ImplicitCardiacMechanicsSolver.cpp

/*

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#include "ImplicitCardiacMechanicsSolver.hpp"
#include "Kerchoffs2003ContractionModel.hpp"
#include "NhsModelWithBackwardSolver.hpp"
#include "NonPhysiologicalContractionModel.hpp"
#include "FakeBathContractionModel.hpp"

template<class ELASTICITY_SOLVER,unsigned DIM>
ImplicitCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::ImplicitCardiacMechanicsSolver(
                                  ContractionModelName contractionModelName,
                                  QuadraticMesh<DIM>& rQuadMesh,
                                  ElectroMechanicsProblemDefinition<DIM>& rProblemDefinition,
                                  std::string outputDirectory)
    : AbstractCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>(rQuadMesh,
                                                            contractionModelName,
                                                            rProblemDefinition,
                                                            outputDirectory)
{

}


template<class ELASTICITY_SOLVER,unsigned DIM>
void ImplicitCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::InitialiseContractionModels(ContractionModelName contractionModelName)
{
    for(std::map<unsigned,DataAtQuadraturePoint>::iterator iter = this->mQuadPointToDataAtQuadPointMap.begin();
        iter != this->mQuadPointToDataAtQuadPointMap.end();
        iter++)
    {
        AbstractContractionModel* p_contraction_model;
        if (iter->second.Active == true)
        {
            switch(contractionModelName)
            {
                case NONPHYSIOL1:
                case NONPHYSIOL2:
                case NONPHYSIOL3:
                {
                    unsigned option = (contractionModelName==NONPHYSIOL1 ? 1 : (contractionModelName==NONPHYSIOL2? 2 : 3));
                    p_contraction_model = new NonPhysiologicalContractionModel(option);
                    break;
                }
                case NHS:
                {
                    p_contraction_model = new NhsModelWithBackwardSolver;
                    break;
                }
                case KERCHOFFS2003: //stretch dependent
                {
                    p_contraction_model = new Kerchoffs2003ContractionModel;
                    break;
                }
                default:
                {
                    #define COVERAGE_IGNORE
                    EXCEPTION("Unknown or disallowed contraction model");
                    #undef COVERAGE_IGNORE
                }
            }
            iter->second.ContractionModel = p_contraction_model;
        }
        else
        {
               //bath
               p_contraction_model = new FakeBathContractionModel;
               iter->second.ContractionModel = p_contraction_model;
        }
    }
}

template<class ELASTICITY_SOLVER,unsigned DIM>
ImplicitCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::~ImplicitCardiacMechanicsSolver()
{
}


template<class ELASTICITY_SOLVER,unsigned DIM>
void ImplicitCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::Solve(double time, double nextTime, double odeTimestep)
{
    // set the times, which are used in AssembleOnElement
    assert(time < nextTime);
    this->mCurrentTime = time;
    this->mNextTime = nextTime;
    this->mOdeTimestep = odeTimestep;

    // solve
    ELASTICITY_SOLVER::Solve();

    // assemble residual again (to solve the cell models implicitly again
    // using the correct value of the deformation x (in case this wasn't the
    // last thing that was done
    if(this->GetNumNewtonIterations() > 0)
    {
        this->AssembleSystem(true,false);
    }

    // now update state variables, and set lambda at last timestep. Note
    // stretches were set in AssembleOnElement
    for(std::map<unsigned,DataAtQuadraturePoint>::iterator iter = this->mQuadPointToDataAtQuadPointMap.begin();
        iter != this->mQuadPointToDataAtQuadPointMap.end();
        iter++)
    {
        AbstractContractionModel* p_contraction_model = iter->second.ContractionModel;
        iter->second.StretchLastTimeStep = iter->second.Stretch;
        p_contraction_model->UpdateStateVariables();
    }

}



template<class ELASTICITY_SOLVER,unsigned DIM>
void ImplicitCardiacMechanicsSolver<ELASTICITY_SOLVER,DIM>::GetActiveTensionAndTensionDerivs(double currentFibreStretch,
                                                                                             unsigned currentQuadPointGlobalIndex,
                                                                                             bool assembleJacobian,
                                                                                             double& rActiveTension,
                                                                                             double& rDerivActiveTensionWrtLambda,
                                                                                             double& rDerivActiveTensionWrtDLambdaDt)
{
    // The iterator should be pointing to the right place (note: it is incremented at the end of this method)
    // This iterator is used so that we don't have to search the map
    assert(this->mMapIterator->first==currentQuadPointGlobalIndex);

    DataAtQuadraturePoint& r_data_at_quad_point = this->mMapIterator->second;

    // save this fibre stretch
    r_data_at_quad_point.Stretch = currentFibreStretch;

    // compute dlam/dt
    double dlam_dt = (currentFibreStretch-r_data_at_quad_point.StretchLastTimeStep)/(this->mNextTime-this->mCurrentTime);

    // Set this stretch and stretch rate on contraction model
    AbstractContractionModel* p_contraction_model = r_data_at_quad_point.ContractionModel;
    p_contraction_model->SetStretchAndStretchRate(currentFibreStretch, dlam_dt);

    // Call RunDoNotUpdate() on the contraction model to solve it using this stretch, and get the active tension
    try
    {
        p_contraction_model->RunDoNotUpdate(this->mCurrentTime,this->mNextTime,this->mOdeTimestep);
        rActiveTension = p_contraction_model->GetNextActiveTension();
    }
    catch (Exception& e)
    {
        #define COVERAGE_IGNORE
        // if this failed during assembling the Jacobian this is a fatal error.
        if(assembleJacobian)
        {
            // probably shouldn't be able to get here
            EXCEPTION("Failure in solving contraction models using current stretches for assembling Jacobian");
        }
        // if this failed during assembling the residual, the stretches are too large, so we just
        // set the active tension to infinity so that the residual will be infinite
        rActiveTension = DBL_MAX;
        std::cout << "WARNING: could not solve contraction model with this stretch and stretch rate. "
                  << "Setting active tension to infinity (DBL_MAX) so that the residual(-norm) is also infinite\n" << std::flush;
        assert(0); // just to see if we ever get here, can be removed..
        return;
        #undef COVERAGE_IGNORE
    }

    // if assembling the Jacobian, numerically evaluate dTa/dlam & dTa/d(lamdot)
    if(assembleJacobian)
    {
        // get active tension for (lam+h,dlamdt)
        double h1 = std::max(1e-6, currentFibreStretch/100);
        p_contraction_model->SetStretchAndStretchRate(currentFibreStretch+h1, dlam_dt);
        p_contraction_model->RunDoNotUpdate(this->mCurrentTime,this->mNextTime,this->mOdeTimestep);
        double active_tension_at_lam_plus_h = p_contraction_model->GetNextActiveTension();

        // get active tension for (lam,dlamdt+h)
        double h2 = std::max(1e-6, dlam_dt/100);
        p_contraction_model->SetStretchAndStretchRate(currentFibreStretch, dlam_dt+h2);
        p_contraction_model->RunDoNotUpdate(this->mCurrentTime,this->mNextTime,this->mOdeTimestep);
        double active_tension_at_dlamdt_plus_h = p_contraction_model->GetNextActiveTension();

        rDerivActiveTensionWrtLambda = (active_tension_at_lam_plus_h - rActiveTension)/h1;
        rDerivActiveTensionWrtDLambdaDt = (active_tension_at_dlamdt_plus_h - rActiveTension)/h2;
    }

    // increment the iterator
    this->mMapIterator++;
    if(this->mMapIterator==this->mQuadPointToDataAtQuadPointMap.end())
    {
        this->mMapIterator = this->mQuadPointToDataAtQuadPointMap.begin();
    }

}



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