MonodomainSolver.cpp

/*

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#include "MonodomainSolver.hpp"
#include "MassMatrixAssembler.hpp"
#include "PetscMatTools.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainSolver<ELEMENT_DIM,SPACE_DIM>::SetupLinearSystem(Vec currentSolution, bool computeMatrix)
{
    assert(this->mpLinearSystem->rGetLhsMatrix() != NULL);
    assert(this->mpLinearSystem->rGetRhsVector() != NULL);


    // set up LHS matrix (and mass matrix)
    if(computeMatrix)
    {
        mpMonodomainAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix());
        mpMonodomainAssembler->AssembleMatrix();

        MassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> mass_matrix_assembler(this->mpMesh, HeartConfig::Instance()->GetUseMassLumping());
        mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
        mass_matrix_assembler.Assemble();

        this->mpLinearSystem->FinaliseLhsMatrix();
        PetscMatTools::Finalise(mMassMatrix);

        if (HeartConfig::Instance()->GetUseMassLumpingForPrecond() && !HeartConfig::Instance()->GetUseMassLumping())
        {
            this->mpLinearSystem->SetPrecondMatrixIsDifferentFromLhs();

            MonodomainAssembler<ELEMENT_DIM,SPACE_DIM> lumped_mass_assembler(this->mpMesh,this->mpMonodomainTissue,this->mNumQuadPoints);
            lumped_mass_assembler.SetMatrixToAssemble(this->mpLinearSystem->rGetPrecondMatrix());

            HeartConfig::Instance()->SetUseMassLumping(true);
            lumped_mass_assembler.AssembleMatrix();
            HeartConfig::Instance()->SetUseMassLumping(false);

            this->mpLinearSystem->FinalisePrecondMatrix();
        }

    }

    HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);

    // Set up z in b=Mz
    DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
    // dist stripe for the current Voltage
    DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
    // dist stripe for z (return value)
    DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);

    double Am = HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio();
    double Cm  = HeartConfig::Instance()->GetCapacitance();

    for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
         index!= dist_vec_matrix_based.End();
         ++index)
    {
        double V = distributed_current_solution[index];
        double F = - Am*this->mpMonodomainTissue->rGetIionicCacheReplicated()[index.Global]
                   - this->mpMonodomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];

        dist_vec_matrix_based[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse() + F;
    }
    dist_vec_matrix_based.Restore();

    // b = Mz
    MatMult(mMassMatrix, mVecForConstructingRhs, this->mpLinearSystem->rGetRhsVector());

    // assembling RHS is not finished yet, as Neumann bcs are added below, but
    // the event will be begun again inside mpMonodomainAssembler->AssembleVector();
    HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);

    // apply Neumann boundary conditions
    mpNeumannSurfaceTermsAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
    mpNeumannSurfaceTermsAssembler->AssembleVector();

    // apply correction term
    if(mpMonodomainCorrectionTermAssembler)
    {
        mpMonodomainCorrectionTermAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
        // don't need to set current solution
        mpMonodomainCorrectionTermAssembler->AssembleVector();
    }

    // finalise
    this->mpLinearSystem->FinaliseRhsVector();
}



template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainSolver<ELEMENT_DIM,SPACE_DIM>::InitialiseForSolve(Vec initialSolution)
{
    if (this->mpLinearSystem != NULL)
    {
        return;
    }

    // call base class version...
    AbstractLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,1>::InitialiseForSolve(initialSolution);

    //..then do a bit extra
    if(HeartConfig::Instance()->GetUseAbsoluteTolerance())
    {
        this->mpLinearSystem->SetAbsoluteTolerance(HeartConfig::Instance()->GetAbsoluteTolerance());
    }
    else
    {
        this->mpLinearSystem->SetRelativeTolerance(HeartConfig::Instance()->GetRelativeTolerance());
    }

    this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
    this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
    this->mpLinearSystem->SetMatrixIsSymmetric(true);
    this->mpLinearSystem->SetUseFixedNumberIterations(HeartConfig::Instance()->GetUseFixedNumberIterationsLinearSolver(), HeartConfig::Instance()->GetEvaluateNumItsEveryNSolves());

    // initialise matrix-based RHS vector and matrix, and use the linear
    // system rhs as a template
    Vec& r_template = this->mpLinearSystem->rGetRhsVector();
    VecDuplicate(r_template, &mVecForConstructingRhs);
    PetscInt ownership_range_lo;
    PetscInt ownership_range_hi;
    VecGetOwnershipRange(r_template, &ownership_range_lo, &ownership_range_hi);
    PetscInt local_size = ownership_range_hi - ownership_range_lo;
    PetscTools::SetupMat(mMassMatrix, this->mpMesh->GetNumNodes(), this->mpMesh->GetNumNodes(),
                         this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
                         local_size, local_size);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainSolver<ELEMENT_DIM,SPACE_DIM>::PrepareForSetupLinearSystem(Vec currentSolution)
{
    // solve cell models
    double time = PdeSimulationTime::GetTime();
    double dt = PdeSimulationTime::GetPdeTimeStep();
    mpMonodomainTissue->SolveCellSystems(currentSolution, time, time+dt);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainSolver<ELEMENT_DIM,SPACE_DIM>::MonodomainSolver(
            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* pTissue,
            BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,1>* pBoundaryConditions,
            unsigned numQuadPoints)
    : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,1>(pMesh),
      mpMonodomainTissue(pTissue),
      mNumQuadPoints(numQuadPoints),
      mpBoundaryConditions(pBoundaryConditions)
{
    assert(pTissue);
    assert(pBoundaryConditions);
    this->mMatrixIsConstant = true;

    mpMonodomainAssembler = new MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpMonodomainTissue,this->mNumQuadPoints);
    mpNeumannSurfaceTermsAssembler = new NaturalNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM,1>(pMesh,pBoundaryConditions);


    // Tell tissue there's no need to replicate ionic caches
    pTissue->SetCacheReplication(false);
    mVecForConstructingRhs = NULL;

    if(HeartConfig::Instance()->GetUseStateVariableInterpolation())
    {
        mpMonodomainCorrectionTermAssembler
            = new MonodomainCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpMonodomainTissue,this->mNumQuadPoints);
        //We are going to need those caches after all
        pTissue->SetCacheReplication(true);
    }
    else
    {
        mpMonodomainCorrectionTermAssembler = NULL;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainSolver<ELEMENT_DIM,SPACE_DIM>::~MonodomainSolver()
{
    delete mpMonodomainAssembler;
    delete mpNeumannSurfaceTermsAssembler;

    if(mVecForConstructingRhs)
    {
        PetscTools::Destroy(mVecForConstructingRhs);
        PetscTools::Destroy(mMassMatrix);
    }

    if(mpMonodomainCorrectionTermAssembler)
    {
        delete mpMonodomainCorrectionTermAssembler;
    }
}


// explicit instantiation

template class MonodomainSolver<1,1>;
template class MonodomainSolver<1,2>;
template class MonodomainSolver<1,3>;
template class MonodomainSolver<2,2>;
template class MonodomainSolver<3,3>;