EllipticGrowingDomainPdeModifier.cpp

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#include "EllipticGrowingDomainPdeModifier.hpp"
#include "CellBasedEllipticPdeSolver.hpp"
#include "AveragedSourceEllipticPde.hpp"

template<unsigned DIM>
EllipticGrowingDomainPdeModifier<DIM>::EllipticGrowingDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde,
                                                                        boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
                                                                        bool isNeumannBoundaryCondition,
                                                                        Vec solution)
    : AbstractGrowingDomainPdeModifier<DIM>(pPde,
                                            pBoundaryCondition,
                                            isNeumannBoundaryCondition,
                                            solution)
{
}

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

template<unsigned DIM>
void EllipticGrowingDomainPdeModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    this->GenerateFeMesh(rCellPopulation);

    // If the solution at the previous timestep exists...
    PetscInt previous_solution_size = 0;
    if (this->mSolution)
    {
        VecGetSize(this->mSolution, &previous_solution_size);
    }

    // ...then record whether it is the correct size...
    bool is_previous_solution_size_correct = (previous_solution_size == (int)this->mpFeMesh->GetNumNodes());

    // ...and if it is, store it as an initial guess for the PDE solver
    Vec initial_guess;
    if (is_previous_solution_size_correct)
    {
        // This Vec is copied by the solver's Solve() method, so must be deleted here too
        VecDuplicate(this->mSolution, &initial_guess);
        VecCopy(this->mSolution, initial_guess);
        PetscTools::Destroy(this->mSolution);
    }

    // Add the BCs to the BCs container
    std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc = this->ConstructBoundaryConditionsContainer();

    // Use CellBasedEllipticPdeSolver as cell wise PDE
    CellBasedEllipticPdeSolver<DIM> solver(this->mpFeMesh,
                                           boost::static_pointer_cast<AbstractLinearEllipticPde<DIM,DIM> >(this->GetPde()).get(),
                                           p_bcc.get());

    // If we have an initial guess, use this when solving the system...
    if (is_previous_solution_size_correct)
    {
        this->mSolution = solver.Solve(initial_guess);
        PetscTools::Destroy(initial_guess);
    }
    else // ...otherwise do not supply one
    {
        // The solver creates a Vec, so we have to keep a handle on the old one to destroy it
        Vec old_solution_copy = this->mSolution;

        this->mSolution = solver.Solve();

        // On the first go round the vector has yet to be initialised, so we don't destroy it
        if (old_solution_copy != nullptr)
        {
            PetscTools::Destroy(old_solution_copy);
        }
    }

    this->UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void EllipticGrowingDomainPdeModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    if (boost::dynamic_pointer_cast<AveragedSourceEllipticPde<DIM> >(this->GetPde()))
    {
        EXCEPTION("EllipticGrowingDomainPdeModifier cannot be used with an AveragedSourceEllipticPde. Use an EllipticBoxDomainPdeModifier instead.");
    }

    AbstractGrowingDomainPdeModifier<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> > EllipticGrowingDomainPdeModifier<DIM>::ConstructBoundaryConditionsContainer()
{
    std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,1>(false));

    // To be well-defined, elliptic PDE problems on growing domains require Dirichlet boundary conditions
    assert(!(this->IsNeumannBoundaryCondition()));
    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 EllipticGrowingDomainPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractGrowingDomainPdeModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

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

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