AbstractBoxDomainPdeModifier.cpp

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#include "AbstractBoxDomainPdeModifier.hpp"
#include "ReplicatableVector.hpp"
#include "LinearBasisFunction.hpp"

template<unsigned DIM>
AbstractBoxDomainPdeModifier<DIM>::AbstractBoxDomainPdeModifier(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)
    : AbstractPdeModifier<DIM>(pPde,
                               pBoundaryCondition,
                               isNeumannBoundaryCondition,
                               solution),
      mpMeshCuboid(pMeshCuboid),
      mStepSize(stepSize),
      mSetBcsOnBoxBoundary(true)
{
    if (pMeshCuboid)
    {
        // We only need to generate mpFeMesh once, as it does not vary with time
        this->GenerateFeMesh(mpMeshCuboid, mStepSize);
        this->mDeleteFeMesh = true;
    }
}

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

template<unsigned DIM>
double AbstractBoxDomainPdeModifier<DIM>::GetStepSize()
{
     return mStepSize;
}

template<unsigned DIM>
void AbstractBoxDomainPdeModifier<DIM>::SetBcsOnBoxBoundary(bool setBcsOnBoxBoundary)
{
    mSetBcsOnBoxBoundary = setBcsOnBoxBoundary;
}

template<unsigned DIM>
bool AbstractBoxDomainPdeModifier<DIM>::AreBcsSetOnBoxBoundary()
{
    return mSetBcsOnBoxBoundary;
}

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

    InitialiseCellPdeElementMap(rCellPopulation);
}

template<unsigned DIM>
void AbstractBoxDomainPdeModifier<DIM>::GenerateFeMesh(boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid, double stepSize)
{
    // Create a regular coarse tetrahedral mesh
    this->mpFeMesh = new TetrahedralMesh<DIM,DIM>();
    switch (DIM)
    {
        case 1:
            this->mpFeMesh->ConstructRegularSlabMesh(stepSize, pMeshCuboid->GetWidth(0));
            break;
        case 2:
            this->mpFeMesh->ConstructRegularSlabMesh(stepSize, pMeshCuboid->GetWidth(0), pMeshCuboid->GetWidth(1));
            break;
        case 3:
            this->mpFeMesh->ConstructRegularSlabMesh(stepSize, pMeshCuboid->GetWidth(0), pMeshCuboid->GetWidth(1), pMeshCuboid->GetWidth(2));
            break;
        default:
            NEVER_REACHED;
    }

    // Get centroid of meshCuboid
    ChastePoint<DIM> upper = pMeshCuboid->rGetUpperCorner();
    ChastePoint<DIM> lower = pMeshCuboid->rGetLowerCorner();
    c_vector<double,DIM> centre_of_cuboid = 0.5*(upper.rGetLocation() + lower.rGetLocation());

    // Find the centre of the PDE mesh
    c_vector<double,DIM> centre_of_coarse_mesh = zero_vector<double>(DIM);
    for (unsigned i=0; i<this->mpFeMesh->GetNumNodes(); i++)
    {
        centre_of_coarse_mesh += this->mpFeMesh->GetNode(i)->rGetLocation();
    }
    centre_of_coarse_mesh /= this->mpFeMesh->GetNumNodes();

    // Now move the mesh to the correct location
    this->mpFeMesh->Translate(centre_of_cuboid - centre_of_coarse_mesh);
}

template<unsigned DIM>
void AbstractBoxDomainPdeModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Store the PDE solution in an accessible form
    ReplicatableVector solution_repl(this->mSolution);

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // The cells are not nodes of the mesh, so we must interpolate
        double solution_at_cell = 0.0;

        // Find the element in the FE mesh that contains this cell. CellElementMap has been updated so use this.
        unsigned elem_index = mCellPdeElementMap[*cell_iter];
        Element<DIM,DIM>* p_element = this->mpFeMesh->GetElement(elem_index);

        const ChastePoint<DIM>& node_location = rCellPopulation.GetLocationOfCellCentre(*cell_iter);

        c_vector<double,DIM+1> weights = p_element->CalculateInterpolationWeights(node_location);

        for (unsigned i=0; i<DIM+1; i++)
        {
            double nodal_value = solution_repl[p_element->GetNodeGlobalIndex(i)];
            solution_at_cell += nodal_value * weights(i);
        }

        cell_iter->GetCellData()->SetItem(this->mDependentVariableName, solution_at_cell);

        if (this->mOutputGradient)
        {
            // Now calculate the gradient of the solution and store this in CellVecData
            c_vector<double, DIM> solution_gradient = zero_vector<double>(DIM);

            // Calculate the basis functions at any point (e.g. zero) in the element
            c_matrix<double, DIM, DIM> jacobian, inverse_jacobian;
            double jacobian_det;
            this->mpFeMesh->GetInverseJacobianForElement(elem_index, jacobian, jacobian_det, inverse_jacobian);
            const ChastePoint<DIM> zero_point;
            c_matrix<double, DIM, DIM+1> grad_phi;
            LinearBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(zero_point, inverse_jacobian, grad_phi);

            for (unsigned node_index=0; node_index<DIM+1; node_index++)
            {
                double nodal_value = solution_repl[p_element->GetNodeGlobalIndex(node_index)];

                for (unsigned j=0; j<DIM; j++)
                {
                    solution_gradient(j) += nodal_value* grad_phi(j, node_index);
                }
            }

            switch (DIM)
            {
                case 1:
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
                    break;
                case 2:
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_y", solution_gradient(1));
                    break;
                case 3:
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_x", solution_gradient(0));
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_y", solution_gradient(1));
                    cell_iter->GetCellData()->SetItem(this->mDependentVariableName+"_grad_z", solution_gradient(2));
                    break;
                default:
                    NEVER_REACHED;
            }
        }
    }
}

template<unsigned DIM>
void AbstractBoxDomainPdeModifier<DIM>::InitialiseCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    mCellPdeElementMap.clear();

    // Find the element of mpFeMesh that contains each cell and populate mCellPdeElementMap
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        const ChastePoint<DIM>& r_position_of_cell = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
        unsigned elem_index = this->mpFeMesh->GetContainingElementIndex(r_position_of_cell);
        mCellPdeElementMap[*cell_iter] = elem_index;
    }
}

template<unsigned DIM>
void AbstractBoxDomainPdeModifier<DIM>::UpdateCellPdeElementMap(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Find the element of mpCoarsePdeMesh that contains each cell and populate mCellPdeElementMap
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        const ChastePoint<DIM>& r_position_of_cell = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
        unsigned elem_index = this->mpFeMesh->GetContainingElementIndexWithInitialGuess(r_position_of_cell, mCellPdeElementMap[*cell_iter]);
        mCellPdeElementMap[*cell_iter] = elem_index;
    }
}

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

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