BuskeElasticForce.cpp

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#include "BuskeElasticForce.hpp"

template<unsigned DIM>
BuskeElasticForce<DIM>::BuskeElasticForce()
   : AbstractTwoBodyInteractionForce<DIM>(),
     mDeformationEnergyParameter(4.0/(3.0*5.0)) // Denoted by D in Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).
{
}

template<unsigned DIM>
double BuskeElasticForce<DIM>::GetDeformationEnergyParameter()
{
    return mDeformationEnergyParameter;
}

template<unsigned DIM>
void BuskeElasticForce<DIM>::SetDeformationEnergyParameter(double deformationEnergyParameter)
{
    mDeformationEnergyParameter = deformationEnergyParameter;
}

template<unsigned DIM>
c_vector<double, DIM> BuskeElasticForce<DIM>::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex,
                                                                             unsigned nodeBGlobalIndex,
                                                                             AbstractCellPopulation<DIM>& rCellPopulation)
{
    // This force class is defined for NodeBasedCellPopulations only
    assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != NULL);

    // We should only ever calculate the force between two distinct nodes
    assert(nodeAGlobalIndex != nodeBGlobalIndex);

    // Get the node locations
    c_vector<double, DIM> node_a_location = rCellPopulation.GetNode(nodeAGlobalIndex)->rGetLocation();
    c_vector<double, DIM> node_b_location = rCellPopulation.GetNode(nodeBGlobalIndex)->rGetLocation();

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

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

    // Account for any cutoff in the force law
    if (this->mUseCutOffLength)
    {
        if (distance_between_nodes >= this->GetCutOffLength())
        {
            return zero_vector<double>(DIM);
        }
    }

    // Assert that the nodes are a finite, non-zero distance apart
    assert(distance_between_nodes > 0);
    assert(!std::isnan(distance_between_nodes));

    // Normalize the unit vector
    unit_vector /= distance_between_nodes;

    // Get the cell radii
    NodesOnlyMesh<DIM>& r_mesh = static_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation)->rGetMesh();
    double radius_of_cell_one = r_mesh.GetCellRadius(nodeAGlobalIndex);
    double radius_of_cell_two = r_mesh.GetCellRadius(nodeBGlobalIndex);

    // Compute the force vector
    c_vector<double, DIM> force_between_nodes = GetMagnitudeOfForce(distance_between_nodes,radius_of_cell_one,radius_of_cell_two) * unit_vector;

    return force_between_nodes;
}

template<unsigned DIM>
double BuskeElasticForce<DIM>::GetMagnitudeOfForce(double distanceBetweenNodes, double radiusOfCellOne, double radiusOfCellTwo)
{
    // Calculate contribution from deformation interaction energy
    double dWDdd;

    if (distanceBetweenNodes < radiusOfCellOne + radiusOfCellTwo)
    {
        dWDdd = -pow(radiusOfCellOne + radiusOfCellTwo - distanceBetweenNodes,1.5)
                *pow(radiusOfCellOne*radiusOfCellTwo/(radiusOfCellOne+radiusOfCellTwo),0.5)
                /mDeformationEnergyParameter;
    }
    else  // no deformation energy contribution as too far apart
    {
        dWDdd = 0.0;
    }

    return dWDdd; //
}

template<unsigned DIM>
void BuskeElasticForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<DeformationEnergyParameter>" << mDeformationEnergyParameter << "</DeformationEnergyParameter>\n";

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

// Explicit instantiation

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

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