ImmersedBoundaryHoneycombMeshGenerator.cpp

 
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#include "ImmersedBoundaryHoneycombMeshGenerator.hpp"
 
ImmersedBoundaryHoneycombMeshGenerator::ImmersedBoundaryHoneycombMeshGenerator(unsigned numElementsX,
                                                                               unsigned numElementsY,
                                                                               unsigned numNodesPerEdge,
                                                                               double proportionalGap,
                                                                               double padding)
        : mpMesh(nullptr)
{
    // Check for sensible input
    assert(numElementsX > 0);
    assert(numElementsY > 0);
    assert(numNodesPerEdge > 2);
    assert(proportionalGap > 0.0);
    assert(padding > 0.0 && padding < 0.5);
 
    // Helper vectors
    unit_vector<double> x_unit(2,0);
    unit_vector<double> y_unit(2,1);
 
    std::vector<Node<2>*> nodes;
    std::vector<ImmersedBoundaryElement<2,2>*>  elements;
 
    double width = 0.5 + 1.5 * numElementsX;
    double height = sqrt(3.0) * numElementsY + 0.5 * sqrt(3.0) * (numElementsY > 1);
 
    double max = width > height ? width : height;
 
    double radius = (1.0 - 2.0 * padding) / max;
 
    // Reset width and height to their scaled values
    width *= radius;
    height *= radius;
 
    // We need to calculate the required centre of each hexagon
    std::vector<c_vector<double, 2> > offsets(numElementsY * numElementsX);
 
    // Specify the centre of the bottom-left most hexagon
    c_vector<double, 2> global_offset;
    if(width > height)
    {
        global_offset[0] = padding + radius;
        global_offset[1] = 0.5 - 0.5 * height + 0.5 * radius * sqrt(3.0);
    }
    else
    {
        global_offset[0] = 0.5 - 0.5 * width + radius;
        global_offset[1] = padding + 0.5 * sqrt(3.0) * radius;
    }
 
    // Calculate the centres
    for (unsigned x = 0; x < numElementsX; x++)
    {
        for (unsigned y = 0; y < numElementsY; y++)
        {
            unsigned idx = x * numElementsY + y;
 
            offsets[idx][0] = global_offset[0] + 1.5 * radius * x;
            offsets[idx][1] = global_offset[1] + 0.5 * sqrt(3.0) * radius * (2.0 * y + (double)(x % 2 == 1));
        }
    }
 
    // Get locations for the reference hexagon
    std::vector<c_vector<double, 2> > node_locations = GetUnitHexagon(numNodesPerEdge);
 
    double scale = 1.0 - proportionalGap;
 
    // For each calculated centre, create the nodes representing each location around that hexagon
    for (unsigned offset = 0; offset < offsets.size(); offset++)
    {
        std::vector<Node<2>*> nodes_this_elem;
 
        for (unsigned location = 0; location < node_locations.size(); location++)
        {
            unsigned index = offset * node_locations.size() + location;
            Node<2>* p_node = new Node<2>(index, offsets[offset] + scale * radius * node_locations[location], true);
 
            nodes_this_elem.push_back(p_node);
            nodes.push_back(p_node);
        }
 
        ImmersedBoundaryElement<2,2>* p_elem = new ImmersedBoundaryElement<2,2>(offset, nodes_this_elem);
 
        // Set whether it's on the boundary
        if (offset < numElementsY ||                        // left edge
            offset >= numElementsY * (numElementsX - 1) ||  // right edge
            offset % numElementsY == 0 ||                   // bottom edge
            (offset + 1) % numElementsY == 0)               // top edge
        {
            p_elem->SetIsBoundaryElement(true);
        }
 
        elements.push_back(p_elem);
    }
 
    // Create the mesh, cells, cell population, and simulation
    mpMesh = new ImmersedBoundaryMesh<2,2>(nodes, elements);
}
 
ImmersedBoundaryHoneycombMeshGenerator::~ImmersedBoundaryHoneycombMeshGenerator()
{
    delete mpMesh;
}
 
ImmersedBoundaryMesh<2,2>* ImmersedBoundaryHoneycombMeshGenerator::GetMesh()
{
    return mpMesh;
}
 
std::vector<c_vector<double, 2> > ImmersedBoundaryHoneycombMeshGenerator::GetUnitHexagon(unsigned numPtsPerSide)
{
    std::vector<c_vector<double, 2> > locations(numPtsPerSide * 6);
 
    // Find locations of the six vertices (and the seventh is the same as the first)
    std::vector<c_vector<double, 2> > vertices(7);
    double sixty_degrees = M_PI / 3.0;
    for (unsigned vertex = 0; vertex < vertices.size(); vertex++)
    {
        vertices[vertex][0] = cos((double)vertex * sixty_degrees);
        vertices[vertex][1] = sin((double)vertex * sixty_degrees);
    }
 
    // Between each pair of vertices, fill in the specified number of locations evenly spaced along the edge
    for (unsigned vertex = 0; vertex < 6; vertex++)
    {
        c_vector<double, 2> this_vertex = vertices[vertex];
        c_vector<double, 2> next_vertex = vertices[vertex + 1];
        c_vector<double, 2> vec_between = next_vertex - this_vertex;
 
        for (unsigned i = 0; i < numPtsPerSide; i++)
        {
            locations[vertex * numPtsPerSide + i] = this_vertex + i * vec_between / (double)numPtsPerSide;
        }
    }
    return locations;
}