BidomainSolver.cpp

/*

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*/


#include "BidomainSolver.hpp"
#include "BidomainAssembler.hpp"
#include "BidomainWithBathAssembler.hpp"
#include "PetscMatTools.hpp"

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

    // 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, 2*this->mpMesh->GetNumNodes(), 2*this->mpMesh->GetNumNodes(),
                         2*this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
                         local_size, local_size);
}


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


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

        // the BidomainMassMatrixAssembler deals with the mass matrix
        // for both bath and nonbath problems
        assert(SPACE_DIM==ELEMENT_DIM);
        BidomainMassMatrixAssembler<SPACE_DIM> mass_matrix_assembler(this->mpMesh);
        mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
        mass_matrix_assembler.Assemble();

        this->mpLinearSystem->SwitchWriteModeLhsMatrix();
        PetscMatTools::Finalise(mMassMatrix);
    }


    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);
    DistributedVector::Stripe distributed_current_solution_vm(distributed_current_solution, 0);

    // dist stripe for z
    DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
    DistributedVector::Stripe dist_vec_matrix_based_vm(dist_vec_matrix_based, 0);
    DistributedVector::Stripe dist_vec_matrix_based_phie(dist_vec_matrix_based, 1);

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

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

            dist_vec_matrix_based_vm[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse() + F;
            dist_vec_matrix_based_phie[index] = 0.0;
        }
    }
    else
    {
        for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
             index!= dist_vec_matrix_based.End();
             ++index)
        {

            if ( !HeartRegionCode::IsRegionBath( this->mpMesh->GetNode(index.Global)->GetRegion() ))
            {
                double V = distributed_current_solution_vm[index];
                double F = - Am*this->mpBidomainTissue->rGetIionicCacheReplicated()[index.Global]
                           - this->mpBidomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];

                dist_vec_matrix_based_vm[index] = Am*Cm*V*PdeSimulationTime::GetPdeTimeStepInverse() + F;
            }
            else
            {
                dist_vec_matrix_based_vm[index] = 0.0;
            }

            dist_vec_matrix_based_phie[index] = 0.0;

        }
    }

    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 mpBidomainAssembler->AssembleVector();
    HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);


    // apply Neumann boundary conditions
    mpBidomainNeumannSurfaceTermAssembler->ResetBoundaryConditionsContainer(this->mpBoundaryConditions); // as the BCC can change
    mpBidomainNeumannSurfaceTermAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
    mpBidomainNeumannSurfaceTermAssembler->AssembleVector();


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

    this->mpLinearSystem->FinaliseRhsVector();

    this->mpBoundaryConditions->ApplyDirichletToLinearProblem(*(this->mpLinearSystem), computeMatrix);

    if(this->mBathSimulation)
    {
        this->mpLinearSystem->FinaliseLhsMatrix();
        this->FinaliseForBath(computeMatrix,true);
    }

    if(computeMatrix)
    {
        this->mpLinearSystem->FinaliseLhsMatrix();
    }
    this->mpLinearSystem->FinaliseRhsVector();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainSolver<ELEMENT_DIM,SPACE_DIM>::BidomainSolver(
        bool bathSimulation,
        AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
        BidomainTissue<SPACE_DIM>* pTissue,
        BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* pBoundaryConditions)
    : AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>(bathSimulation,pMesh,pTissue,pBoundaryConditions)
{
    // Tell tissue there's no need to replicate ionic caches
    pTissue->SetCacheReplication(false);
    mVecForConstructingRhs = NULL;

    // create assembler
    if(bathSimulation)
    {
        mpBidomainAssembler = new BidomainWithBathAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpBidomainTissue);
    }
    else
    {
        mpBidomainAssembler = new BidomainAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpBidomainTissue);
    }


    mpBidomainNeumannSurfaceTermAssembler = new BidomainNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM>(pMesh,pBoundaryConditions);

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainSolver<ELEMENT_DIM,SPACE_DIM>::~BidomainSolver()
{
    delete mpBidomainAssembler;
    delete mpBidomainNeumannSurfaceTermAssembler;

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

    if(mpBidomainCorrectionTermAssembler)
    {
        delete mpBidomainCorrectionTermAssembler;
    }
}

// explicit instantiation

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