MonodomainPurkinjeSolver.cpp

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#include "MonodomainPurkinjeSolver.hpp"
#include "MonodomainPurkinjeVolumeMassMatrixAssembler.hpp"
#include "MonodomainPurkinjeCableMassMatrixAssembler.hpp"
#include "PetscMatTools.hpp"



template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeSolver<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)
    {
        mpVolumeAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix(),false);
        mpVolumeAssembler->AssembleMatrix();

        mpCableAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix(),false);
        // False here is to say to the cable assembler don't zero the matrix before assembling,
        // just add the terms to the previous value of the matrix.
        mpCableAssembler->AssembleMatrix();

        SetIdentityBlockToLhsMatrix();
        this->mpLinearSystem->FinaliseLhsMatrix();


        MonodomainPurkinjeVolumeMassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> volume_mass_matrix_assembler(mpMixedMesh, HeartConfig::Instance()->GetUseMassLumping());
        volume_mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
        volume_mass_matrix_assembler.Assemble();

        MonodomainPurkinjeCableMassMatrixAssembler<ELEMENT_DIM,SPACE_DIM> cable_mass_matrix_assembler(mpMixedMesh, HeartConfig::Instance()->GetUseMassLumping());
        cable_mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix,false /* don't zero the matrix*/);
        cable_mass_matrix_assembler.Assemble();

        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_volume(distributed_current_solution, 0);
    DistributedVector::Stripe distributed_current_solution_cable(distributed_current_solution, 1);
    // dist stripe for z
    DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
    DistributedVector::Stripe dist_vec_matrix_based_volume(dist_vec_matrix_based, 0);
    DistributedVector::Stripe dist_vec_matrix_based_cable(dist_vec_matrix_based, 1);

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

    double Am_purkinje = HeartConfig::Instance()->GetPurkinjeSurfaceAreaToVolumeRatio();
    double Cm_purkinje  = HeartConfig::Instance()->GetPurkinjeCapacitance();


    for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
         index!= dist_vec_matrix_based.End();
         ++index)
    {
        double V_volume = distributed_current_solution_volume[index];
        double F_volume = - Am*this->mpMonodomainTissue->rGetIionicCacheReplicated()[index.Global]
                          - this->mpMonodomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
        dist_vec_matrix_based_volume[index] = Am*Cm*V_volume*PdeSimulationTime::GetPdeTimeStepInverse() + F_volume;

        double V_cable = distributed_current_solution_cable[index];
        double F_cable = - Am*this->mpMonodomainTissue->rGetPurkinjeIionicCacheReplicated()[index.Global] //Purkinje intra-cell stimulus not defined yet
                         - this->mpMonodomainTissue->rGetPurkinjeIntracellularStimulusCacheReplicated()[index.Global];

        dist_vec_matrix_based_cable[index] = Am_purkinje*Cm_purkinje*V_cable*PdeSimulationTime::GetPdeTimeStepInverse() + F_cable;
    }

    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();

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


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeSolver<ELEMENT_DIM,SPACE_DIM>::SetIdentityBlockToLhsMatrix()
{
    this->mpLinearSystem->FinaliseLhsMatrix();

    Vec diagonal;
    VecDuplicate(mVecForConstructingRhs, &diagonal);
    MatGetDiagonal(this->mpLinearSystem->rGetLhsMatrix(), diagonal);

    // if A(i,i)=0, i must be within the block to be altered, so set A(i,i)=1.
    PetscMatTools::SwitchWriteMode(this->mpLinearSystem->rGetLhsMatrix());
    PetscInt lo, hi;
    this->mpLinearSystem->GetOwnershipRange(lo, hi);
    for (int row=lo; row<hi; row++)
    {
        if ( fabs( PetscVecTools::GetElement(diagonal, row)) < 1e-8 )
        {
            PetscMatTools::SetElement(this->mpLinearSystem->rGetLhsMatrix(),row, row, 1.0);
        }
    }

    PetscTools::Destroy(diagonal);
}

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

    // call base class version...
    AbstractLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>::InitialiseForSolve(initialSolution);

    //..then do a bit extra
    if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
    {
        this->mpLinearSystem->SetAbsoluteTolerance(HeartConfig::Instance()->GetAbsoluteTolerance());
    }
    else
    {
        NEVER_REACHED;
//        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 sizes/partitioning of mass matrix & vector, using the initial condition as a template
    VecDuplicate(initialSolution, &mVecForConstructingRhs);
    PetscInt ownership_range_lo;
    PetscInt ownership_range_hi;
    VecGetOwnershipRange(initialSolution, &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 MonodomainPurkinjeSolver<ELEMENT_DIM,SPACE_DIM>::PrepareForSetupLinearSystem(Vec currentSolution)
{
    // solve cell models
    mpMonodomainTissue->SolveCellSystems(currentSolution, PdeSimulationTime::GetTime(), PdeSimulationTime::GetNextTime());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainPurkinjeSolver<ELEMENT_DIM,SPACE_DIM>::MonodomainPurkinjeSolver(
            MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* pTissue,
            BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* pBoundaryConditions)
    : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>(pMesh),
      mpMixedMesh(pMesh),
      mpMonodomainTissue(pTissue),
      mpBoundaryConditions(pBoundaryConditions)
{
    assert(pTissue);
    assert(pBoundaryConditions);
    if(HeartConfig::Instance()->GetUseStateVariableInterpolation())
    {
        EXCEPTION("State-variable interpolation is not yet supported with Purkinje");
    }
    this->mMatrixIsConstant = true;

    mpVolumeAssembler = new MonodomainPurkinjeVolumeAssembler<ELEMENT_DIM,SPACE_DIM>(mpMixedMesh,this->mpMonodomainTissue);
    mpCableAssembler = new MonodomainPurkinjeCableAssembler<ELEMENT_DIM,SPACE_DIM>(mpMixedMesh);
    mpNeumannSurfaceTermsAssembler = new NaturalNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM,2>(pMesh,pBoundaryConditions);

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

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainPurkinjeSolver<ELEMENT_DIM,SPACE_DIM>::~MonodomainPurkinjeSolver()
{
    delete mpVolumeAssembler;
    delete mpCableAssembler;
    delete mpNeumannSurfaceTermsAssembler;

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


// explicit instantiation

template class MonodomainPurkinjeSolver<2,2>;
template class MonodomainPurkinjeSolver<3,3>;