mOutputDirectory{};
 
    bool mOutputGradient = false;
 
    bool mOutputSolutionAtPdeNodes = false;
 
    out_stream mpVizPdeSolutionResultsFile;
 
    bool mDeleteFeMesh = false;
 
    std::vector<double> mIsDirichletBoundaryNode;
 
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);
 
    ~AbstractPdeModifier() override;
 
    boost::shared_ptr<AbstractLinearPde<DIM,DIM> > GetPde();
 
    boost::shared_ptr<AbstractBoundaryCondition<DIM> > GetBoundaryCondition();
 
    bool IsNeumannBoundaryCondition() const;
 
    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;
 
    void SetupSolve(AbstractCellPopulation<DIM, DIM>& rCellPopulation, std::string outputDirectory) override;
 
    void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM, DIM>& rCellPopulation) override = 0;
 
    void UpdateAtEndOfOutputTimeStep(AbstractCellPopulation<DIM, DIM>& rCellPopulation) override;
 
    void UpdateAtEndOfSolve(AbstractCellPopulation<DIM, DIM>& rCellPopulation) override;
 
    bool GetOutputGradient() const;
 
    void SetOutputGradient(bool outputGradient);
 
    void SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes);
 
    void OutputSimulationModifierParameters(out_stream& rParamsFile) override;
};
 
#include "SerializationExportWrapper.hpp"
TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractPdeModifier)
 
#endif /*ABSTRACTPDEMODIFIER_HPP_*/