DiffusionForce.cpp

/*

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*/

#include "DiffusionForce.hpp"
#include "NodeBasedCellPopulation.hpp"

template<unsigned DIM>
DiffusionForce<DIM>::DiffusionForce()
    : AbstractForce<DIM>(),
      mDiffusionConstant(0.01),
      mAbsoluteTemperature(296.0), // default to room temperature
      mViscosity(3.204e-6), // default to viscosity of water at room temperature in (using microns and hours)
      mMechanicsCutOffLength(10.0)
{
}

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

template<unsigned DIM>
void DiffusionForce<DIM>::SetCutOffLength(double cutOffLength)
{
    assert(cutOffLength > 0.0);
    mMechanicsCutOffLength=cutOffLength;
}


template<unsigned DIM>
double DiffusionForce<DIM>::GetCutOffLength()
{
    return mMechanicsCutOffLength;
}

template<unsigned DIM>
void DiffusionForce<DIM>::SetDiffusionConstant(double diffusionConstant)
{
    assert(diffusionConstant > 0.0);
    mDiffusionConstant = diffusionConstant;
}

template<unsigned DIM>
double DiffusionForce<DIM>::GetDiffusionConstant()
{
    return mDiffusionConstant;
}

template<unsigned DIM>
void DiffusionForce<DIM>::SetAbsoluteTemperature(double newValue)
{
    assert(newValue > 0.0);
    mAbsoluteTemperature = newValue;
}

template<unsigned DIM>
double DiffusionForce<DIM>::GetAbsoluteTemperature()
{
    return mAbsoluteTemperature;
}

template<unsigned DIM>
void DiffusionForce<DIM>::SetViscosity(double newValue)
{
    assert(newValue > 0.0);
    mViscosity = newValue;
}

template<unsigned DIM>
double DiffusionForce<DIM>::GetViscosity()
{
    return mViscosity;
}

template<unsigned DIM>
void DiffusionForce<DIM>::AddForceContribution(std::vector<c_vector<double, DIM> >& rForces,
                          AbstractCellPopulation<DIM>& rCellPopulation)
{
    double dt = SimulationTime::Instance()->GetTimeStep();

    // Loop over the cells
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // Get the radius, damping constant and node index associated with this cell
        unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
        double nu = dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(&rCellPopulation)->GetDampingConstant(node_index);
        double cell_radius = dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation)->rGetMesh().GetCellRadius(node_index);

        /*
         * Compute the diffusion coefficient D as D = k*T/(6*pi*eta*r), where
         *
         * k = Boltzmann's constant,
         * T = absolute temperature,
         * eta = dynamic viscosity,
         * r = cell radius.
         */
        double boltzmann_constant = 1.3806488e-23;
        double diffusion_const_scaling = boltzmann_constant*mAbsoluteTemperature/(6.0*mViscosity*M_PI);
        double diffusion_constant = diffusion_const_scaling/cell_radius;

        c_vector<double, DIM> force_contribution;
        for (unsigned i=0; i<DIM; i++)
        {
            /*
             * The force on this cell is scaled with the timestep such that when it is
             * used in the discretised equation of motion for the cell, we obtain the
             * correct formula
             *
             * x_new = x_old + sqrt(2*D*dt)*W
             *
             * where W is a standard normal random variable.
             */
            double xi = RandomNumberGenerator::Instance()->StandardNormalRandomDeviate();

            force_contribution[i] = (nu*sqrt(2.0*diffusion_constant*dt)/dt)*xi;
        }
        rForces[node_index] += force_contribution;
    }
}

template<unsigned DIM>
void DiffusionForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<DiffusionConstant>" << mDiffusionConstant << "</DiffusionConstant> \n";
    *rParamsFile << "\t\t\t<MechanicsCutOffLength>" << mMechanicsCutOffLength << "</MechanicsCutOffLength> \n";

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

// Explicit instantiation

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

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