AbstractBidomainSolver.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef ABSTRACTBIDOMAINSOLVER_HPP_
#define ABSTRACTBIDOMAINSOLVER_HPP_

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

    BidomainAssembler<ELEMENT_DIM,SPACE_DIM>* mpBidomainAssembler;
    
    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, we can't reset the bcc on the assembler (even if this
        // method was implemented in the concrete classes), as the assembler 
        // might not be created (eg when grounded electrodes are switched off).
        // Therefore we just reset our own copy. This means that
        // in SetupLinearSystem() 
        //   mpAssembler->SetApplyNeumannBcs(mpBcc) 
        // MUST be called every timestep, in case the bcc was reset. 
    }
};




#endif /*ABSTRACTBIDOMAINSOLVER_HPP_*/

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