NodeBasedCellPopulationWithBuskeUpdate.cpp

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#include "NodeBasedCellPopulationWithBuskeUpdate.hpp"

#include "ReplicatableVector.hpp"
#include "OdeLinearSystemSolver.hpp"

template<unsigned DIM>
NodeBasedCellPopulationWithBuskeUpdate<DIM>::NodeBasedCellPopulationWithBuskeUpdate(NodesOnlyMesh<DIM>& rMesh,
                                      std::vector<CellPtr>& rCells,
                                      const std::vector<unsigned> locationIndices,
                                      bool deleteMesh)
    : NodeBasedCellPopulation<DIM>(rMesh, rCells, locationIndices, deleteMesh)
{
}

template<unsigned DIM>
NodeBasedCellPopulationWithBuskeUpdate<DIM>::NodeBasedCellPopulationWithBuskeUpdate(NodesOnlyMesh<DIM>& rMesh)
    : NodeBasedCellPopulation<DIM>(rMesh)
{
    // No Validate() because the cells are not associated with the cell population yet in archiving
}

template<unsigned DIM>
void NodeBasedCellPopulationWithBuskeUpdate<DIM>::UpdateNodeLocations(double dt)
{
    // Declare solver and give the size of the system and timestep
    unsigned system_size = this->GetNumNodes()*DIM;

    OdeLinearSystemSolver solver(system_size, dt);

    // Set up the matrix
    Mat& r_matrix = solver.rGetLhsMatrix();

    // Initial condition
    Vec initial_condition = PetscTools::CreateAndSetVec(system_size, 0.0);

    // Then an rGetForceVector for RHS
    Vec& r_vector = solver.rGetForceVector();

    // Iterate over all nodes associated with real cells to construct the matrix A.
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get index of node associated with cell
        unsigned global_node_index = this->GetLocationIndexUsingCell((*cell_iter));

        // Get the local index using the mesh
        unsigned node_index = this->rGetMesh().SolveNodeMapping(global_node_index);

        Node<DIM>* p_node_i = this->GetNode(global_node_index);

        // Get the location of this node
        c_vector<double, DIM> node_i_location = p_node_i->rGetLocation();

        // Get the radius of this cell
        double radius_of_cell_i = p_node_i->GetRadius();

        // Get damping constant for node
        double damping_const = this->GetDampingConstant(global_node_index);

        // loop over neighbours to add contribution

        // Get the set of node indices corresponding to this cell's neighbours
        std::set<unsigned> neighbouring_node_indices = this->GetNeighbouringNodeIndices(global_node_index);

        for (std::set<unsigned>::iterator iter = neighbouring_node_indices.begin();
             iter != neighbouring_node_indices.end();
             ++iter)
        {
            unsigned neighbour_node_global_index = *iter;

            unsigned neighbour_node_index = this->rGetMesh().SolveNodeMapping(neighbour_node_global_index);

            // Calculate Aij
            double Aij = 0.0;

            Node<DIM>* p_node_j = this->GetNode(neighbour_node_global_index);

            // Get the location of this node
            c_vector<double, DIM> node_j_location = p_node_j->rGetLocation();

            // Get the unit vector parallel to the line joining the two nodes (assuming no periodicities etc.)
            c_vector<double, DIM> unit_vector = node_j_location - node_i_location;

            // Calculate the distance between the two nodes
            double dij = norm_2(unit_vector);

            unit_vector /= dij;

            // Get the radius of the cell corresponding to this node
            double radius_of_cell_j = p_node_j->GetRadius();

            if (dij < radius_of_cell_i + radius_of_cell_j)
            {
                // ...then compute the adhesion force and add it to the vector of forces...
                double xij = 0.5*(radius_of_cell_i*radius_of_cell_i - radius_of_cell_j*radius_of_cell_j + dij*dij)/dij;

                Aij = M_PI*(radius_of_cell_i*radius_of_cell_i - xij*xij);

                // This is contribution from the sum term in (A7)
                for (unsigned i=0; i<DIM; i++)
                {
                    PetscMatTools::AddToElement(r_matrix, DIM*neighbour_node_index+i, DIM*neighbour_node_index+i, -damping_const*Aij);
                    PetscMatTools::AddToElement(r_matrix, DIM*node_index+i, DIM*node_index+i, damping_const*Aij);
                }
            }
        }

        // This is the standard contribution (i.e. not in the sum) in (A7)
        for (unsigned i=0; i<DIM; i++)
        {
            PetscMatTools::AddToElement(r_matrix, DIM*node_index+i, DIM*node_index+i, damping_const);
        }

        // Add current positions to initial_conditions and RHS vector

        // Note that we define these vectors before setting them as otherwise the profiling build will break (see #2367)
        c_vector<double, DIM> current_location;
        c_vector<double, DIM> forces;
        current_location = this->GetNode(global_node_index)->rGetLocation();
        forces = this->GetNode(global_node_index)->rGetAppliedForce();

        for (unsigned i=0; i<DIM; i++)
        {
            PetscVecTools::SetElement(initial_condition, DIM*node_index+i, current_location(i));
            PetscVecTools::SetElement(r_vector, DIM*node_index+i, forces(i));
        }
    }
    PetscMatTools::Finalise(r_matrix);

    solver.SetInitialConditionVector(initial_condition);

    // Solve to get solution at next timestep
    Vec soln_next_timestep = solver.SolveOneTimeStep();

    ReplicatableVector soln_next_timestep_repl(soln_next_timestep);

    // Iterate over all nodes associated with real cells to update the node locations
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get index of node associated with cell
        unsigned global_node_index = this->GetLocationIndexUsingCell((*cell_iter));

        unsigned node_index = this->rGetMesh().SolveNodeMapping(global_node_index);

        c_vector<double, DIM> new_node_location;

        // Get new node location
        for (unsigned i=0; i<DIM; i++)
        {
            new_node_location(i) = soln_next_timestep_repl[DIM*node_index+i];
        }

        // Create ChastePoint for new node location
        ChastePoint<DIM> new_point(new_node_location);

        // Move the node
        this->SetNode(global_node_index, new_point);
    }

    // Tidy up
    PetscTools::Destroy(initial_condition);
}

template<unsigned DIM>
void NodeBasedCellPopulationWithBuskeUpdate<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    // Currently no specific parameters to output all come from parent classes

    // Call method on direct parent class
    NodeBasedCellPopulation<DIM>::OutputCellPopulationParameters(rParamsFile);
}

// Explicit instantiation

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

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