ExtendedBidomainSolver.cpp

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#include "ExtendedBidomainSolver.hpp"
#include "ExtendedBidomainMassMatrixAssembler.hpp"
#include "ExtendedBidomainAssembler.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::InitialiseForSolve(Vec initialSolution)
{
    if (this->mpLinearSystem != NULL)
    {
        return;
    }
    AbstractExtendedBidomainSolver<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, 3*this->mpMesh->GetNumNodes(), 3*this->mpMesh->GetNumNodes(),
                         3*this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
                         local_size, local_size);
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver<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)
    {
        mpExtendedBidomainAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix());
        mpExtendedBidomainAssembler->AssembleMatrix();

        // the ExtendedBidomainMassMatrixAssembler deals with the mass matrix
        // for both bath and nonbath problems
        assert(SPACE_DIM==ELEMENT_DIM);
        ExtendedBidomainMassMatrixAssembler<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();

    // get bidomain parameters
    double Am1 = this->mpExtendedBidomainTissue->GetAmFirstCell();
    double Am2 = this->mpExtendedBidomainTissue->GetAmSecondCell();
    double AmGap = this->mpExtendedBidomainTissue->GetAmGap();
    double Cm1 = this->mpExtendedBidomainTissue->GetCmFirstCell();
    double Cm2 = this->mpExtendedBidomainTissue->GetCmSecondCell();

    // dist stripe for the current Voltage
    DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
    DistributedVector::Stripe distributed_current_solution_v_first_cell(distributed_current_solution, 0);
    DistributedVector::Stripe distributed_current_solution_v_second_cell(distributed_current_solution, 1);
    DistributedVector::Stripe distributed_current_solution_phi_e(distributed_current_solution, 2);

    // dist stripe for z
    DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
    DistributedVector::Stripe dist_vec_matrix_based_v_first_cell(dist_vec_matrix_based, 0);
    DistributedVector::Stripe dist_vec_matrix_based_v_second_cell(dist_vec_matrix_based, 1);
    DistributedVector::Stripe dist_vec_matrix_based_phi_e(dist_vec_matrix_based, 2);

    for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
         index!= dist_vec_matrix_based.End();
         ++index)
    {
        double V_first_cell = distributed_current_solution_v_first_cell[index];
        double V_second_Cell = distributed_current_solution_v_second_cell[index];
        double Phi_e = distributed_current_solution_phi_e[index];

        double i_ionic_first_cell = this->mpExtendedBidomainTissue->rGetIionicCacheReplicated()[index.Global];
        double i_ionic_second_cell = this->mpExtendedBidomainTissue->rGetIionicCacheReplicatedSecondCell()[index.Global];
        double intracellular_stimulus_first_cell = this->mpExtendedBidomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
        double intracellular_stimulus_second_cell = this->mpExtendedBidomainTissue->rGetIntracellularStimulusCacheReplicatedSecondCell()[index.Global];
        double extracellular_stimulus =  this->mpExtendedBidomainTissue->rGetExtracellularStimulusCacheReplicated()[index.Global];
        double g_gap = this->mpExtendedBidomainTissue->rGetGgapCacheReplicated()[index.Global];
        double delta_t = PdeSimulationTime::GetPdeTimeStep();
        dist_vec_matrix_based_v_first_cell[index] = Am1*Cm1*V_first_cell/delta_t - Am1*Cm1*Phi_e/delta_t - Am1*i_ionic_first_cell + AmGap*g_gap*(V_second_Cell - V_first_cell) -  intracellular_stimulus_first_cell;
        dist_vec_matrix_based_v_second_cell[index] = Am2*Cm2*V_second_Cell/delta_t- Am2*Cm2*Phi_e/delta_t - Am2*i_ionic_second_cell + AmGap*g_gap*(V_first_cell - V_second_Cell) - intracellular_stimulus_second_cell;

        if (this->mpExtendedBidomainTissue->HasTheUserSuppliedExtracellularStimulus() )
        {
            assert((fabs(intracellular_stimulus_first_cell) < 1e-12)
            && (fabs(intracellular_stimulus_second_cell) < 1e-12));

            dist_vec_matrix_based_phi_e[index] = -extracellular_stimulus;
        }
        else
        {
            dist_vec_matrix_based_phi_e[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 mpExtendedBidomainAssembler->AssembleVector();
    HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);

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

    this->mpLinearSystem->FinaliseRhsVector();

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

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


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::ExtendedBidomainSolver(
        bool bathSimulation,
        AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
        ExtendedBidomainTissue<SPACE_DIM>* pTissue,
        BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* pBoundaryConditions)
    : AbstractExtendedBidomainSolver<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(this->mBathSimulation)
    {
        //this->mpExtendedExtendedBidomainAssembler = new ExtendedExtendedBidomainWithBathAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpExtendedExtendedBidomainTissue,this->mDt);
        EXCEPTION("Bath simulations are not yet supported for extended bidomain problems");
    }
    else
    {
        mpExtendedBidomainAssembler = new ExtendedBidomainAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpExtendedBidomainTissue);
    }

    mpExtendedBidomainNeumannSurfaceTermAssembler = new ExtendedBidomainNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM>(pMesh,pBoundaryConditions);

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::~ExtendedBidomainSolver()
{
    delete mpExtendedBidomainAssembler;
    delete mpExtendedBidomainNeumannSurfaceTermAssembler;

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

// explicit instantiation

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