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)
{
}
EllipticBoxDomainPdeModifier<DIM>::EllipticBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde, {…}
 
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);
}
void EllipticBoxDomainPdeModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& 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);
}
void EllipticBoxDomainPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory) {…}
 
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()));
 
    this->ConstructBoundaryConditionsContainerHelper(rCellPopulation,p_bcc);
    
    return p_bcc;
}
std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > EllipticBoxDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation) {…}
 
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);
}
void EllipticBoxDomainPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& 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)