EllipticBoxDomainPdeModifier.cpp

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#include "EllipticBoxDomainPdeModifier.hpp"
#include "SimpleLinearEllipticSolver.hpp"

template<unsigned DIM>
EllipticBoxDomainPdeModifier<DIM>::EllipticBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde,
                                                                boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
                                                                bool isNeumannBoundaryCondition,
                                                                boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid,
                                                                double stepSize,
                                                                Vec solution)
    : AbstractBoxDomainPdeModifier<DIM>(pPde,
                                        pBoundaryCondition,
                                         isNeumannBoundaryCondition,
                                        pMeshCuboid,
                                        stepSize,
                                        solution)
{
}

template<unsigned DIM>
EllipticBoxDomainPdeModifier<DIM>::~EllipticBoxDomainPdeModifier()
{
}

template<unsigned DIM>
void EllipticBoxDomainPdeModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Set up boundary conditions
    std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc = ConstructBoundaryConditionsContainer(rCellPopulation);

    this->UpdateCellPdeElementMap(rCellPopulation);

    // When using a PDE mesh which doesn't coincide with the cells, we must set up the source terms before solving the PDE.
    // Pass in already updated CellPdeElementMap to speed up finding cells.
    this->SetUpSourceTermsForAveragedSourcePde(this->mpFeMesh, &this->mCellPdeElementMap);

    // Use SimpleLinearEllipticSolver as Averaged Source PDE
    SimpleLinearEllipticSolver<DIM,DIM> solver(this->mpFeMesh,
                                               boost::static_pointer_cast<AbstractLinearEllipticPde<DIM,DIM> >(this->GetPde()).get(),
                                               p_bcc.get());

    Vec old_solution_copy = this->mSolution;
    this->mSolution = solver.Solve();
    if (old_solution_copy != nullptr)
    {
        PetscTools::Destroy(old_solution_copy);
    }

    this->UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void EllipticBoxDomainPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    AbstractBoxDomainPdeModifier<DIM>::SetupSolve(rCellPopulation,outputDirectory);

    // Call these  methods to solve the PDE on the initial step and output the results
    UpdateAtEndOfTimeStep(rCellPopulation);
    this->UpdateAtEndOfOutputTimeStep(rCellPopulation);
}

template<unsigned DIM>
std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > EllipticBoxDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));

    // To be well-defined, elliptic PDE problems on box domains require at least some Dirichlet boundary conditions
    assert(!(this->IsNeumannBoundaryCondition()));

    if (!this->mSetBcsOnBoxBoundary)
    {
        // Get the set of coarse element indices that contain cells
        std::set<unsigned> coarse_element_indices_in_map;
        for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
             cell_iter != rCellPopulation.End();
             ++cell_iter)
        {
            coarse_element_indices_in_map.insert(this->mCellPdeElementMap[*cell_iter]);
        }

        // Find the node indices associated with elements whose indices are NOT in the set coarse_element_indices_in_map
        std::set<unsigned> coarse_mesh_boundary_node_indices;
        for (unsigned i=0; i<this->mpFeMesh->GetNumElements(); i++)
        {
            if (coarse_element_indices_in_map.find(i) == coarse_element_indices_in_map.end())
            {
                Element<DIM,DIM>* p_element = this->mpFeMesh->GetElement(i);
                for (unsigned j=0; j<DIM+1; j++)
                {
                    unsigned node_index = p_element->GetNodeGlobalIndex(j);
                    coarse_mesh_boundary_node_indices.insert(node_index);
                }
            }
        }

        // Apply boundary condition to the nodes in the set coarse_mesh_boundary_node_indices
        for (std::set<unsigned>::iterator iter = coarse_mesh_boundary_node_indices.begin();
             iter != coarse_mesh_boundary_node_indices.end();
             ++iter)
        {
            p_bcc->AddDirichletBoundaryCondition(this->mpFeMesh->GetNode(*iter), this->mpBoundaryCondition.get(), 0, false);
        }
    }
    else // Apply BC at boundary nodes of box domain FE mesh
    {
        for (typename TetrahedralMesh<DIM,DIM>::BoundaryNodeIterator node_iter = this->mpFeMesh->GetBoundaryNodeIteratorBegin();
             node_iter != this->mpFeMesh->GetBoundaryNodeIteratorEnd();
             ++node_iter)
        {
            p_bcc->AddDirichletBoundaryCondition(*node_iter, this->mpBoundaryCondition.get());
        }
    }

    return p_bcc;
}

template<unsigned DIM>
void EllipticBoxDomainPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractBoxDomainPdeModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

// Explicit instantiation
template class EllipticBoxDomainPdeModifier<1>;
template class EllipticBoxDomainPdeModifier<2>;
template class EllipticBoxDomainPdeModifier<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(EllipticBoxDomainPdeModifier)