CardiacElectroMechanicsProblem.hpp

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*/


#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 "AbstractCardiacMechanicsSolverInterface.hpp"
#include "FineCoarseMeshPair.hpp"
#include "AbstractConductivityModifier.hpp"
#include "ElectroMechanicsProblemDefinition.hpp"

typedef enum ElectricsProblemType_
{
    MONODOMAIN,
    BIDOMAIN,   
    BIDOMAIN_WITH_BATH
    //EXTENDED_BIDOMAIN
} ElectricsProblemType;

template<unsigned DIM, unsigned ELEC_PROB_DIM=1>
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 TestAbstractContractionCellFactory;
friend class TestCardiacElectroMechanicsProblem;
friend class TestCardiacElectroMechanicsFurtherFunctionality;
friend class TestElectroMechanicsExactSolution;

protected :
    CompressibilityType mCompressibilityType;

    AbstractCardiacProblem<DIM,DIM,ELEC_PROB_DIM>* mpElectricsProblem;

    AbstractCardiacMechanicsSolverInterface<DIM>* mpCardiacMechSolver;
    AbstractNonlinearElasticitySolver<DIM>* mpMechanicsSolver;

    unsigned mNumElecTimestepsPerMechTimestep;

    std::vector<double> mInterpolatedCalciumConcs;

    std::vector<double> mInterpolatedVoltages;

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

    ElectroMechanicsProblemDefinition<DIM>* mpProblemDefinition;

    bool mHasBath;

    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;

    unsigned mNumTimestepsToOutputDeformationGradientsAndStress;

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

    c_matrix<double,DIM,DIM> mModifiedConductivityTensor;

    void DetermineWatchedNodes();


    void WriteWatchedLocationData(double time, Vec voltage);


public :

    CardiacElectroMechanicsProblem(CompressibilityType compressibilityType,
                                   ElectricsProblemType electricsProblemType,
                                   TetrahedralMesh<DIM,DIM>* pElectricsMesh,
                                   QuadraticMesh<DIM>* pMechanicsMesh,
                                   AbstractCardiacCellFactory<DIM>* pCellFactory,
                                   ElectroMechanicsProblemDefinition<DIM>* pProblemDefinition,
                                   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 SetOutputDeformationGradientsAndStress(double timestep);

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


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


    virtual void PrepareForSolve(){}

    virtual void OnEndOfTimeStep(unsigned counter)
    {
    }

    AbstractNonlinearElasticitySolver<DIM>* GetMechanicsSolver()
    {
        assert(mpMechanicsSolver);
        return mpMechanicsSolver;
    }
};

#endif /*CARDIACELECTROMECHANICSPROBLEM_HPP_*/