AbstractExtendedBidomainSolver.cpp

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#include "AbstractExtendedBidomainSolver.hpp"
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM, SPACE_DIM>::InitialiseForSolve(Vec initialSolution)
{
    // The base class method that calls this function will only call it with a null linear system
    assert(this->mpLinearSystem == NULL);
 
    // linear system created here
    AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, 3>::InitialiseForSolve(initialSolution);
 
    if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
    {
#ifdef TRACE_KSP
        std::cout << "Using absolute tolerance: " << mpConfig->GetAbsoluteTolerance() << "\n";
#endif
        this->mpLinearSystem->SetAbsoluteTolerance(mpConfig->GetAbsoluteTolerance());
    }
    else
    {
#ifdef TRACE_KSP
        std::cout << "Using relative tolerance: " << mpConfig->GetRelativeTolerance() << "\n";
#endif
        this->mpLinearSystem->SetRelativeTolerance(mpConfig->GetRelativeTolerance());
    }
 
    this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
    this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
 
    if (mRowForAverageOfPhiZeroed == INT_MAX)
    {
        // not applying average(phi)=0 constraint, so matrix is symmetric
        this->mpLinearSystem->SetMatrixIsSymmetric(true);
    }
    else
    {
        //Turn off preallocation so that we can have one dense row in the matrix.
        PetscMatTools::TurnOffVariableAllocationError(this->mpLinearSystem->rGetLhsMatrix());
        // applying average(phi)=0 constraint, so matrix is not symmetric
        this->mpLinearSystem->SetMatrixIsSymmetric(false);
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::PrepareForSetupLinearSystem(Vec existingSolution)
{
    mpExtendedBidomainTissue->SolveCellSystems(existingSolution, PdeSimulationTime::GetTime(), PdeSimulationTime::GetNextTime());
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Vec AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::GenerateNullBasis() const
{
    double sqrrt_num_nodes = sqrt(  this->mpMesh->GetNumNodes());
    double normalised_basis_value = 1.0 / sqrrt_num_nodes;
 
    Vec nullbasis;
    DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
    nullbasis=p_factory->CreateVec(3);
    DistributedVector dist_null_basis = p_factory->CreateDistributedVector(nullbasis);
    DistributedVector::Stripe null_basis_stripe_0(dist_null_basis,0);
    DistributedVector::Stripe null_basis_stripe_1(dist_null_basis,1);
    DistributedVector::Stripe null_basis_stripe_2(dist_null_basis,2);
    for (DistributedVector::Iterator index = dist_null_basis.Begin();
         index != dist_null_basis.End();
         ++index)
    {
        null_basis_stripe_0[index] = 0.0;
        null_basis_stripe_1[index] = 0.0;
        null_basis_stripe_2[index] = normalised_basis_value;
    }
    dist_null_basis.Restore();
    return nullbasis;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::FinaliseLinearSystem(Vec existingSolution)
{
    if (!(this->mpBoundaryConditions->HasDirichletBoundaryConditions()))
    {
        // We're not pinning any nodes.
        if (mRowForAverageOfPhiZeroed==INT_MAX)
        {
            // We're not using the 'Average phi_e = 0' method, hence use a null space
            if (!mNullSpaceCreated)
            {
                // No null space set up, so create one and pass it to the linear system
                Vec nullbasis[] = {GenerateNullBasis()};
 
                this->mpLinearSystem->SetNullBasis(nullbasis, 1);
 
                PetscTools::Destroy(nullbasis[0]);
                mNullSpaceCreated = true;
            }
        }
        else  // mRowForAverageOfPhiZeroed!=INT_MAX, i.e. we're using the 'Average phi_e = 0' method
        {
            // CG (default solver) won't work since the system isn't symmetric anymore. Switch to GMRES
            this->mpLinearSystem->SetKspType("gmres"); // Switches the solver
            mpConfig->SetKSPSolver("gmres", true); // Makes sure this change will be reflected in the XML file written to disk at the end of the simulation.
            //(If the user doesn't have gmres then the "true" warns the user about the switch)
 
            // Set average phi_e to zero
            unsigned matrix_size = this->mpLinearSystem->GetSize();
            if (!this->mMatrixIsAssembled)
            {
 
                // Set the mRowForAverageOfPhiZeroed-th matrix row to 0 0 1 0 0 1 ...
                std::vector<unsigned> row_for_average;
                row_for_average.push_back(mRowForAverageOfPhiZeroed);
                this->mpLinearSystem->ZeroMatrixRowsWithValueOnDiagonal(row_for_average, 0.0);
                for (unsigned col_index=0; col_index<matrix_size; col_index++)
                {
                    if (((col_index-2)%3 == 0) && (col_index>1))//phi_e column indices are 2,5,8,11 etc....
                    {
                        this->mpLinearSystem->SetMatrixElement(mRowForAverageOfPhiZeroed, col_index, 1);
                    }
 
                }
                this->mpLinearSystem->FinaliseLhsMatrix();
            }
            // Set the mRowForAverageOfPhiZeroed-th rhs vector row to 0
            this->mpLinearSystem->SetRhsVectorElement(mRowForAverageOfPhiZeroed, 0);
 
            this->mpLinearSystem->FinaliseRhsVector();
        }
    }
    CheckCompatibilityCondition();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::CheckCompatibilityCondition()
{
    if (this->mpBoundaryConditions->HasDirichletBoundaryConditions() || mRowForAverageOfPhiZeroed!=INT_MAX )
    {
        // not a singular system, no compability condition
        return;
    }
 
#ifndef NDEBUG
    DistributedVector distributed_rhs=this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mpLinearSystem->rGetRhsVector());
    DistributedVector::Stripe distributed_rhs_phi_entries(distributed_rhs,2); // stripe number 2 -> phi_e
 
    double local_sum=0;
    for (DistributedVector::Iterator index = distributed_rhs.Begin();
         index!= distributed_rhs.End();
         ++index)
    {
        local_sum += distributed_rhs_phi_entries[index];
    }
 
    double global_sum;
    int mpi_ret = MPI_Allreduce(&local_sum, &global_sum, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
    assert(mpi_ret == MPI_SUCCESS);
 
    if (fabs(global_sum)>1e-6) // magic number! sum should really be a sum of zeros and exactly zero though anyway (or a-a+b-b+c-c.. etc in the case of electrodes)
    {
        // LCOV_EXCL_START
        // shouldn't ever reach this line but useful to have the error printed out if you do
        std::cout << "Sum of b_{every 3 items} = " << global_sum << " (should be zero for compatibility)\n";
        EXCEPTION("Linear system does not satisfy compatibility constraint!");
        // LCOV_EXCL_STOP
    }
#endif
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::AbstractExtendedBidomainSolver(
        bool bathSimulation,
        AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
        ExtendedBidomainTissue<SPACE_DIM>* pTissue,
        BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 3>* pBcc)
    : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,3>(pMesh),
              mBathSimulation(bathSimulation),
              mpExtendedBidomainTissue(pTissue),
              mpBoundaryConditions(pBcc)
{
    assert(pTissue != NULL);
    assert(pBcc != NULL);
 
    mNullSpaceCreated = false;
 
    // important!
    this->mMatrixIsConstant = true;
 
    mRowForAverageOfPhiZeroed = INT_MAX; //this->mpLinearSystem->GetSize() - 1;
    mpConfig = HeartConfig::Instance();
 
    mpExtendedBidomainAssembler = NULL; // can't initialise until know what dt is
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::~AbstractExtendedBidomainSolver()
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::SetFixedExtracellularPotentialNodes(
            std::vector<unsigned> fixedExtracellularPotentialNodes)
{
    for (unsigned i=0; i<fixedExtracellularPotentialNodes.size(); i++)
    {
        if (fixedExtracellularPotentialNodes[i] >= this->mpMesh->GetNumNodes() )
        {
            EXCEPTION("Fixed node number must be less than total number nodes");
        }
    }
 
    mFixedExtracellularPotentialNodes = fixedExtracellularPotentialNodes;
 
    // We will need to recalculate this when HasDirichletBoundaryConditions() is called.
    this->mpBoundaryConditions->ResetDirichletCommunication();
 
    for (unsigned i=0; i<mFixedExtracellularPotentialNodes.size(); i++)
    {
        if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(mFixedExtracellularPotentialNodes[i]))
        {
            ConstBoundaryCondition<SPACE_DIM>* p_boundary_condition = new ConstBoundaryCondition<SPACE_DIM>(0.0);
 
            //Throws if node is not owned locally
            Node<SPACE_DIM>* p_node = this->mpMesh->GetNode(mFixedExtracellularPotentialNodes[i]);
 
            //the "false" passed in tells not to check that it is a boundary node (since we might have grounded electrodes within the tissue)
            GetBoundaryConditions()->AddDirichletBoundaryCondition(p_node, p_boundary_condition, 2, false);
        }
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::SetRowForAverageOfPhiZeroed(unsigned row)
{
    // Row should be every 3 entries, starting from zero...
    if (((row-2)%3 != 0) && row!=INT_MAX)
    {
        EXCEPTION("Row for applying the constraint 'Average of phi_e = zero' should be every 3 rows");
    }
 
    mRowForAverageOfPhiZeroed = row;
}
 
// Explicit instantiation
template class AbstractExtendedBidomainSolver<1,1>;
template class AbstractExtendedBidomainSolver<2,2>;
template class AbstractExtendedBidomainSolver<3,3>;