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"
#include "CardiacElectroMechanicsVtkHandler.hpp"
#include "VoltageInterpolaterOntoMechanicsMesh.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;
 
    CardiacElectroMechanicsVtkHandler<DIM,ELEC_PROB_DIM>* mpCardiacVtkWriter; 
 
    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_*/