ImmersedBoundaryMorseInteractionForce.cpp

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*/
 
#include "ImmersedBoundaryMorseInteractionForce.hpp"
#include "ImmersedBoundaryEnumerations.hpp"
 
template <unsigned DIM>
ImmersedBoundaryMorseInteractionForce<DIM>::ImmersedBoundaryMorseInteractionForce()
    : AbstractImmersedBoundaryForce<DIM>(),
      mWellDepth(1e3),
      mRestLength(0.25),
      mLaminaWellDepthMult(1.0),
      mLaminaRestLengthMult(1.0),
      mWellWidth(0.25)
{
}
 
template <unsigned DIM>
ImmersedBoundaryMorseInteractionForce<DIM>::~ImmersedBoundaryMorseInteractionForce()
{
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::AddImmersedBoundaryForceContribution(
    std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs,
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation)
{
    for (unsigned pair = 0; pair < rNodePairs.size(); ++pair)
    {
        // Interactions only exist between pairs of nodes that are not in the same boundary / lamina
        if (rCellPopulation.rGetMesh().NodesInDifferentElementOrLamina(rNodePairs[pair].first, rNodePairs[pair].second))
        {
            Node<DIM>* p_node_a = rNodePairs[pair].first;
            Node<DIM>* p_node_b = rNodePairs[pair].second;
 
            c_vector<double, DIM> vec_a2b = rCellPopulation.rGetMesh().GetVectorFromAtoB(p_node_a->rGetLocation(),
                                                                                         p_node_b->rGetLocation());
            double normed_dist = norm_2(vec_a2b);
 
            // Force non-zero only within interaction distance, by definition
            if (normed_dist < rCellPopulation.GetInteractionDistance())
            {
                // Need the average spacing of the containing element; this depends on whether it's a lamina or element
                bool a_lamina = p_node_a->GetRegion() == LAMINA_REGION;
                bool b_lamina = p_node_b->GetRegion() == LAMINA_REGION;
 
                unsigned a_idx = *(p_node_a->ContainingElementsBegin());
                unsigned b_idx = *(p_node_b->ContainingElementsBegin());
 
                double node_a_elem_spacing = a_lamina ? rCellPopulation.rGetMesh().GetAverageNodeSpacingOfLamina(a_idx, false)
                                                      : rCellPopulation.rGetMesh().GetAverageNodeSpacingOfElement(a_idx, false);
 
                double node_b_elem_spacing = b_lamina ? rCellPopulation.rGetMesh().GetAverageNodeSpacingOfLamina(b_idx, false)
                                                      : rCellPopulation.rGetMesh().GetAverageNodeSpacingOfElement(b_idx, false);
 
                double elem_spacing = 0.5 * (node_a_elem_spacing + node_b_elem_spacing);
 
                double eff_well_depth = mWellDepth * elem_spacing / rCellPopulation.GetIntrinsicSpacing();
                double eff_rest_length = mRestLength * rCellPopulation.GetInteractionDistance();
                double eff_well_width = mWellWidth * rCellPopulation.GetInteractionDistance();
 
                if (a_lamina || b_lamina)
                {
                    eff_well_depth *= mLaminaWellDepthMult;
                    eff_rest_length *= mLaminaRestLengthMult;
 
                    // Bit of a hack
                    bool apical_lam = (a_lamina && p_node_a->rGetLocation()[1] > 0.5) ||
                                      (b_lamina && p_node_b->rGetLocation()[1] > 0.5);
 
                    if (apical_lam)
                    {
                        eff_well_depth *= 1.0;
                    }
                }
 
                double morse_exp = exp((eff_rest_length - normed_dist) / eff_well_width);
 
                /*
                 * We must scale each applied force by a factor of elem_spacing / local spacing, so that forces
                 * balance when spread to the grid later (where the multiplicative factor is the local spacing)
                 */
                vec_a2b *= 2.0 * eff_well_width * eff_well_depth * morse_exp * (1.0 - morse_exp) / normed_dist;
 
                c_vector<double, DIM> force_a2b = vec_a2b * (elem_spacing / node_a_elem_spacing);
                p_node_a->AddAppliedForceContribution(force_a2b);
 
                c_vector<double, DIM> force_b2a = vec_a2b * (-1.0 * elem_spacing / node_b_elem_spacing);
                p_node_b->AddAppliedForceContribution(force_b2a);
            }
        }
    }
 
    if (this->mAdditiveNormalNoise)
    {
        this->AddNormalNoiseToNodes(rCellPopulation);
    }
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::OutputImmersedBoundaryForceParameters(
    out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<WellDepth>" << mWellDepth << "</WellDepth>\n";
    *rParamsFile << "\t\t\t<RestLength>" << mRestLength << "</RestLength>\n";
    *rParamsFile << "\t\t\t<LaminaWellDepthMult>" << mLaminaWellDepthMult << "</LaminaWellDepthMult>\n";
    *rParamsFile << "\t\t\t<LaminaRestLengthMult>" << mLaminaRestLengthMult << "</LaminaRestLengthMult>\n";
    *rParamsFile << "\t\t\t<WellWidth>" << mWellWidth << "</WellWidth>\n";
 
    // Call method on direct parent class
    AbstractImmersedBoundaryForce<DIM>::OutputImmersedBoundaryForceParameters(rParamsFile);
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseInteractionForce<DIM>::GetWellDepth() const
{
    return mWellDepth;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::SetWellDepth(double wellDepth)
{
    mWellDepth = wellDepth;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseInteractionForce<DIM>::GetRestLength() const
{
    return mRestLength;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::SetRestLength(double restLength)
{
    mRestLength = restLength;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseInteractionForce<DIM>::GetLaminaWellDepthMult() const
{
    return mLaminaWellDepthMult;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::SetLaminaWellDepthMult(
    double laminaWellDepthMult)
{
    mLaminaWellDepthMult = laminaWellDepthMult;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseInteractionForce<DIM>::GetLaminaRestLengthMult() const
{
    return mLaminaRestLengthMult;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::SetLaminaRestLengthMult(
    double laminaRestLengthMult)
{
    mLaminaRestLengthMult = laminaRestLengthMult;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseInteractionForce<DIM>::GetWellWidth() const
{
    return mWellWidth;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseInteractionForce<DIM>::SetWellWidth(double wellWidth)
{
    mWellWidth = wellWidth;
}
 
// Explicit instantiation
template class ImmersedBoundaryMorseInteractionForce<1>;
template class ImmersedBoundaryMorseInteractionForce<2>;
template class ImmersedBoundaryMorseInteractionForce<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundaryMorseInteractionForce)