CardiacElectroMechanicsProblem.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 CARDIACELECTROMECHANICSPROBLEM_HPP_
#define CARDIACELECTROMECHANICSPROBLEM_HPP_

#include <vector>
#include <string>
#include "UblasIncludes.hpp"

#include "AbstractCardiacCellFactory.hpp"
#include "MonodomainProblem.hpp"
#include "TetrahedralMesh.hpp"
#include "QuadraticMesh.hpp"
#include "AbstractOdeBasedContractionModel.hpp"
#include "AbstractCardiacMechanicsSolver.hpp"
#include "FineCoarseMeshPair.hpp"
#include "AbstractConductivityModifier.hpp"

template<unsigned DIM>
class CardiacElectroMechanicsProblem
    : public AbstractConductivityModifier<DIM,DIM> // this only inherits from this class so it can be passed to the tissue to
                                                   // allow deformation-based altering of the conductivity
{

friend class TestCardiacElectroMechanicsProblem;

protected :
    ContractionModel mContractionModel;
    MonodomainProblem<DIM>* mpMonodomainProblem;
    AbstractCardiacMechanicsSolver<DIM>* mpCardiacMechSolver;

    double mEndTime;
    double mElectricsTimeStep;
    double mMechanicsTimeStep;
    unsigned mNumElecTimestepsPerMechTimestep;
    double mContractionModelOdeTimeStep;

    TetrahedralMesh<DIM,DIM>* mpElectricsMesh;
    QuadraticMesh<DIM>* mpMechanicsMesh;

    FineCoarseMeshPair<DIM>* mpMeshPair;

    std::string mOutputDirectory;
    std::string mDeformationOutputDirectory;
    bool mWriteOutput;
    bool mNoElectricsOutput;

    static const int WRITE_EVERY_NTH_TIME = 1; //hardcoded for the time being ///\todo, allow user to set this

    bool mIsWatchedLocation;
    c_vector<double,DIM> mWatchedLocation;
    unsigned mWatchedElectricsNodeIndex;
    unsigned mWatchedMechanicsNodeIndex;
    out_stream mpWatchedLocationFile;

    std::vector<unsigned> mFixedNodes;
    std::string mFibreSheetDirectionsFile;
    bool mFibreSheetDirectionsDefinedPerQuadraturePoint;

    std::vector<double> mStretchesForEachMechanicsElement;
    std::vector<c_matrix<double,DIM,DIM> > mDeformationGradientsForEachMechanicsElement;

    std::pair<unsigned, c_matrix<double,DIM,DIM> > mLastModifiedConductivity;

    bool mConductivityAffectedByDeformationMef;

    bool mCellModelsAffectedByDeformationMef;


    void DetermineWatchedNodes();


    void WriteWatchedLocationData(double time, Vec voltage);


//    std::vector<BoundaryElement<DIM-1,DIM>*>* mpImpactRegion;
//    std::vector<c_vector<double,DIM> > mImpactTractions;
//    void ApplyImpactTractions(double time);

public :

    CardiacElectroMechanicsProblem(ContractionModel contractionModel,
                                   TetrahedralMesh<DIM,DIM>* pElectricsMesh,
                                   QuadraticMesh<DIM>* pMechanicsMesh,
                                   std::vector<unsigned> fixedMechanicsNodes,
                                   AbstractCardiacCellFactory<DIM>* pCellFactory,
                                   double endTime,
                                   double electricsPdeTimeStep,
                                   double mechanicsSolveTimestep,
                                   double contractionModelOdeTimeStep,
                                   std::string outputDirectory);

    virtual ~CardiacElectroMechanicsProblem();

    void Initialise();

    void Solve();

    double Max(std::vector<double>& vec);

    void SetNoElectricsOutput();

    void SetWatchedPosition(c_vector<double,DIM> watchedLocation);

    void SetVariableFibreSheetDirectionsFile(std::string orthoFile, bool definedPerQuadPoint);

    std::vector<c_vector<double,DIM> >& rGetDeformedPosition();

    void UseMechanoElectricFeedback()
    {
        mConductivityAffectedByDeformationMef = true;
        mCellModelsAffectedByDeformationMef = true;
    }

    c_matrix<double,DIM,DIM>& rGetModifiedConductivityTensor(unsigned elementIndex, const c_matrix<double,DIM,DIM>& rOriginalConductivity);

//    void SetImpactRegion(std::vector<BoundaryElement<DIM-1,DIM>*>& rImpactRegion);

    virtual void PrepareForSolve(){}

    virtual void OnEndOfTimeStep(unsigned counter){}

    AbstractCardiacMechanicsSolver<DIM>* GetCardiacMechanicsSolver()
    {
        assert(mpCardiacMechSolver);
        return mpCardiacMechSolver;
    }

};



#endif /*CARDIACELECTROMECHANICSPROBLEM_HPP_*/

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