AbstractGrowingDomainPdeModifier.cpp

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#include "AbstractGrowingDomainPdeModifier.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "CaBasedCellPopulation.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "ReplicatableVector.hpp"
#include "LinearBasisFunction.hpp"
 
template <unsigned DIM>
AbstractGrowingDomainPdeModifier<DIM>::AbstractGrowingDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM, DIM> > pPde,
                                                                        boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition,
                                                                        bool isNeumannBoundaryCondition,
                                                                        Vec solution)
        : AbstractPdeModifier<DIM>(pPde,
                                   pBoundaryCondition,
                                   isNeumannBoundaryCondition,
                                   solution)
{
}
AbstractGrowingDomainPdeModifier<DIM>::AbstractGrowingDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM, DIM> > pPde, {…}
 
template<unsigned DIM>
void AbstractGrowingDomainPdeModifier<DIM>::GenerateFeMesh(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    if (this->mDeleteFeMesh)
    {
        // If a mesh has been created on a previous time step then we need to tidy it up
        assert(this->mpFeMesh != nullptr);
        delete this->mpFeMesh;
    }
    else
    {
        // This placement assumes that if this->mDeleteFeMesh is false it is uninitialised and needs to
        // be checked. If true, it has been checked elsewhere.
        this->mDeleteFeMesh = (dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation) == nullptr);
    }
 
    // Get the finite element mesh via the cell population. Set to NULL first in case mesh generation fails.
    this->mpFeMesh = nullptr;
    this->mpFeMesh = rCellPopulation.GetTetrahedralMeshForPdeModifier();
 
    // initialise Dirichlet boundary node tracking
    this->mIsDirichletBoundaryNode = std::vector<double>(this->mpFeMesh->GetNumNodes(), 0.0);
}
void AbstractGrowingDomainPdeModifier<DIM>::GenerateFeMesh(AbstractCellPopulation<DIM,DIM>& rCellPopulation) {…}
 
template<unsigned DIM>
void AbstractGrowingDomainPdeModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Store the PDE solution in an accessible form
    ReplicatableVector solution_repl(this->mSolution);
 
    // Local cell index used by the CA simulation
    unsigned cell_index = 0;
 
    unsigned index_in_solution_repl = 0;
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        unsigned tet_node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
 
        if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
        {
            // Offset to relate elements in vertex mesh to nodes in tetrahedral mesh
            tet_node_index += rCellPopulation.GetNumNodes();
        }
        else if (dynamic_cast<CaBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
        {
            // Here local cell index corresponds to tet node
            tet_node_index = cell_index;
            cell_index++;
        }
        else if (dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != nullptr)
        {
            tet_node_index = index_in_solution_repl;
            index_in_solution_repl++;
        }
 
        double solution_at_node = solution_repl[tet_node_index];
 
        cell_iter->GetCellData()->SetItem(this->mDependentVariableName, solution_at_node);
 
        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);
 
            Node<DIM>* p_tet_node = this->mpFeMesh->GetNode(tet_node_index);
 
            // Get the containing elements and average the contribution from each one
            for (typename Node<DIM>::ContainingElementIterator element_iter = p_tet_node->ContainingElementsBegin();
                 element_iter != p_tet_node->ContainingElementsEnd();
                 ++element_iter)
            {
                // 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(*element_iter, 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);
 
                // Add the contribution from this element
                for (unsigned node_index=0; node_index<DIM+1; node_index++)
                {
                    double nodal_value = solution_repl[this->mpFeMesh->GetElement(*element_iter)->GetNodeGlobalIndex(node_index)];
 
                    for (unsigned j=0; j<DIM; j++)
                    {
                        solution_gradient(j) += nodal_value* grad_phi(j, node_index);
                    }
                }
            }
 
            // Divide by number of containing elements
            solution_gradient /= p_tet_node->GetNumContainingElements();
 
            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;
            }
        }
    }
}
void AbstractGrowingDomainPdeModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation) {…}
 
template<unsigned DIM>
void AbstractGrowingDomainPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractPdeModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
void AbstractGrowingDomainPdeModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile) {…}
 
// Explicit instantiation
template class AbstractGrowingDomainPdeModifier<1>;
template class AbstractGrowingDomainPdeModifier<2>;
template class AbstractGrowingDomainPdeModifier<3>;