ImmersedBoundaryKinematicFeedbackForce.cpp

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*/
 
#include "ImmersedBoundaryKinematicFeedbackForce.hpp"
#include "ImmersedBoundaryEnumerations.hpp"
#include "UblasCustomFunctions.hpp"
 
template <unsigned DIM>
ImmersedBoundaryKinematicFeedbackForce<DIM>::ImmersedBoundaryKinematicFeedbackForce()
    : AbstractImmersedBoundaryForce<DIM>(),
      mSpringConst(1e3),
      mPreviousLocations()
{
}
 
template <unsigned DIM>
void ImmersedBoundaryKinematicFeedbackForce<DIM>::AddImmersedBoundaryForceContribution(
    std::vector<std::pair<Node<DIM>*, Node<DIM>*> >& rNodePairs,
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation)
{
    // Update memory allocation if number of nodes has changed/on first call
    if (mPreviousLocations.size() != rCellPopulation.GetNumNodes())
    {
        mPreviousLocations.resize(rCellPopulation.GetNumNodes());
        UpdatePreviousLocations(rCellPopulation);
    }
 
    /*
     * Calculate force only if neither node is in a lamina, and if nodes are in
     * different elements.
     */
    auto condition_satisfied = [&rCellPopulation](const std::pair<Node<DIM>*, Node<DIM>*>& pair) -> bool
    {
        // Laminas do not participate in this force class
        if (pair.first->GetRegion() == LAMINA_REGION || pair.second->GetRegion() == LAMINA_REGION)
        {
            return false;
        }
        // This force only acts on nodes in different elements
        if (*(pair.first->ContainingElementsBegin()) == *(pair.second->ContainingElementsBegin()))
        {
            return false;
        }
        // Return true if the nodes are within threshold distance, else false
        auto vec_a2b = rCellPopulation.rGetMesh().GetVectorFromAtoB(pair.first->rGetLocation(), pair.second->rGetLocation());
        return norm_2(vec_a2b) < rCellPopulation.GetInteractionDistance();
    };
 
    for (auto&& pair : rNodePairs)
    {
        if (condition_satisfied(pair))
        {
            Node<DIM>* p_node_a = pair.first;
            Node<DIM>* p_node_b = pair.second;
 
            // Get the current and previous displacement between nodes
            auto previous_disp = rCellPopulation.rGetMesh().GetVectorFromAtoB(mPreviousLocations[p_node_a->GetIndex()],
                                                                              mPreviousLocations[p_node_b->GetIndex()]);
            auto current_disp = rCellPopulation.rGetMesh().GetVectorFromAtoB(p_node_a->rGetLocation(),
                                                                             p_node_b->rGetLocation());
 
            // Calculate the relative velocity and fill in unit_perp, the direction of the force that will act
            c_vector<double, DIM> unit_perp;
            double relative_vel_comp = CalculateRelativeVelocityComponent(previous_disp, current_disp, unit_perp);
 
            unsigned a_idx = *(p_node_a->ContainingElementsBegin());
            unsigned b_idx = *(p_node_b->ContainingElementsBegin());
 
            double node_a_elem_spacing = rCellPopulation.rGetMesh().GetAverageNodeSpacingOfElement(a_idx, false);
            double node_b_elem_spacing = rCellPopulation.rGetMesh().GetAverageNodeSpacingOfElement(b_idx, false);
 
            double elem_spacing = 0.5 * (node_a_elem_spacing + node_b_elem_spacing);
 
            double eff_spring_const = mSpringConst * elem_spacing / rCellPopulation.GetIntrinsicSpacing();
 
            /*
             * 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)
             */
            // df = K dx
            c_vector<double, DIM> force = unit_perp * (relative_vel_comp * eff_spring_const);
 
            c_vector<double, DIM> force_on_b = force * (elem_spacing / node_a_elem_spacing);
            p_node_b->AddAppliedForceContribution(force_on_b);
 
            c_vector<double, DIM> force_on_a = force * (-1.0 * elem_spacing / node_b_elem_spacing);
            p_node_a->AddAppliedForceContribution(force_on_a);
        }
    }
 
    UpdatePreviousLocations(rCellPopulation);
 
    if (this->mAdditiveNormalNoise)
    {
        this->AddNormalNoiseToNodes(rCellPopulation);
    }
}
 
template <unsigned DIM>
double ImmersedBoundaryKinematicFeedbackForce<DIM>::CalculateRelativeVelocityComponent(
    const c_vector<double, DIM>& rPreviousDisp,
    const c_vector<double, DIM>& rCurrentDisp,
    c_vector<double, DIM>& rUnitPerp)
{
    // Get a unit vector perpendicular to the line joining the nodes at the previous time step
    rUnitPerp = Create_c_vector(-rPreviousDisp[1], rPreviousDisp[0]);
    rUnitPerp /= norm_2(rUnitPerp);
 
    // Calculate the relative velocity component in the direction of the perpendicular
    return inner_prod(rCurrentDisp / SimulationTime::Instance()->GetTimeStep(), rUnitPerp);
}
 
template<unsigned DIM>
void ImmersedBoundaryKinematicFeedbackForce<DIM>::UpdatePreviousLocations(
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation)
{
    /*
     * Populate the mPreviousLocations vector with the current location of
     * nodes, so it's ready for next time step.
     */
    for (const auto& p_node : rCellPopulation.rGetMesh().rGetNodes())
    {
        if (p_node->GetRegion() != LAMINA_REGION)
        {
            if (p_node->GetIndex() >= mPreviousLocations.size())
            {
                mPreviousLocations.resize(p_node->GetIndex() + 1);
            }
 
            mPreviousLocations[p_node->GetIndex()] = p_node->rGetLocation();
        }
    }
}
 
template<unsigned DIM>
void ImmersedBoundaryKinematicFeedbackForce<DIM>::OutputImmersedBoundaryForceParameters(
    out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<SpringConstant>" << mSpringConst << "</SpringConstant>\n";
 
    // Call method on direct parent class
    AbstractImmersedBoundaryForce<DIM>::OutputImmersedBoundaryForceParameters(rParamsFile);
}
 
template<unsigned DIM>
double ImmersedBoundaryKinematicFeedbackForce<DIM>::GetSpringConst() const
{
    return mSpringConst;
}
 
template<unsigned DIM>
void ImmersedBoundaryKinematicFeedbackForce<DIM>::SetSpringConst(
    double springConst)
{
    mSpringConst = springConst;
}
 
// Explicit instantiation
template class ImmersedBoundaryKinematicFeedbackForce<1>;
template class ImmersedBoundaryKinematicFeedbackForce<2>;
template class ImmersedBoundaryKinematicFeedbackForce<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundaryKinematicFeedbackForce)