DiffusionForce.cpp

/*

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*/

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

//Static constant is instantiated here.
template<unsigned DIM>
const double DiffusionForce<DIM>::msBoltzmannConstant = 4.97033568e-7;

template<unsigned DIM>
DiffusionForce<DIM>::DiffusionForce()
    : AbstractForce<DIM>(),
      mAbsoluteTemperature(296.0), // default to room temperature
      mViscosity(3.204e-6) // default to viscosity of water at room temperature in (using 10 microns and hours)
{
}

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

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>
double DiffusionForce<DIM>::GetDiffusionScalingConstant()
{
    return msBoltzmannConstant*mAbsoluteTemperature/(6.0*mViscosity*M_PI);
}

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

    // Iterate over the nodes
    for (typename AbstractMesh<DIM, DIM>::NodeIterator node_iter = rCellPopulation.rGetMesh().GetNodeIteratorBegin();
         node_iter != rCellPopulation.rGetMesh().GetNodeIteratorEnd();
         ++node_iter)
    {
        // Get the index, radius and damping constant of this node
        unsigned node_index = node_iter->GetIndex();
        double node_radius = node_iter->GetRadius();

        // If the node radius is zero, then it has not been set...
        if (node_radius == 0.0)
        {
            // ...so throw an exception to avoid dividing by zero when we compute diffusion_constant below
            EXCEPTION("SetRadius() must be called on each Node before calling DiffusionForce::AddForceContribution() to avoid a division by zero error");
        }

        double nu = dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(&rCellPopulation)->GetDampingConstant(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 diffusion_const_scaling = GetDiffusionScalingConstant();
        double diffusion_constant = diffusion_const_scaling/node_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;
        }
        node_iter->AddAppliedForceContribution(force_contribution);
    }
}

template<unsigned DIM>
void DiffusionForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<AbsoluteTemperature>" << mAbsoluteTemperature << "</AbsoluteTemperature> \n";
    *rParamsFile << "\t\t\t<Viscosity>" << mViscosity << "</Viscosity> \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)