ChemotacticForce.cpp

/*

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*/

#include "ChemotacticForce.hpp"
#include "CellwiseDataGradient.hpp"

template<unsigned DIM>
ChemotacticForce<DIM>::ChemotacticForce()
    : AbstractForce<DIM>()
{
}

template<unsigned DIM>
ChemotacticForce<DIM>::~ChemotacticForce()
{
}

template<unsigned DIM>
double ChemotacticForce<DIM>::GetChemotacticForceMagnitude(const double concentration, const double concentrationGradientMagnitude)
{
    return concentration; // temporary force law - can be changed to something realistic
                          // without tests failing
}

template<unsigned DIM>
void ChemotacticForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
    CellwiseDataGradient<DIM> gradients;
    gradients.SetupGradients(rCellPopulation, "nutrient");

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // Only labelled cells move chemotactically
        if (cell_iter->template HasCellProperty<CellLabel>())
        {
            unsigned node_global_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);

            c_vector<double,DIM>& r_gradient = gradients.rGetGradient(node_global_index);
            double nutrient_concentration = cell_iter->GetCellData()->GetItem("nutrient");
            double magnitude_of_gradient = norm_2(r_gradient);

            double force_magnitude = GetChemotacticForceMagnitude(nutrient_concentration, magnitude_of_gradient);

            // force += chi * gradC/|gradC|
            if (magnitude_of_gradient > 0)
            {
                c_vector<double,DIM> force = (force_magnitude/magnitude_of_gradient)*r_gradient;
                rCellPopulation.GetNode(node_global_index)->AddAppliedForceContribution(force);
            }
            // else Fc=0
        }
    }
}

template<unsigned DIM>
void ChemotacticForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    // No parameters to include

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

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

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