NodeBasedCellPopulationWithBuskeUpdate.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#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(const std::vector< c_vector<double, DIM> >& rNodeForces, double dt)
{
    // Declare solver and give the size of the system and timestep
    unsigned system_size = rNodeForces.size()*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 node_index = this->mCellLocationMap[(*cell_iter).get()];

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

        // Get the radius of this cell
        double radius_of_cell_i = this->rGetMesh().GetCellRadius(node_index);

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

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

            // Calculate Aij
            double Aij = 0.0;

            // Get the location of this node
            c_vector<double, DIM> node_j_location = this->GetNode(neighbour_node_index)->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 = this->rGetMesh().GetCellRadius(neighbour_node_index);

            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
        c_vector<double, DIM> current_location = this->GetNode(node_index)->rGetLocation();
        c_vector<double, DIM> forces = rNodeForces[node_index];

        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 node_index = this->mCellLocationMap[(*cell_iter).get()];

        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(node_index, new_point);
    }

    // Tidy up
    VecDestroy(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)