ImmersedBoundaryPalisadeMeshGenerator.cpp

 
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#include "ImmersedBoundaryPalisadeMeshGenerator.hpp"
#include "ImmersedBoundaryEnumerations.hpp"
#include "RandomNumberGenerator.hpp"
 
ImmersedBoundaryPalisadeMeshGenerator::ImmersedBoundaryPalisadeMeshGenerator(unsigned numCellsWide,
                                                                             unsigned numNodesPerCell,
                                                                             double ellipseExponent,
                                                                             double cellAspectRatio,
                                                                             double randomYMult,
                                                                             bool basalLamina,
                                                                             bool apicalLamina,
                                                                             bool leakyLaminas,
                                                                             unsigned numFluidMeshPoints,
                                                                             double absoluteGap)
    : mpMesh(NULL)
{
    // Check for sensible input
    assert(numCellsWide > 0);
    assert(numNodesPerCell > 3);
    assert(ellipseExponent > 0.0);
    assert(cellAspectRatio > 0.0); // aspect ratio is cell height / cell width
    assert(fabs(randomYMult) < 2.0);
    assert( (leakyLaminas && numFluidMeshPoints < UINT_MAX) || (!leakyLaminas) );
 
    // If the number of fluid mesh points is specified, calculate an appropriate number of nodes per cell automatically
    bool override_nodes_per_cell = numFluidMeshPoints < UINT_MAX;
 
    // Helper vectors
    unit_vector<double> x_unit(2,0);
    unit_vector<double> y_unit(2,1);
 
    // Calculate cell sizes and rescale if necessary
    double cell_width = 1.0 / double(numCellsWide);
    double cell_height = cellAspectRatio * cell_width;
 
    if (cell_height > 0.8)
    {
        cell_height = 0.8;
        cell_width = cell_height / cellAspectRatio;
    }
 
    // If we are overriding the number of nodes per cell, alter it so that the spacing ratio is approx 0.5
    if (override_nodes_per_cell)
    {
        double cell_perimeter = 2.0 * (cell_height + cell_width);
        double fluid_mesh_spacing = 1.0 / static_cast<double>(numFluidMeshPoints);
        double target_node_spacing = 0.5 * fluid_mesh_spacing;
        numNodesPerCell = static_cast<unsigned>(cell_perimeter / target_node_spacing);
    }
 
    const double width_scale_fac = absoluteGap == DOUBLE_UNSET ? 0.95 : (cell_width - absoluteGap) / cell_width;
 
    // Generate a reference superellipse
    std::unique_ptr<SuperellipseGenerator> p_gen(new SuperellipseGenerator(numNodesPerCell, ellipseExponent, cell_width, cell_height, 0.0, 0.0));
    std::vector<c_vector<double, 2> > locations = p_gen->GetPointsAsVectors();
 
    /*
     * The top and bottom heights are the heights at which there is maximum curvature in the superellipse.
     * These define the apical and basal domains.
     *       _____
     *    __/_____\__ Apical cutoff
     *    __|_____|__ Periapical cutoff
     *      |     |
     *      |     |
     *    __|_____|__ Basal cutoff
     *      \_____/__ y = 0
     */
    double apical_cutoff = p_gen->GetHeightOfTopSurface();
    double basal_cutoff = cell_height - apical_cutoff;
    double periapical_cutoff = apical_cutoff - basal_cutoff;
 
    if (apical_cutoff < 0.5 * cell_height || apical_cutoff > cell_height || periapical_cutoff < basal_cutoff)
    {
        EXCEPTION("Something went wrong calculating the height of top surface of the cell."); //LCOV_EXCL_LINE
    }
 
    // Corner 0 is left-apical, 1 is right-apical, 2 is right-basal, 3 is left-basal
    std::vector<unsigned> corner_indices(4, UINT_MAX);
 
    // Node 0 is middle of right lateral side
 
    // First anticlockwise is RIGHT_APICAL_CORNER
    for (unsigned location = 0; location < locations.size(); location++)
    {
        if (locations[location][1] > apical_cutoff)
        {
            corner_indices[RIGHT_APICAL_CORNER] = location;
            break;
        }
    }
 
    // Second anticlockwise is LEFT_APICAL_CORNER
    for (unsigned location = unsigned(0.25 * numNodesPerCell); location < locations.size(); location++)
    {
        if (locations[location][1] < apical_cutoff)
        {
            corner_indices[LEFT_APICAL_CORNER] = location - 1;
            break;
        }
    }
 
    // Third anticlockwise is LEFT_BASAL_CORNER
    for (unsigned location = unsigned(0.5 * numNodesPerCell); location < locations.size(); location++)
    {
        if (locations[location][1] < basal_cutoff)
        {
            corner_indices[LEFT_BASAL_CORNER] = location;
            break;
        }
    }
 
    // Fourth anticlockwise is RIGHT_BASAL_CORNER
    for (unsigned location = unsigned(0.75 * numNodesPerCell); location < locations.size(); location++)
    {
        if (locations[location][1] > basal_cutoff)
        {
            corner_indices[RIGHT_BASAL_CORNER] = location - 1;
            break;
        }
    }
 
    if ( (corner_indices[0] == UINT_MAX) ||
         (corner_indices[1] == UINT_MAX) ||
         (corner_indices[2] == UINT_MAX) ||
         (corner_indices[3] == UINT_MAX) )
    {
        EXCEPTION("At least one corner not tagged"); //LCOV_EXCL_LINE
    }
 
    // Should have RIGHT_APICAL_CORNER < LEFT_APICAL_CORNER < LEFT_BASAL_CORNER < RIGHT_BASAL_CORNER
    if ( (corner_indices[RIGHT_APICAL_CORNER] > corner_indices[LEFT_APICAL_CORNER]) ||
         (corner_indices[LEFT_APICAL_CORNER] > corner_indices[LEFT_BASAL_CORNER]) ||
         (corner_indices[LEFT_BASAL_CORNER] > corner_indices[RIGHT_BASAL_CORNER]) )
    {
        EXCEPTION("Something went wrong when tagging corner locations"); //LCOV_EXCL_LINE
    }
 
    if ( corner_indices[LEFT_APICAL_CORNER] - corner_indices[RIGHT_APICAL_CORNER] !=
         corner_indices[RIGHT_BASAL_CORNER] - corner_indices[LEFT_BASAL_CORNER] )
    {
        EXCEPTION("Apical and basal surfaces are different sizes"); //LCOV_EXCL_LINE
    }
 
    // Create vectors of immersed boundary elements, laminas, nodes
    std::vector<ImmersedBoundaryElement<2,2>*> ib_elements;
    std::vector<ImmersedBoundaryElement<1,2>*> ib_laminas;
    std::vector<Node<2>*> nodes;
 
    // Helper c_vector for offsets in x and y
    c_vector<double, 2> x_offset = x_unit * cell_width;
    c_vector<double, 2> y_offset = y_unit * (1.0 - cell_height) / 2.0;
 
    // Aim to give the laminas roughly the same node-spacing as the other cells...
    double lamina_node_spacing = 2.0 * (cell_height + cell_width) / numNodesPerCell;
    //... unless the laminas are to be leaky, in which case the spacing should be bigger
    if (leakyLaminas && override_nodes_per_cell)
    {
        // If laminas are leaky, increase the spacing so fluid can flow through
        lamina_node_spacing = 2.0 / static_cast<double>(numFluidMeshPoints);
    }
 
    // Add the basal lamina, if there is one
    if (basalLamina)
    {
        // The height of the lamina is offset by a proportion of the cell height
        double lam_height = absoluteGap == DOUBLE_UNSET ? y_offset[1] - 0.05 * cell_height : y_offset[1] - absoluteGap;
 
        unsigned num_lamina_nodes = static_cast<unsigned>(floor(1.0 / lamina_node_spacing));
 
        std::vector<Node<2>*> nodes_this_elem;
 
        for (unsigned node_idx = 0; node_idx < num_lamina_nodes; node_idx++)
        {
            // Calculate location of node
            c_vector<double, 2> location = lam_height * y_unit + ( 0.5 / num_lamina_nodes + double(node_idx) / num_lamina_nodes ) * x_unit;
 
            // Create the new node
            Node<2>* p_node = new Node<2>(nodes.size(), location, true);
            p_node->SetRegion(LAMINA_REGION);
 
            nodes.push_back(p_node);
            nodes_this_elem.push_back(p_node);
        }
 
        // Create the lamina element
        ib_laminas.push_back(new ImmersedBoundaryElement<1,2>(0, nodes_this_elem));
    }
 
    // Add the apical lamina, if there is one
    if (apicalLamina)
    {
        if (randomYMult != 0.0)
        {
            for (auto& p_node : nodes)
            {
                delete p_node;
            }
            for (auto& p_lam : ib_laminas)
            {
                delete p_lam;
            }
            EXCEPTION("Currently no random y variation allowed with an apical lamina");
        }
 
        // The height of the lamina is offset by a proportion of the cell height
        double lam_height = y_offset[1] + cell_height;
 
        unsigned num_lamina_nodes = static_cast<unsigned>(floor(1.0 / lamina_node_spacing));
 
        std::vector<Node<2>*> nodes_this_elem;
 
        for (unsigned node_idx = 0; node_idx < num_lamina_nodes; node_idx++)
        {
            // Calculate location of node
            c_vector<double, 2> location = lam_height * y_unit + ( 0.5 / num_lamina_nodes + double(node_idx) / num_lamina_nodes ) * x_unit;
 
            // Create the new node
            Node<2>* p_node = new Node<2>(nodes.size(), location, true);
            p_node->SetRegion(LAMINA_REGION);
 
            nodes.push_back(p_node);
            nodes_this_elem.push_back(p_node);
        }
 
        // Create the lamina element
        ib_laminas.push_back(new ImmersedBoundaryElement<1,2>(1, nodes_this_elem));
    }
 
    RandomNumberGenerator* p_rand_gen = RandomNumberGenerator::Instance();
 
    for (unsigned elem_idx = 0; elem_idx < numCellsWide; elem_idx++)
    {
        std::vector<Node<2>*> nodes_this_elem;
        double random_variation = p_rand_gen->ranf() * randomYMult;
        c_vector<double, 2> scaled_location;
 
        for (unsigned location = 0; location < locations.size(); location++)
        {
            unsigned node_index = nodes.size();
            scaled_location = width_scale_fac * locations[location] + x_offset * (elem_idx + 0.5);
            scaled_location[0] = fmod(scaled_location[0], 1.0);
            scaled_location[1] *= (1.0 + random_variation);
            scaled_location[1] += y_offset[1];
 
            // Create the new node
            Node<2>* p_node = new Node<2>(node_index, scaled_location, true);
 
            // Tag the node region
            if (locations[location][1] <= basal_cutoff)
            {
                if (locations[location][0] < 0.5 * cell_width)
                {
                    p_node->SetRegion(LEFT_BASAL_REGION);
                }
                else
                {
                    p_node->SetRegion(RIGHT_BASAL_REGION);
                }
            }
            else if (locations[location][1] <= periapical_cutoff)
            {
                if (locations[location][0] < 0.5 * cell_width)
                {
                    p_node->SetRegion(LEFT_LATERAL_REGION);
                }
                else
                {
                    p_node->SetRegion(RIGHT_LATERAL_REGION);
                }
            }
            else if (locations[location][1] < apical_cutoff)
            {
                if (locations[location][0] < 0.5 * cell_width)
                {
                    p_node->SetRegion(LEFT_PERIAPICAL_REGION);
                }
                else
                {
                    p_node->SetRegion(RIGHT_PERIAPICAL_REGION);
                }
            }
            else
            {
                if (locations[location][0] < 0.5 * cell_width)
                {
                    p_node->SetRegion(LEFT_APICAL_REGION);
                }
                else
                {
                    p_node->SetRegion(RIGHT_APICAL_REGION);
                }
            }
 
            nodes.push_back(p_node);
            nodes_this_elem.push_back(p_node);
        }
 
        ib_elements.push_back(new ImmersedBoundaryElement<2,2>(elem_idx, nodes_this_elem));
 
        // Pass in the corners calculated above
        std::vector<Node<2>*>& r_elem_corners = ib_elements.back()->rGetCornerNodes();
        for (unsigned corner = 0; corner < 4; corner++)
        {
            r_elem_corners.push_back(ib_elements.back()->GetNode(corner_indices[corner]));
        }
    }
 
    if (override_nodes_per_cell)
    {
        mpMesh = new ImmersedBoundaryMesh<2, 2>(nodes, ib_elements, ib_laminas, numFluidMeshPoints, numFluidMeshPoints);
    }
    else
    {
        mpMesh = new ImmersedBoundaryMesh<2, 2>(nodes, ib_elements, ib_laminas);
    }
}
 
ImmersedBoundaryPalisadeMeshGenerator::~ImmersedBoundaryPalisadeMeshGenerator()
{
    delete mpMesh;
}
 
ImmersedBoundaryMesh<2,2>* ImmersedBoundaryPalisadeMeshGenerator::GetMesh()
{
    return mpMesh;
}