AbstractBidomainSolver.cpp

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#include "AbstractBidomainSolver.hpp"
#include "TetrahedralMesh.hpp"
#include "PetscMatTools.hpp"
#include "PetscVecTools.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<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, 2>::InitialiseForSolve(initialSolution);
 
    if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
    {
#ifdef TRACE_KSP
        if (PetscTools::AmMaster())
        {
            std::cout << "Using absolute tolerance: " << mpConfig->GetAbsoluteTolerance() << "\n";
        }
#endif
        this->mpLinearSystem->SetAbsoluteTolerance(mpConfig->GetAbsoluteTolerance());
    }
    else
    {
#ifdef TRACE_KSP
        if (PetscTools::AmMaster())
        {
            std::cout << "Using relative tolerance: " << mpConfig->GetRelativeTolerance() << "\n";
        }
#endif
        this->mpLinearSystem->SetRelativeTolerance(mpConfig->GetRelativeTolerance());
    }
 
    this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
 
    // Note that twolevelblockdiagonal was never finished.  It was a preconditioner specific to the Parabolic-Parabolic formulation of Bidomain
    // Two levels block diagonal only worked in serial with TetrahedralMesh.
    assert(std::string(HeartConfig::Instance()->GetKSPPreconditioner()) != std::string("twolevelsblockdiagonal"));
    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);
    }
 
    this->mpLinearSystem->SetUseFixedNumberIterations(
        HeartConfig::Instance()->GetUseFixedNumberIterationsLinearSolver(),
        HeartConfig::Instance()->GetEvaluateNumItsEveryNSolves());
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::PrepareForSetupLinearSystem(Vec existingSolution)
{
    mpBidomainTissue->SolveCellSystems(existingSolution, PdeSimulationTime::GetTime(), PdeSimulationTime::GetNextTime());
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Vec AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::GenerateNullBasis() const
{
    double sqrt_num_nodes = sqrt((double) this->mpMesh->GetNumNodes());
 
    Vec null_basis;
    DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
    null_basis = p_factory->CreateVec(2);
 
    DistributedVector dist_null_basis = p_factory->CreateDistributedVector(null_basis);
    DistributedVector::Stripe null_basis_stripe_0(dist_null_basis,0);
    DistributedVector::Stripe null_basis_stripe_1(dist_null_basis,1);
    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] = 1.0/sqrt_num_nodes; // normalised vector
    }
    dist_null_basis.Restore();
 
    return null_basis;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::FinaliseLinearSystem(Vec existingSolution)
{
    // If no dirichlet boundary conditions
    //  (i) Check compatibility condition to check we are solving
    //      a linear system that can be solved
    // Then either
    //  (a) If not setting average(phi)=0, we are solving a singular system,
    //      so set up a null space
    //  (b) Apply average(phi)=0 constraint by altering the last row, to
    //      get a non-singular system
    //
    if (!(GetBoundaryConditions()->HasDirichletBoundaryConditions()))
    {
        // first check compatibility condition
        CheckCompatibilityCondition();
 
        // Check whether applying average(phi_e)=0 constraint
        if (mRowForAverageOfPhiZeroed==INT_MAX)
        {
            // We're not using the constraint, hence use a null space
            if (!mNullSpaceCreated)
            {
                // No null space set up, so create one and pass it to the linear system
                Vec null_basis[] = {GenerateNullBasis()};
 
                this->mpLinearSystem->SetNullBasis(null_basis, 1);
 
                PetscTools::Destroy(null_basis[0]);
                mNullSpaceCreated = true;
            }
        }
        else
        {
            // Using the average(phi_e)=0 constraint
 
            // 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 1 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 == 1)
                    {
                        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();
        }
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::CheckCompatibilityCondition()
{
    if (GetBoundaryConditions()->HasDirichletBoundaryConditions() || this->mRowForAverageOfPhiZeroed!=INT_MAX)
    {
        // not a singular system, no compatibility condition
        return;
    }
 
#ifndef NDEBUG
    DistributedVector distributed_rhs=this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mpLinearSystem->rGetRhsVector());
    DistributedVector::Stripe distributed_rhs_phi_entries(distributed_rhs,1);
 
    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_{2i+1} = " << 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>
AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::AbstractBidomainSolver(
            bool bathSimulation,
            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            BidomainTissue<SPACE_DIM>* pTissue,
            BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,2>* pBoundaryConditions)
    : AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>(pMesh),
      mBathSimulation(bathSimulation),
      mpBidomainTissue(pTissue),
      mpBoundaryConditions(pBoundaryConditions)
{
    assert(pTissue != NULL);
    assert(pBoundaryConditions != NULL);
 
    mNullSpaceCreated = false;
 
    // important!
    this->mMatrixIsConstant = true;
 
    mRowForAverageOfPhiZeroed = INT_MAX; //this->mpLinearSystem->GetSize() - 1;
    mpConfig = HeartConfig::Instance();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::~AbstractBidomainSolver()
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<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.
    GetBoundaryConditions()->ResetDirichletCommunication();
 
    for (unsigned i=0; i<mFixedExtracellularPotentialNodes.size(); i++)
    {
        if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(mFixedExtracellularPotentialNodes[i]))
        {
            auto* 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]);
 
            GetBoundaryConditions()->AddDirichletBoundaryCondition(p_node, p_boundary_condition, 1);
 
        }
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::SetRowForAverageOfPhiZeroed(unsigned row)
{
    // Row should be odd in C++-like indexing
    if (row%2 == 0)
    {
        EXCEPTION("Row for applying the constraint 'Average of phi_e = zero' should be odd in C++ like indexing");
    }
 
    mRowForAverageOfPhiZeroed = row;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractBidomainSolver<ELEMENT_DIM,SPACE_DIM>::FinaliseForBath(bool computeMatrix, bool computeVector)
{
    assert(mBathSimulation);
    PetscBool is_matrix_assembled;
    MatAssembled(this->mpLinearSystem->GetLhsMatrix(), &is_matrix_assembled);
    assert(is_matrix_assembled == PETSC_TRUE);
 
    /*
     *  Before revision 6516, we used to zero out i-th row and column here. It seems to be redundant because they are already zero after assembly.
     *  When assembling a bath element you get a matrix subblock that looks like (2D example):
     *
     *     Vm   0 0 0 0 0 0
     *     Vm   0 0 0 0 0 0
     *     Vm   0 0 0 0 0 0
     *     Phie 0 0 0 x x x
     *     Phie 0 0 0 x x x  -> the x subblock is assembled from div(grad_phi) = 0
     *     Phie 0 0 0 x x x
     *
     *  Therefore, all the Vm entries of this node are already 0.
     *
     *  Explicitly checking it in non-production builds.
     */
#ifndef NDEBUG
    if (computeMatrix)
    {
        for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator iter=this->mpMesh->GetNodeIteratorBegin();
             iter != this->mpMesh->GetNodeIteratorEnd();
             ++iter)
        {
            if (HeartRegionCode::IsRegionBath( (*iter).GetRegion() ))
            {
                int num_equation = 2*iter->GetIndex(); // assumes Vm and Phie are interleaved
 
                PetscInt local_lo, local_hi;
                this->mpLinearSystem->GetOwnershipRange(local_lo, local_hi);
 
                // If this processor owns i-th row, check it.
                if ((local_lo <= (int)num_equation) && ((int)num_equation < local_hi))
                {
                    for (unsigned column=0; column < this->mpLinearSystem->GetSize(); column++)
                    {
                        assert(this->mpLinearSystem->GetMatrixElement(num_equation, column)==0.0);
                    }
                }
 
                // Check the local entries of the i-th column
                for (int row=local_lo; row<local_hi; row++)
                {
                    assert(this->mpLinearSystem->GetMatrixElement(row, num_equation)==0);
                }
            }
        }
    }
#endif
 
    /*
     *  These two loops are decoupled because interleaving calls to GetMatrixElement and MatSetValue
     *  require reassembling the matrix before GetMatrixElement which generates massive communication
     *  overhead for large models and/or large core counts.
     */
 
    for (typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator iter=this->mpMesh->GetNodeIteratorBegin();
         iter != this->mpMesh->GetNodeIteratorEnd();
         ++iter)
    {
        if (HeartRegionCode::IsRegionBath((*iter).GetRegion() ))
        {
            PetscInt index = 2*iter->GetIndex(); // assumes Vm and Phie are interleaved
 
            if (computeMatrix)
            {
                // put 1.0 on the diagonal
                PetscMatTools::SetElement(this->mpLinearSystem->rGetLhsMatrix(), index, index, 1.0);
            }
 
            if (computeVector)
            {
                // zero rhs vector entry
                PetscVecTools::SetElement(this->mpLinearSystem->rGetRhsVector(), index, 0.0);
            }
        }
    }
}
 
// Explicit instantiation
template class AbstractBidomainSolver<1,1>;
template class AbstractBidomainSolver<2,2>;
template class AbstractBidomainSolver<3,3>;