AbstractCardiacMechanicsSolver.cpp

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#include "AbstractCardiacMechanicsSolver.hpp"
#include "AbstractContractionCellFactory.hpp"
#include "FakeBathContractionModel.hpp"

template<class ELASTICITY_SOLVER,unsigned DIM>
AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::AbstractCardiacMechanicsSolver(QuadraticMesh<DIM>& rQuadMesh,
                                                                                      ElectroMechanicsProblemDefinition<DIM>& rProblemDefinition,
                                                                                      std::string outputDirectory)
   : ELASTICITY_SOLVER(rQuadMesh,
                       rProblemDefinition,
                       outputDirectory),
     mpMeshPair(NULL),
     mCurrentTime(DBL_MAX),
     mNextTime(DBL_MAX),
     mOdeTimestep(DBL_MAX),
     mrElectroMechanicsProblemDefinition(rProblemDefinition)
{
}

template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::Initialise()
{
    // compute total num quad points
    unsigned num_quad_pts_per_element = this->mpQuadratureRule->GetNumQuadPoints();
    mTotalQuadPoints = this->mrQuadMesh.GetNumElements()*num_quad_pts_per_element;

    std::vector<ElementAndWeights<DIM> > fine_elements = mpMeshPair->rGetElementsAndWeights();
    assert(fine_elements.size()==mTotalQuadPoints);
    assert(mpMeshPair!=NULL);

    AbstractContractionCellFactory<DIM>* p_factory = mrElectroMechanicsProblemDefinition.GetContractionCellFactory();

    for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = this->mrQuadMesh.GetElementIteratorBegin();
         iter != this->mrQuadMesh.GetElementIteratorEnd();
         ++iter)
    {
        Element<DIM, DIM>& element = *iter;

        if (element.GetOwnership() == true)
        {
            for(unsigned j=0; j<num_quad_pts_per_element; j++)
            {
                unsigned quad_pt_global_index = element.GetIndex()*num_quad_pts_per_element + j;

                // We construct a set of data to be assigned to each quadrature point
                // this includes a contraction cell model set as bath or by the contraction
                // cell factory.
                DataAtQuadraturePoint data_at_quad_point;
                data_at_quad_point.Stretch = 1.0;
                data_at_quad_point.StretchLastTimeStep = 1.0;

                if ( mpMeshPair->GetFineMesh().GetElement(fine_elements[quad_pt_global_index].ElementNum)
                        ->GetUnsignedAttribute() == HeartRegionCode::GetValidBathId() )
                {
                    // Bath
                    data_at_quad_point.ContractionModel = new FakeBathContractionModel;
                }
                else
                {
                    // Tissue
                    data_at_quad_point.ContractionModel = p_factory->CreateContractionCellForElement( &element );
                }
                mQuadPointToDataAtQuadPointMap[quad_pt_global_index] = data_at_quad_point;
            }
        }
    }

    // initialise the iterator to point at the beginning
    mMapIterator = mQuadPointToDataAtQuadPointMap.begin();

    // initialise fibre/sheet direction matrix to be the identity, fibres in X-direction, and sheet in XY-plane
    mConstantFibreSheetDirections = zero_matrix<double>(DIM,DIM);
    for(unsigned i=0; i<DIM; i++)
    {
        mConstantFibreSheetDirections(i,i) = 1.0;
    }

    mpVariableFibreSheetDirections = NULL;

    // Check that we are using the right kind of solver.
    for(std::map<unsigned,DataAtQuadraturePoint>::iterator iter = this->mQuadPointToDataAtQuadPointMap.begin();
            iter != this->mQuadPointToDataAtQuadPointMap.end();
            iter++)
    {
        if (!IsImplicitSolver() && (*iter).second.ContractionModel->IsStretchRateDependent())
        {
            EXCEPTION("stretch-rate-dependent contraction model requires an IMPLICIT cardiac mechanics solver.");
        }

        if (!IsImplicitSolver() && (*iter).second.ContractionModel->IsStretchDependent())
        {
            WARN_ONCE_ONLY("stretch-dependent contraction model may require an IMPLICIT cardiac mechanics solver.");
        }
    }
}


template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::SetFineCoarseMeshPair(FineCoarseMeshPair<DIM>* pMeshPair)
{
    assert(pMeshPair!=NULL);
    if (pMeshPair->GetCoarseMesh().GetNumElements() != this->mrQuadMesh.GetNumElements())
    {
        EXCEPTION("When setting a mesh pair into the solver, the coarse mesh of the mesh pair must be the same as the quadratic mesh");
    }
    mpMeshPair = pMeshPair;
}

template<class ELASTICITY_SOLVER,unsigned DIM>
AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::~AbstractCardiacMechanicsSolver()
{
    for(mMapIterator = mQuadPointToDataAtQuadPointMap.begin();
        mMapIterator != mQuadPointToDataAtQuadPointMap.end();
        ++mMapIterator)
    {
        AbstractContractionModel* p_model = mMapIterator->second.ContractionModel;
        if (p_model)
        {
            delete p_model;
        }
    }

    if(mpVariableFibreSheetDirections)
    {
        delete mpVariableFibreSheetDirections;
    }
}



template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::SetCalciumAndVoltage(std::vector<double>& rCalciumConcentrations,
                                                                                 std::vector<double>& rVoltages)

{
    assert(rCalciumConcentrations.size() == mTotalQuadPoints);
    assert(rVoltages.size() == mTotalQuadPoints);

    ContractionModelInputParameters input_parameters;

    for(unsigned i=0; i<rCalciumConcentrations.size(); i++)
    {
        input_parameters.intracellularCalciumConcentration = rCalciumConcentrations[i];
        input_parameters.voltage = rVoltages[i];

        std::map<unsigned,DataAtQuadraturePoint>::iterator iter = mQuadPointToDataAtQuadPointMap.find(i);
        if(iter != mQuadPointToDataAtQuadPointMap.end())
        {
            iter->second.ContractionModel->SetInputParameters(input_parameters);
        }
    }
}


template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::SetupChangeOfBasisMatrix(unsigned elementIndex,
                                                                                     unsigned currentQuadPointGlobalIndex)
{
    if(!mpVariableFibreSheetDirections) // constant fibre directions
    {
        this->mChangeOfBasisMatrix = mConstantFibreSheetDirections;
    }
    else if(!mFibreSheetDirectionsDefinedByQuadraturePoint) // fibre directions defined for each mechanics mesh element
    {
        this->mChangeOfBasisMatrix = (*mpVariableFibreSheetDirections)[elementIndex];
    }
    else // fibre directions defined for each mechanics mesh quadrature point
    {
        this->mChangeOfBasisMatrix = (*mpVariableFibreSheetDirections)[currentQuadPointGlobalIndex];
    }
}



template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::AddActiveStressAndStressDerivative(c_matrix<double,DIM,DIM>& rC,
                                                                                               unsigned elementIndex,
                                                                                               unsigned currentQuadPointGlobalIndex,
                                                                                               c_matrix<double,DIM,DIM>& rT,
                                                                                               FourthOrderTensor<DIM,DIM,DIM,DIM>& rDTdE,
                                                                                               bool addToDTdE)
{
    for(unsigned i=0; i<DIM; i++)
    {
        mCurrentElementFibreDirection(i) = this->mChangeOfBasisMatrix(i,0);
    }

    //Compute the active tension and add to the stress and stress-derivative
    double I4_fibre = inner_prod(mCurrentElementFibreDirection, prod(rC, mCurrentElementFibreDirection));
    double lambda_fibre = sqrt(I4_fibre);

    double active_tension = 0;
    double d_act_tension_dlam = 0.0;     // Set and used if assembleJacobian==true
    double d_act_tension_d_dlamdt = 0.0; // Set and used if assembleJacobian==true

    GetActiveTensionAndTensionDerivs(lambda_fibre, currentQuadPointGlobalIndex, addToDTdE,
                                     active_tension, d_act_tension_dlam, d_act_tension_d_dlamdt);


    double detF = sqrt(Determinant(rC));
    rT += (active_tension*detF/I4_fibre)*outer_prod(mCurrentElementFibreDirection,mCurrentElementFibreDirection);

    // amend the stress and dTdE using the active tension
    double dTdE_coeff1 = -2*active_tension*detF/(I4_fibre*I4_fibre); // note: I4_fibre*I4_fibre = lam^4
    double dTdE_coeff2 = active_tension*detF/I4_fibre;
    double dTdE_coeff_s1 = 0.0; // only set non-zero if we apply cross fibre tension (in 2/3D)
    double dTdE_coeff_s2 = 0.0; // only set non-zero if we apply cross fibre tension (in 2/3D)
    double dTdE_coeff_s3 = 0.0; // only set non-zero if we apply cross fibre tension and implicit (in 2/3D)
    double dTdE_coeff_n1 = 0.0; // only set non-zero if we apply cross fibre tension in 3D
    double dTdE_coeff_n2 = 0.0; // only set non-zero if we apply cross fibre tension in 3D
    double dTdE_coeff_n3 = 0.0; // only set non-zero if we apply cross fibre tension in 3D and implicit

    if(IsImplicitSolver())
    {
        double dt = mNextTime-mCurrentTime;
        //std::cout << "d sigma / d lamda = " << d_act_tension_dlam << ", d sigma / d lamdat = " << d_act_tension_d_dlamdt << "\n" << std::flush;
        dTdE_coeff1 += (d_act_tension_dlam + d_act_tension_d_dlamdt/dt)*detF/(lambda_fibre*I4_fibre); // note: I4_fibre*lam = lam^3
    }

    bool apply_cross_fibre_tension = (this->mrElectroMechanicsProblemDefinition.GetApplyCrossFibreTension()) && (DIM > 1);
    if(apply_cross_fibre_tension)
    {
        double sheet_cross_fraction = mrElectroMechanicsProblemDefinition.GetSheetTensionFraction();

        for(unsigned i=0; i<DIM; i++)
        {
            mCurrentElementSheetDirection(i) = this->mChangeOfBasisMatrix(i,1);
        }

        double I4_sheet = inner_prod(mCurrentElementSheetDirection, prod(rC, mCurrentElementSheetDirection));

        // amend the stress and dTdE using the active tension
        dTdE_coeff_s1 = -2*sheet_cross_fraction*detF*active_tension/(I4_sheet*I4_sheet); // note: I4*I4 = lam^4

        if(IsImplicitSolver())
        {
            double dt = mNextTime-mCurrentTime;
            dTdE_coeff_s3 = sheet_cross_fraction*(d_act_tension_dlam + d_act_tension_d_dlamdt/dt)*detF/(lambda_fibre*I4_sheet); // note: I4*lam = lam^3
        }

        rT += sheet_cross_fraction*(active_tension*detF/I4_sheet)*outer_prod(mCurrentElementSheetDirection,mCurrentElementSheetDirection);

        dTdE_coeff_s2 = active_tension*sheet_cross_fraction*detF/I4_sheet;

        if (DIM>2)
        {
            double sheet_normal_cross_fraction = mrElectroMechanicsProblemDefinition.GetSheetNormalTensionFraction();
            for(unsigned i=0; i<DIM; i++)
            {
                mCurrentElementSheetNormalDirection(i) = this->mChangeOfBasisMatrix(i,2);
            }

            double I4_sheet_normal = inner_prod(mCurrentElementSheetNormalDirection, prod(rC, mCurrentElementSheetNormalDirection));

            dTdE_coeff_n1 =-2*sheet_normal_cross_fraction*detF*active_tension/(I4_sheet_normal*I4_sheet_normal); // note: I4*I4 = lam^4

            rT += sheet_normal_cross_fraction*(active_tension*detF/I4_sheet_normal)*outer_prod(mCurrentElementSheetNormalDirection,mCurrentElementSheetNormalDirection);

            dTdE_coeff_n2 = active_tension*sheet_normal_cross_fraction*detF/I4_sheet_normal;
            if(IsImplicitSolver())
            {
                double dt = mNextTime-mCurrentTime;
                dTdE_coeff_n3 = sheet_normal_cross_fraction*(d_act_tension_dlam + d_act_tension_d_dlamdt/dt)*detF/(lambda_fibre*I4_sheet_normal); // note: I4*lam = lam^3
            }
        }
    }


    if(addToDTdE)
    {
        c_matrix<double,DIM,DIM> invC = Inverse(rC);

        for (unsigned M=0; M<DIM; M++)
        {
            for (unsigned N=0; N<DIM; N++)
            {
                for (unsigned P=0; P<DIM; P++)
                {
                    for (unsigned Q=0; Q<DIM; Q++)
                    {
                        rDTdE(M,N,P,Q) +=   dTdE_coeff1 * mCurrentElementFibreDirection(M)
                                                        * mCurrentElementFibreDirection(N)
                                                        * mCurrentElementFibreDirection(P)
                                                        * mCurrentElementFibreDirection(Q)

                                         +  dTdE_coeff2 * mCurrentElementFibreDirection(M)
                                                        * mCurrentElementFibreDirection(N)
                                                        * invC(P,Q);
                        if(apply_cross_fibre_tension)
                        {
                            rDTdE(M,N,P,Q) += dTdE_coeff_s1 * mCurrentElementSheetDirection(M)
                                                            * mCurrentElementSheetDirection(N)
                                                            * mCurrentElementSheetDirection(P)
                                                            * mCurrentElementSheetDirection(Q)

                                           +  dTdE_coeff_s2 * mCurrentElementSheetDirection(M)
                                                            * mCurrentElementSheetDirection(N)
                                                            * invC(P,Q)

                                           + dTdE_coeff_s3 * mCurrentElementSheetDirection(M)
                                                           * mCurrentElementSheetDirection(N)
                                                           * mCurrentElementFibreDirection(P)
                                                           * mCurrentElementFibreDirection(Q);
                            if (DIM>2)
                            {
                                rDTdE(M,N,P,Q) += dTdE_coeff_n1 * mCurrentElementSheetNormalDirection(M)
                                                                * mCurrentElementSheetNormalDirection(N)
                                                                * mCurrentElementSheetNormalDirection(P)
                                                                * mCurrentElementSheetNormalDirection(Q)

                                                + dTdE_coeff_n2 * mCurrentElementSheetNormalDirection(M)
                                                                * mCurrentElementSheetNormalDirection(N)
                                                                * invC(P,Q)

                                                + dTdE_coeff_n3 * mCurrentElementSheetNormalDirection(M)
                                                                * mCurrentElementSheetNormalDirection(N)
                                                                * mCurrentElementFibreDirection(P)
                                                                * mCurrentElementFibreDirection(Q);
                            }
                        }
                    }
                }
            }
        }
    }

//    ///\todo #2180 The code below applies a cross fibre tension in the 2D case. Things that need doing:
//    // * Refactor the common code between the block below and the block above to avoid duplication.
//    // * Handle the 3D case.
//    if(this->mrElectroMechanicsProblemDefinition.GetApplyCrossFibreTension() && DIM > 1)
//    {
//        double sheet_cross_fraction = mrElectroMechanicsProblemDefinition.GetSheetTensionFraction();
//
//        for(unsigned i=0; i<DIM; i++)
//        {
//            mCurrentElementSheetDirection(i) = this->mChangeOfBasisMatrix(i,1);
//        }
//
//        double I4_sheet = inner_prod(mCurrentElementSheetDirection, prod(rC, mCurrentElementSheetDirection));
//
//        // amend the stress and dTdE using the active tension
//        double dTdE_coeff_s1 = -2*sheet_cross_fraction*detF*active_tension/(I4_sheet*I4_sheet); // note: I4*I4 = lam^4
//
//        ///\todo #2180 The code below is specific to the implicit cardiac mechanics solver. Currently
//        // the cross-fibre code is only tested using the explicit solver so the code below fails coverage.
//        // This will need to be added back in once an implicit test is in place.
//        double lambda_sheet = sqrt(I4_sheet);
//        if(IsImplicitSolver())
//        {
//           double dt = mNextTime-mCurrentTime;
//           dTdE_coeff_s1 += (d_act_tension_dlam + d_act_tension_d_dlamdt/dt)/(lambda_sheet*I4_sheet); // note: I4*lam = lam^3
//        }
//
//        rT += sheet_cross_fraction*(active_tension*detF/I4_sheet)*outer_prod(mCurrentElementSheetDirection,mCurrentElementSheetDirection);
//
//        double dTdE_coeff_s2 = active_tension*detF/I4_sheet;
//        if(addToDTdE)
//        {
//           for (unsigned M=0; M<DIM; M++)
//           {
//               for (unsigned N=0; N<DIM; N++)
//               {
//                   for (unsigned P=0; P<DIM; P++)
//                   {
//                       for (unsigned Q=0; Q<DIM; Q++)
//                       {
//                           rDTdE(M,N,P,Q) +=  dTdE_coeff_s1 * mCurrentElementSheetDirection(M)
//                                                            * mCurrentElementSheetDirection(N)
//                                                            * mCurrentElementSheetDirection(P)
//                                                            * mCurrentElementSheetDirection(Q)
//
//                                           +  dTdE_coeff_s2 * mCurrentElementFibreDirection(M)
//                                                            * mCurrentElementFibreDirection(N)
//                                                            * invC(P,Q);
//
//                       }
//                   }
//               }
//           }
//        }
//    }
}


template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::ComputeDeformationGradientAndStretchInEachElement(
    std::vector<c_matrix<double,DIM,DIM> >& rDeformationGradients,
    std::vector<double>& rStretches)
{
    assert(rStretches.size()==this->mrQuadMesh.GetNumElements());

    // this will only work currently if the coarse mesh fibre info is defined per element, not per quad point
    assert(!mpVariableFibreSheetDirections || !mFibreSheetDirectionsDefinedByQuadraturePoint);

    static c_matrix<double,DIM,NUM_VERTICES_PER_ELEMENT> element_current_displacements;
    static c_matrix<double,DIM,NUM_VERTICES_PER_ELEMENT> grad_lin_phi;
    static c_matrix<double,DIM,DIM> F;      // the deformation gradient, F = dx/dX, F_{iM} = dx_i/dX_M

    static c_matrix<double,DIM,DIM> jacobian;
    static c_matrix<double,DIM,DIM> inverse_jacobian;
    double jacobian_determinant;
    ChastePoint<DIM> quadrature_point; // not needed, but has to be passed in

    // loop over all the elements
    for(unsigned elem_index=0; elem_index<this->mrQuadMesh.GetNumElements(); elem_index++)
    {
        Element<DIM,DIM>* p_elem = this->mrQuadMesh.GetElement(elem_index);

        // get the fibre direction for this element
        SetupChangeOfBasisMatrix(elem_index, 0); // 0 is quad index, and doesn't matter as checked that fibres not defined by quad pt above.
        for(unsigned i=0; i<DIM; i++)
        {
            mCurrentElementFibreDirection(i) = this->mChangeOfBasisMatrix(i,0);
        }

        // get the displacement at this element
        for (unsigned II=0; II<NUM_VERTICES_PER_ELEMENT; II++)
        {
            for (unsigned JJ=0; JJ<DIM; JJ++)
            {
                // mProblemDimension = DIM for compressible elasticity and DIM+1 for incompressible elasticity
                element_current_displacements(JJ,II) = this->mCurrentSolution[this->mProblemDimension*p_elem->GetNodeGlobalIndex(II) + JJ];
            }
        }

        // set up the linear basis functions
        this->mrQuadMesh.GetInverseJacobianForElement(elem_index, jacobian, jacobian_determinant, inverse_jacobian);
        LinearBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_lin_phi);

        F = identity_matrix<double>(DIM,DIM);

        // loop over the vertices and interpolate F, the deformation gradient
        // (note: could use matrix-mult if this becomes inefficient
        for (unsigned node_index=0; node_index<NUM_VERTICES_PER_ELEMENT; node_index++)
        {
            for (unsigned i=0; i<DIM; i++)
            {
                for (unsigned M=0; M<DIM; M++)
                {
                    F(i,M) += grad_lin_phi(M,node_index)*element_current_displacements(i,node_index);
                }
            }
        }

        rDeformationGradients[elem_index] = F;

        // compute and save the stretch: m^T C m = ||Fm||
        c_vector<double,DIM> deformed_fibre = prod(F, mCurrentElementFibreDirection);
        rStretches[elem_index] = norm_2(deformed_fibre);
    }
}


template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::SetVariableFibreSheetDirections(const FileFinder& rOrthoFile, bool definedPerQuadraturePoint)
{
    mFibreSheetDirectionsDefinedByQuadraturePoint = definedPerQuadraturePoint;

    FibreReader<DIM> reader(rOrthoFile, ORTHO);

    unsigned num_entries = reader.GetNumLinesOfData();

    if (!mFibreSheetDirectionsDefinedByQuadraturePoint && (num_entries!=this->mrQuadMesh.GetNumElements()) )
    {
        EXCEPTION("Number of entries defined at top of file " << rOrthoFile.GetAbsolutePath() <<
                  " does not match number of elements in the mesh, " << "found " <<  num_entries <<
                  ", expected " << this->mrQuadMesh.GetNumElements());
    }

    if (mFibreSheetDirectionsDefinedByQuadraturePoint && (num_entries!=mTotalQuadPoints) )
    {
        EXCEPTION("Number of entries defined at top of file " << rOrthoFile.GetAbsolutePath() <<
                  " does not match number of quadrature points defined, " << "found " <<  num_entries <<
                  ", expected " << mTotalQuadPoints);
    }

    mpVariableFibreSheetDirections = new std::vector<c_matrix<double,DIM,DIM> >(num_entries, zero_matrix<double>(DIM,DIM));
    for(unsigned index=0; index<num_entries; index++)
    {
        reader.GetFibreSheetAndNormalMatrix(index, (*mpVariableFibreSheetDirections)[index] );
    }
}

template<class ELASTICITY_SOLVER,unsigned DIM>
void AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::SetConstantFibreSheetDirections(const c_matrix<double,DIM,DIM>& rFibreSheetMatrix)
{
    mConstantFibreSheetDirections = rFibreSheetMatrix;
    // check orthogonality
    c_matrix<double,DIM,DIM>  temp = prod(trans(rFibreSheetMatrix),rFibreSheetMatrix);
    for(unsigned i=0; i<DIM; i++)
    {
        for(unsigned j=0; j<DIM; j++)
        {
            double val = (i==j ? 1.0 : 0.0);
            if(fabs(temp(i,j)-val)>1e-4)
            {
                EXCEPTION("The given fibre-sheet matrix, " << rFibreSheetMatrix << ", is not orthogonal");
            }
        }
    }
}

template class AbstractCardiacMechanicsSolver<IncompressibleNonlinearElasticitySolver<2>,2>;
template class AbstractCardiacMechanicsSolver<IncompressibleNonlinearElasticitySolver<3>,3>;
template class AbstractCardiacMechanicsSolver<CompressibleNonlinearElasticitySolver<2>,2>;
template class AbstractCardiacMechanicsSolver<CompressibleNonlinearElasticitySolver<3>,3>;