CellwiseDataGradient.cpp

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#include "CellwiseDataGradient.hpp"
#include "LinearBasisFunction.hpp"

template<unsigned DIM>
c_vector<double, DIM>& CellwiseDataGradient<DIM>::rGetGradient(unsigned nodeIndex)
{
    return mGradients[nodeIndex];
}


template<unsigned DIM>
void CellwiseDataGradient<DIM>::SetupGradients(AbstractCellPopulation<DIM>& rCellPopulation, const std::string& rItemName)
{
    MeshBasedCellPopulation<DIM>* pCellPopulation = static_cast<MeshBasedCellPopulation<DIM>*>(&(rCellPopulation));
    TetrahedralMesh<DIM,DIM>& r_mesh = pCellPopulation->rGetMesh();

    // Initialise gradients size
    unsigned num_nodes = pCellPopulation->GetNumNodes();
    mGradients.resize(num_nodes, zero_vector<double>(DIM));

    // The constant gradients at each element
    std::vector<c_vector<double, DIM> > gradients_on_elements;
    unsigned num_elements = r_mesh.GetNumElements();
    gradients_on_elements.resize(num_elements, zero_vector<double>(DIM));

    // The number of elements containing a given node (excl ghost elements)
    std::vector<unsigned> num_real_elems_for_node(num_nodes, 0);

    for (unsigned elem_index=0; elem_index<num_elements; elem_index++)
    {
        Element<DIM,DIM>& r_elem = *(r_mesh.GetElement(elem_index));

        // Calculate the basis functions at any point (eg zero) in the element
        c_matrix<double, DIM, DIM> jacobian, inverse_jacobian;
        double jacobian_det;
        r_mesh.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);

        bool is_ghost_element = false;

        for (unsigned node_index=0; node_index<DIM+1; node_index++)
        {
            unsigned node_global_index = r_elem.GetNodeGlobalIndex(node_index);

            // This code is commented because CellData can't deal with ghost nodes see #1975
            assert(pCellPopulation->IsGhostNode(node_global_index) == false);
            //if (pCellPopulation->IsGhostNode(node_global_index) == true)
            //{
            //    is_ghost_element = true;
            //    break;
            //}

            // If no ghost element, get PDE solution
            CellPtr p_cell = pCellPopulation->GetCellUsingLocationIndex(node_global_index);
            double pde_solution = p_cell->GetCellData()->GetItem(rItemName);

            // Interpolate gradient
            for (unsigned i=0; i<DIM; i++)
            {
                gradients_on_elements[elem_index](i) += pde_solution* grad_phi(i, node_index);
            }
        }

        // Add gradient at element to gradient at node
        if (!is_ghost_element)
        {
            for (unsigned node_index=0; node_index<DIM+1; node_index++)
            {
                unsigned node_global_index = r_elem.GetNodeGlobalIndex(node_index);
                mGradients[node_global_index] += gradients_on_elements[elem_index];
                num_real_elems_for_node[node_global_index]++;
            }
        }
    }

    // Divide to obtain average gradient
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        unsigned node_global_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        if (!num_real_elems_for_node[node_global_index] > 0)
        {
            NEVER_REACHED;
            // This code is commented because CellwiseData Can't deal with ghost nodes so won't ever come into this statement see #1975
            //Node<DIM>& this_node = *(pCellPopulation->GetNodeCorrespondingToCell(*cell_iter));
            //
            //mGradients[node_global_index] = zero_vector<double>(DIM);
            //unsigned num_real_adjacent_nodes = 0;
            //
            //std::set<Node<DIM>*> real_adjacent_nodes;
            //real_adjacent_nodes.clear();
            //
            //for (typename Node<DIM>::ContainingElementIterator element_iter = this_node.ContainingElementsBegin();
            //     element_iter != this_node.ContainingElementsEnd();
            //     ++element_iter)
            //{
            //    // Then loop over nodes therein
            //    Element<DIM,DIM>& r_adjacent_elem = *(r_mesh.GetElement(*element_iter));
            //    for (unsigned local_node_index=0; local_node_index<DIM+1; local_node_index++)
            //    {
            //        unsigned adjacent_node_global_index = r_adjacent_elem.GetNodeGlobalIndex(local_node_index);
            //
            //        // If not a ghost node and not the node we started with
            //        if (    !(pCellPopulation->IsGhostNode(adjacent_node_global_index))
            //             && adjacent_node_global_index != node_global_index )
            //        {
            //
            //            // Calculate the contribution of gradient from this node
            //            Node<DIM>& adjacent_node = *(r_mesh.GetNode(adjacent_node_global_index));
            //
            //            double this_cell_concentration = CellwiseData<DIM>::Instance()->GetValue(*cell_iter, 0);
            //            CellPtr p_adjacent_cell = pCellPopulation->GetCellUsingLocationIndex(adjacent_node_global_index);
            //            double adjacent_cell_concentration = CellwiseData<DIM>::Instance()->GetValue(p_adjacent_cell, 0);
            //
            //            c_vector<double, DIM> gradient_contribution = zero_vector<double>(DIM);
            //
            //            if (fabs(this_cell_concentration-adjacent_cell_concentration) > 100*DBL_EPSILON)
            //            {
            //                c_vector<double, DIM> edge_vector = r_mesh.GetVectorFromAtoB(this_node.rGetLocation(), adjacent_node.rGetLocation());
            //                double norm_edge_vector = norm_2(edge_vector);
            //                gradient_contribution = edge_vector
            //                                            * (adjacent_cell_concentration - this_cell_concentration)
            //                                            / (norm_edge_vector * norm_edge_vector);
            //            }
            //
            //            mGradients[node_global_index] += gradient_contribution;
            //            num_real_adjacent_nodes++;
            //        }
            //    }
            //}
            //mGradients[node_global_index] /= num_real_adjacent_nodes;
        }
        else
        {
            mGradients[node_global_index] /= num_real_elems_for_node[node_global_index];
        }
    }
}

// Explicit instantiation

template class CellwiseDataGradient<1>;
template class CellwiseDataGradient<2>;
template class CellwiseDataGradient<3>;