AbstractBidomainSolver.hpp

/*

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*/

#ifndef ABSTRACTBIDOMAINSOLVER_HPP_
#define ABSTRACTBIDOMAINSOLVER_HPP_

#include "AbstractDynamicLinearPdeSolver.hpp"
#include "BidomainTissue.hpp"
#include "HeartConfig.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractBidomainSolver : public AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>
{
protected:
    bool mBathSimulation;

    BidomainTissue<SPACE_DIM>* mpBidomainTissue;

    BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* mpBoundaryConditions;

    unsigned mNumQuadPoints;

    bool mNullSpaceCreated;

    HeartConfig* mpConfig;

    std::vector<unsigned> mFixedExtracellularPotentialNodes;

    unsigned mRowForAverageOfPhiZeroed;

    void InitialiseForSolve(Vec initialSolution);

    virtual void CheckCompatibilityCondition();

    void PrepareForSetupLinearSystem(Vec existingSolution);

    virtual void FinaliseLinearSystem(Vec existingSolution);

    virtual Vec GenerateNullBasis() const;

    void FinaliseForBath(bool computeMatrix, bool computeVector);

public:
    AbstractBidomainSolver(bool bathSimulation,
                           AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                           BidomainTissue<SPACE_DIM>* pTissue,
                           BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* pBoundaryConditions,
                           unsigned numQuadPoints = 2);

    virtual ~AbstractBidomainSolver();

    void SetFixedExtracellularPotentialNodes(std::vector<unsigned> fixedExtracellularPotentialNodes);

     void SetRowForAverageOfPhiZeroed(unsigned rowMeanPhiEZero);

    BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* GetBoundaryConditions()
    {
        return mpBoundaryConditions;
    }

    void ResetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* pBcc)
    {
        assert(pBcc);
        mpBoundaryConditions = pBcc;
        // Note, in SetupLinearSystem()
        //   neumann_assembler->ResetBoundaryConditionsContainer(mpBcc)
        // MUST be called every timestep, in case the bcc was reset.
    }
};




#endif /*ABSTRACTBIDOMAINSOLVER_HPP_*/