BuskeAdhesiveForce.cpp

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#include "BuskeAdhesiveForce.hpp"
#include "IsNan.hpp"

template<unsigned DIM>
BuskeAdhesiveForce<DIM>::BuskeAdhesiveForce()
   : AbstractTwoBodyInteractionForce<DIM>(),
     mAdhesionEnergyParameter(0.2)        // Denoted by epsilon in Buske et al (2011) (doi:10.1371/journal.pcbi.1001045).
{
}

template<unsigned DIM>
double BuskeAdhesiveForce<DIM>::GetAdhesionEnergyParameter()
{
    return mAdhesionEnergyParameter;
}

template<unsigned DIM>
void BuskeAdhesiveForce<DIM>::SetAdhesionEnergyParameter(double adhesionEnergyParameter)
{
    mAdhesionEnergyParameter = adhesionEnergyParameter;
}

template<unsigned DIM>
c_vector<double, DIM> BuskeAdhesiveForce<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);

    Node<DIM>* p_node_a = rCellPopulation.GetNode(nodeAGlobalIndex);
    Node<DIM>* p_node_b = rCellPopulation.GetNode(nodeBGlobalIndex);

    // Get the node locations
    c_vector<double, DIM> node_a_location = p_node_a->rGetLocation();
    c_vector<double, DIM> node_b_location = p_node_b->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;

    double radius_of_cell_one = p_node_a->GetRadius();
    double radius_of_cell_two = p_node_b->GetRadius();

    // 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 BuskeAdhesiveForce<DIM>::GetMagnitudeOfForce(double distanceBetweenNodes, double radiusOfCellOne, double radiusOfCellTwo)
{
    double dWAdd = 0.0;

    // If the cells are close enough...
    if (distanceBetweenNodes < radiusOfCellOne + radiusOfCellTwo)
    {
        // ...calculate the force contribution from their adhesive interaction energy
        double xij = 0.5*(radiusOfCellOne*radiusOfCellOne - radiusOfCellTwo*radiusOfCellTwo + distanceBetweenNodes*distanceBetweenNodes)/distanceBetweenNodes;
        double dxijdd = 1.0 - xij/distanceBetweenNodes;
        dWAdd = 2.0*mAdhesionEnergyParameter*M_PI*xij*dxijdd;
    }

    return dWAdd;
}

template<unsigned DIM>
void BuskeAdhesiveForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<AdhesionEnergyParameter>" << mAdhesionEnergyParameter << "</AdhesionEnergyParameter>\n";

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

// Explicit instantiation
template class BuskeAdhesiveForce<1>;
template class BuskeAdhesiveForce<2>;
template class BuskeAdhesiveForce<3>;

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