ImmersedBoundaryMorseMembraneForce.cpp

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*/
 
#include "ImmersedBoundaryMorseMembraneForce.hpp"
 
template <unsigned DIM>
ImmersedBoundaryMorseMembraneForce<DIM>::ImmersedBoundaryMorseMembraneForce()
    : AbstractImmersedBoundaryForce<DIM>(),
      mElementWellDepth(1e6),
      mElementRestLength(0.5),
      mLaminaWellDepth(1e6),
      mLaminaRestLength(0.5),
      mWellWidth(0.25)
{
}
 
template <unsigned DIM>
ImmersedBoundaryMorseMembraneForce<DIM>::~ImmersedBoundaryMorseMembraneForce()
{
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::AddImmersedBoundaryForceContribution(
    std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs,
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation)
{
    // Data common across the entire cell population
    double intrinsic_spacing_squared = rCellPopulation.GetIntrinsicSpacing() * rCellPopulation.GetIntrinsicSpacing();
 
    // Loop over all elements ( <DIM, DIM> )
    for (auto elem_it = rCellPopulation.rGetMesh().GetElementIteratorBegin();
         elem_it != rCellPopulation.rGetMesh().GetElementIteratorEnd();
         ++elem_it)
    {
        CalculateForcesOnElement(*elem_it, rCellPopulation, intrinsic_spacing_squared);
    }
 
    // Loop over all laminas ( <DIM-1, DIM> )
    for (auto lam_it = rCellPopulation.rGetMesh().GetLaminaIteratorBegin();
         lam_it != rCellPopulation.rGetMesh().GetLaminaIteratorEnd();
         ++lam_it)
    {
        CalculateForcesOnElement(*lam_it, rCellPopulation, intrinsic_spacing_squared);
    }
 
    if (this->mAdditiveNormalNoise)
    {
        this->AddNormalNoiseToNodes(rCellPopulation);
    }
}
 
template <unsigned DIM>
template <unsigned ELEMENT_DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::CalculateForcesOnElement(
    ImmersedBoundaryElement<ELEMENT_DIM, DIM>& rElement,
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation,
    double intrinsicSpacingSquared)
{
    // Get index and number of nodes of current element
    unsigned elem_idx = rElement.GetIndex();
    unsigned num_nodes = rElement.GetNumNodes();
 
    // Make a vector to store the force on node i+1 from node i
    std::vector<c_vector<double, DIM> > force_to_next(num_nodes);
 
    /*
     * Get the node spacing ratio for this element. The rest length and spring
     * constant are derived from this characteristic length.
     *
     * The spring constant is derived with reference to the intrinsic spacing,
     * so that with different node spacings the user-defined parameters do not
     * have to be updated.
     *
     * The correct factor to increase the spring constant by is (intrinsic
     * spacing / node_spacing)^2. One factor takes into account the energy
     * considerations of the elastic springs, and the other takes account of the
     * factor of node_spacing used in discretising the force relation.
     */
    double node_spacing = 0.0;
    double well_depth = 0.0;
    double rest_length = 0.0;
    double well_width = mWellWidth;
 
    // Determine if we're in a lamina or not
    if (ELEMENT_DIM < DIM)
    {
        node_spacing = rCellPopulation.rGetMesh().GetAverageNodeSpacingOfLamina(elem_idx, false);
 
        well_depth = mLaminaWellDepth * intrinsicSpacingSquared / (node_spacing * node_spacing);
        rest_length = mLaminaRestLength * node_spacing;
        well_width *= node_spacing;
    }
    else // regular element
    {
        node_spacing = rCellPopulation.rGetMesh().GetAverageNodeSpacingOfElement(elem_idx, false);
 
        well_depth = mElementWellDepth * intrinsicSpacingSquared / (node_spacing * node_spacing);
        rest_length = mElementRestLength * node_spacing;
        well_width *= node_spacing;
    }
 
    // Loop over nodes and calculate the force exerted on node i+1 by node i
    for (unsigned node_idx = 0; node_idx < num_nodes; node_idx++)
    {
        // Index of the next node, calculated modulo number of nodes in this element
        unsigned next_idx = (node_idx + 1) % num_nodes;
 
        // Morse force (derivative of Morse potential wrt distance between nodes
        force_to_next[node_idx] = rCellPopulation.rGetMesh().GetVectorFromAtoB(rElement.GetNodeLocation(node_idx),
                                                                               rElement.GetNodeLocation(next_idx));
        double normed_dist = norm_2(force_to_next[node_idx]);
 
        double morse_exp = exp((rest_length - normed_dist) / well_width);
        force_to_next[node_idx] *= 2.0 * well_width * well_depth * morse_exp * (1.0 - morse_exp) / normed_dist;
    }
 
    // Add the contributions of springs adjacent to each node
    for (unsigned node_idx = 0; node_idx < num_nodes; node_idx++)
    {
        // Get index of previous node
        unsigned prev_idx = (node_idx + num_nodes - 1) % num_nodes;
 
        c_vector<double, DIM> aggregate_force = force_to_next[node_idx] - force_to_next[prev_idx];
 
        // Add the aggregate force contribution to the node
        rElement.GetNode(node_idx)->AddAppliedForceContribution(aggregate_force);
    }
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::OutputImmersedBoundaryForceParameters(
    out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<ElementWellDepth>" << mElementWellDepth << "</ElementWellDepth>\n";
    *rParamsFile << "\t\t\t<ElementRestLength>" << mElementRestLength << "</ElementRestLength>\n";
    *rParamsFile << "\t\t\t<LaminaWellDepth>" << mLaminaWellDepth << "</LaminaWellDepth>\n";
    *rParamsFile << "\t\t\t<LaminaRestLength>" << mLaminaRestLength << "</LaminaRestLength>\n";
    *rParamsFile << "\t\t\t<WellWidth>" << mWellWidth << "</WellWidth>\n";
 
    // Call method on direct parent class
    AbstractImmersedBoundaryForce<DIM>::OutputImmersedBoundaryForceParameters(rParamsFile);
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseMembraneForce<DIM>::GetElementWellDepth() const
{
    return mElementWellDepth;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::SetElementWellDepth(
    double elementWellDepth)
{
    mElementWellDepth = elementWellDepth;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseMembraneForce<DIM>::GetElementRestLength() const
{
    return mElementRestLength;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::SetElementRestLength(
    double elementRestLength)
{
    mElementRestLength = elementRestLength;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseMembraneForce<DIM>::GetLaminaWellDepth() const
{
    return mLaminaWellDepth;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::SetLaminaWellDepth(
    double laminaWellDepth)
{
    mLaminaWellDepth = laminaWellDepth;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseMembraneForce<DIM>::GetLaminaRestLength() const
{
    return mLaminaRestLength;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::SetLaminaRestLength(
    double laminaRestLength)
{
    mLaminaRestLength = laminaRestLength;
}
 
template <unsigned DIM>
double ImmersedBoundaryMorseMembraneForce<DIM>::GetWellWidth() const
{
    return mWellWidth;
}
 
template <unsigned DIM>
void ImmersedBoundaryMorseMembraneForce<DIM>::SetWellWidth(double wellWidth)
{
    mWellWidth = wellWidth;
}
 
// Explicit instantiation
template class ImmersedBoundaryMorseMembraneForce<1>;
template class ImmersedBoundaryMorseMembraneForce<2>;
template class ImmersedBoundaryMorseMembraneForce<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundaryMorseMembraneForce)