AbstractImmersedBoundaryForce.cpp

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*/
 
#include <random>
 
#include "AbstractImmersedBoundaryForce.hpp"
 
template <unsigned DIM>
AbstractImmersedBoundaryForce<DIM>::AbstractImmersedBoundaryForce()
    : mAdditiveNormalNoise(false),
      mNormalNoiseMean(1.0),
      mNormalNoiseStdDev(0.0)
{
}
 
template<unsigned DIM>
AbstractImmersedBoundaryForce<DIM>::~AbstractImmersedBoundaryForce()
{
}
 
template<unsigned DIM>
void AbstractImmersedBoundaryForce<DIM>::AddNormalNoiseToNodes(
    ImmersedBoundaryCellPopulation<DIM>& rCellPopulation)
{
    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
 
    // Add random forces to elements
    for (unsigned elem_idx = 0; elem_idx < rCellPopulation.GetNumElements(); ++elem_idx)
    {
        unsigned num_nodes_this_elem = rCellPopulation.GetElement(elem_idx)->GetNumNodes();
 
        // Generate a vector with 0, 1, 2, ..., num_nodes-1
        std::vector<unsigned> random_node_order;
        random_node_order.reserve(num_nodes_this_elem);
        for (unsigned node_idx = 0; node_idx < num_nodes_this_elem; ++node_idx)
        {
            random_node_order.push_back(node_idx);
        }
 
        // Shuffle the vector
        std::shuffle(random_node_order.begin(), random_node_order.end(), std::mt19937(std::random_device()()));
 
        // Only go to half way (rounded down - forget about the very last node for now)
        unsigned half_way = num_nodes_this_elem / 2;
        for (unsigned i = 0; i < half_way; ++i)
        {
            unsigned rand_node_a = random_node_order[2 * i];
            unsigned rand_node_b = random_node_order[2 * i + 1];
 
            c_vector<double, DIM> random_force;
            for (unsigned dim = 0; dim < DIM; ++dim)
            {
                random_force[dim] = p_gen->NormalRandomDeviate(mNormalNoiseMean, mNormalNoiseStdDev);
            }
 
            Node<DIM>* p_node_a = rCellPopulation.GetElement(elem_idx)->GetNode(rand_node_a);
            Node<DIM>* p_node_b = rCellPopulation.GetElement(elem_idx)->GetNode(rand_node_b);
 
            double avg_magnitude = 0.5 * (norm_2(p_node_a->rGetAppliedForce()) +
                                          norm_2(p_node_b->rGetAppliedForce()));
 
            random_force *= avg_magnitude;
            p_node_a->AddAppliedForceContribution(random_force);
 
            random_force *= -1.0;
            p_node_b->AddAppliedForceContribution(random_force);
        }
    }
 
    // Do the same for laminas
    for (unsigned lam_idx = 0; lam_idx < rCellPopulation.GetNumLaminas(); ++lam_idx)
    {
        unsigned num_nodes_this_elem = rCellPopulation.GetLamina(lam_idx)->GetNumNodes();
 
        // Generate a vector with 0, 1, 2, ..., num_nodes-1
        std::vector<unsigned> random_node_order;
        random_node_order.reserve(num_nodes_this_elem);
        for (unsigned node_idx = 0; node_idx < num_nodes_this_elem; ++node_idx)
        {
            random_node_order.push_back(node_idx);
        }
 
        // Shuffle the vector
        std::shuffle(random_node_order.begin(), random_node_order.end(), std::mt19937(std::random_device()()));
 
        // Only go to half way (rounded down - forget about the very last node for now)
        unsigned half_way = num_nodes_this_elem / 2;
        for (unsigned i = 0; i < half_way; ++i)
        {
            unsigned rand_node_a = random_node_order[2 * i];
            unsigned rand_node_b = random_node_order[2 * i + 1];
 
            c_vector<double, DIM> random_force;
            for (unsigned dim = 0; dim < DIM; ++dim)
            {
                random_force[dim] = p_gen->NormalRandomDeviate(mNormalNoiseMean, mNormalNoiseStdDev);
            }
 
            Node<DIM>* p_node_a = rCellPopulation.GetLamina(lam_idx)->GetNode(rand_node_a);
            Node<DIM>* p_node_b = rCellPopulation.GetLamina(lam_idx)->GetNode(rand_node_b);
 
            double avg_magnitude = 0.5 * (norm_2(p_node_a->rGetAppliedForce()) +
                                          norm_2(p_node_b->rGetAppliedForce()));
 
            random_force *= avg_magnitude;
            p_node_a->AddAppliedForceContribution(random_force);
 
            random_force *= -1.0;
            p_node_b->AddAppliedForceContribution(random_force);
        }
    }
}
 
template <unsigned DIM>
bool AbstractImmersedBoundaryForce<DIM>::GetAdditiveNormalNoise() const
{
    return mAdditiveNormalNoise;
}
 
template <unsigned DIM>
void AbstractImmersedBoundaryForce<DIM>::SetAdditiveNormalNoise(
    bool additiveNormalNoise)
{
    mAdditiveNormalNoise = additiveNormalNoise;
}
 
template <unsigned DIM>
double AbstractImmersedBoundaryForce<DIM>::GetNormalNoiseMean() const
{
    return mNormalNoiseMean;
}
 
template <unsigned DIM>
void AbstractImmersedBoundaryForce<DIM>::SetNormalNoiseMean(
    double normalNoiseMean)
{
    mNormalNoiseMean = normalNoiseMean;
}
 
template <unsigned DIM>
double AbstractImmersedBoundaryForce<DIM>::GetNormalNoiseStdDev() const
{
    return mNormalNoiseStdDev;
}
 
template <unsigned DIM>
void AbstractImmersedBoundaryForce<DIM>::SetNormalNoiseStdDev(
    double normalNoiseStdDev)
{
    mNormalNoiseStdDev = normalNoiseStdDev;
}
 
template<unsigned DIM>
void AbstractImmersedBoundaryForce<DIM>::OutputImmersedBoundaryForceParameters(
    out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<AdditiveNormalNoise>" << mAdditiveNormalNoise << "</AdditiveNormalNoise>\n";
    *rParamsFile << "\t\t\t<NormalNoiseMean>" << mNormalNoiseMean << "</NormalNoiseMean>\n";
    *rParamsFile << "\t\t\t<NormalNoiseStdDev>" << mNormalNoiseStdDev << "</NormalNoiseStdDev>\n";
}
 
// Explicit instantiation
template class AbstractImmersedBoundaryForce<1>;
template class AbstractImmersedBoundaryForce<2>;
template class AbstractImmersedBoundaryForce<3>;