ElectroMechanicsProblemDefinition.cpp

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#include "ElectroMechanicsProblemDefinition.hpp"
#include "LabelBasedContractionCellFactory.hpp"

template<unsigned DIM>
ElectroMechanicsProblemDefinition<DIM>::ElectroMechanicsProblemDefinition(QuadraticMesh<DIM>& rMesh)
    : SolidMechanicsProblemDefinition<DIM>(rMesh),
      mContractionModelOdeTimeStep(-1.0),
      mMechanicsSolveTimestep(-1.0),
      mDeformationAffectsConductivity(false),
      mDeformationAffectsCellModels(false),
      mpDefaultMaterialLaw(NULL),
      mReadFibreSheetInformationFromFile(false),
      mNumIncrementsForInitialDeformation(1),
      mApplyCrossFibreTension(false),
      mSheetTensionFraction(DOUBLE_UNSET),
      mSheetNormalTensionFraction(DOUBLE_UNSET),
      mpContractionCellFactory(NULL),
      mWeMadeCellFactory(false),
      mSolverType(IMPLICIT) // default solver is implicit
{
}

template<unsigned DIM>
ElectroMechanicsProblemDefinition<DIM>::~ElectroMechanicsProblemDefinition()
{
    if(mpDefaultMaterialLaw)
    {
        delete mpDefaultMaterialLaw;
    }

    if (mWeMadeCellFactory)
    {
        delete mpContractionCellFactory;
    }
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetContractionModel(ContractionModelName contractionModel, double timestep)
{
    assert(timestep > 0.0);
    SetContractionModelOdeTimestep(timestep);

    if (contractionModel == NASH2004 || contractionModel == CONSTANT)
    {
        // These models can use an Explicit solver, default is Implicit.
        SetSolverType(EXPLICIT);
    }

    // Make sure we aren't overwriting a problem that has been set up with a cell factory.
    assert(mpContractionCellFactory==NULL);

    AbstractContractionCellFactory<DIM>* p_factory = new LabelBasedContractionCellFactory<DIM>(contractionModel);
    mWeMadeCellFactory = true;
    SetContractionCellFactory(p_factory);
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetUseDefaultCardiacMaterialLaw(CompressibilityType compressibilityType)
{
    if(mpDefaultMaterialLaw)
    {
        delete mpDefaultMaterialLaw;
    }

    if(compressibilityType == INCOMPRESSIBLE)
    {
        mpDefaultMaterialLaw = new NashHunterPoleZeroLaw<DIM>();
        this->SetMaterialLaw(INCOMPRESSIBLE, mpDefaultMaterialLaw);
    }
    else
    {
        mpDefaultMaterialLaw = new CompressibleExponentialLaw<DIM>();
        this->SetMaterialLaw(COMPRESSIBLE, mpDefaultMaterialLaw);
    }
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetDeformationAffectsElectrophysiology(bool deformationAffectsConductivity, bool deformationAffectsCellModels)
{
    mDeformationAffectsConductivity = deformationAffectsConductivity;
    mDeformationAffectsCellModels = deformationAffectsCellModels;
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetMechanicsSolveTimestep(double timestep)
{
    assert(timestep > 0.0);
    mMechanicsSolveTimestep = timestep;
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetVariableFibreSheetDirectionsFile(const FileFinder& rFibreSheetDirectionsFile, bool definedPerQuadraturePoint)
{
    mReadFibreSheetInformationFromFile = true;
    mFibreSheetDirectionsFile = rFibreSheetDirectionsFile;
    mFibreSheetDirectionsDefinedPerQuadraturePoint = definedPerQuadraturePoint;
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetApplyIsotropicCrossFibreTension(bool applyCrossFibreTension, double crossFibreTensionFraction)
{
    mApplyCrossFibreTension = applyCrossFibreTension;
    mSheetTensionFraction = crossFibreTensionFraction;
    mSheetNormalTensionFraction = crossFibreTensionFraction;
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetApplyAnisotropicCrossFibreTension(bool applyCrossFibreTension, double sheetTensionFraction, double sheetNormalTensionFraction)
{
    if (DIM!=3)
    {
        EXCEPTION("You can only apply anisotropic cross fibre tensions in a 3D simulation.");
    }
    mApplyCrossFibreTension = applyCrossFibreTension;
    mSheetTensionFraction = sheetTensionFraction;
    mSheetNormalTensionFraction = sheetNormalTensionFraction;
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::SetContractionCellFactory(AbstractContractionCellFactory<DIM>* pCellFactory)
{
    // Make sure we aren't overwriting a problem that has been set up with a cell factory already.
    assert(mpContractionCellFactory == NULL);

    mpContractionCellFactory = pCellFactory;
    mpContractionCellFactory->SetMechanicsMesh(static_cast<QuadraticMesh<DIM>*>(&(this->mrMesh)));
}

template<unsigned DIM>
void ElectroMechanicsProblemDefinition<DIM>::Validate()
{
    SolidMechanicsProblemDefinition<DIM>::Validate();

    if(mMechanicsSolveTimestep < 0.0)
    {
        EXCEPTION("Timestep for mechanics solve hasn't been set yet");
    }

    if(mContractionModelOdeTimeStep < 0.0)
    {
        std::string message =  "Contraction model or contraction model ODE timestep have not been set. "
                               "Make sure SetContractionModel(), or SetContractionCellFactory() AND SetContractionModelOdeTimestep "
                               "are called. (Pass in a timestep even if contraction model is algebraic and won't use it). ";
        EXCEPTION(message);
    }

    if(mDeformationAffectsConductivity && this->GetCompressibilityType()==COMPRESSIBLE)
    {
        // the conductivity depends on the deformation gradient and also scales in some way with
        // J=det(F), which is not equal to 1 in the compressible case. The F dependence
        // is implemented but the J dependence is not yet.
        EXCEPTION("Deformation affecting the conductivity is currently not implemented fully for compressible problems");
    }

    if(mDeformationAffectsCellModels && mReadFibreSheetInformationFromFile && mFibreSheetDirectionsDefinedPerQuadraturePoint)
    {
        // This combination is not allowed. For explanation see doxygen for SetDeformationAffectsElectrophysiology()
        std::stringstream message;
        message << "Deformation affecting cell models cannot be done when fibres-sheet information is defined for each quadrature point.";
        message << "Define fibre-sheet information for each element instead.";
        EXCEPTION(message.str());
    }
}

// Explicit instantiation

template class ElectroMechanicsProblemDefinition<2>;
template class ElectroMechanicsProblemDefinition<3>;