CylindricalHoneycombMeshGenerator.cpp

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#include "CylindricalHoneycombMeshGenerator.hpp"
 
#include <boost/foreach.hpp>
#include <boost/make_shared.hpp>
#include <boost/shared_ptr.hpp>
#include "RandomNumberGenerator.hpp"
#include "MathsCustomFunctions.hpp"
#include "ChasteSyscalls.hpp"
 
CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(unsigned numNodesAlongWidth, unsigned numNodesAlongLength, unsigned ghosts, double scaleFactor)
{
    mpMesh = nullptr;
    mDomainWidth = numNodesAlongWidth*scaleFactor;
    mNumCellWidth = numNodesAlongWidth; //*1 because cells are considered to be size one
    mNumCellLength = numNodesAlongLength;
    mMeshFilename = "mesh";
    mGhostNodeIndices.clear();
    // The code below won't work in parallel
    assert(PetscTools::IsSequential());
 
    // An older version of the constructor might allow the wrong argument through to the scale factor
    assert(scaleFactor > 0.0);
 
    // Get a unique mesh filename
    std::stringstream pid;
    pid << getpid();
 
    OutputFileHandler output_file_handler("2D_temporary_honeycomb_mesh_"+ pid.str());
 
    unsigned num_nodes_along_width = mNumCellWidth;
    unsigned num_nodes_along_length = mNumCellLength;
    double horizontal_spacing = mDomainWidth / (double)num_nodes_along_width;
    double vertical_spacing = (sqrt(3.0)/2)*horizontal_spacing;
 
    // This line is needed to define ghost nodes later
    mDomainDepth = (double)(num_nodes_along_length) * vertical_spacing;
 
    // Take account of ghost nodes
    num_nodes_along_length += 2*ghosts;
 
    unsigned num_nodes            = num_nodes_along_width*num_nodes_along_length;
    unsigned num_elem_along_width = num_nodes_along_width-1;
    unsigned num_elem_along_length = num_nodes_along_length-1;
    unsigned num_elem             = 2*num_elem_along_width*num_elem_along_length;
    unsigned num_edges            = 3*num_elem_along_width*num_elem_along_length + num_elem_along_width + num_elem_along_length;
 
    double x0 = 0;
    double y0 = -vertical_spacing*ghosts;
 
    mBottom = -vertical_spacing*ghosts;
    mTop = mBottom + vertical_spacing*(num_nodes_along_length-1);
 
    // Write node file
    out_stream p_node_file = output_file_handler.OpenOutputFile(mMeshFilename+".node");
    (*p_node_file) << std::scientific;
    //(*p_node_file) << std::setprecision(20);
    (*p_node_file) << num_nodes << "\t2\t0\t1" << std::endl;
 
    unsigned node = 0;
    for (unsigned i=0; i<num_nodes_along_length; i++)
    {
        for (unsigned j=0; j<num_nodes_along_width; j++)
        {
            if (i<ghosts || i>=(ghosts+mNumCellLength))
            {
                mGhostNodeIndices.insert(node);
            }
            unsigned boundary = 0;
            if ((i==0) || (i==num_nodes_along_length-1))
            {
                boundary = 1;
            }
 
            const double adjustment = i % 2 != 0 ? 0.5 : 0.0;
            double x = x0 + horizontal_spacing*((double)j + adjustment);
            double y = y0 + vertical_spacing*(double)i;
 
            // Avoid floating point errors which upset OffLatticeSimulation
            if ((y<0.0) && (y>-1e-12))
            {
                // Difficult to cover - just corrects floating point errors that have occurred from time to time!
                // LCOV_EXCL_START
                y = 0.0;
                // LCOV_EXCL_STOP
            }
 
            (*p_node_file) << node++ << "\t" << x << "\t" << y << "\t" << boundary << std::endl;
        }
    }
    p_node_file->close();
 
    // Write element file and edge file
    out_stream p_elem_file = output_file_handler.OpenOutputFile(mMeshFilename+".ele");
    (*p_elem_file) << std::scientific;
 
    out_stream p_edge_file = output_file_handler.OpenOutputFile(mMeshFilename+".edge");
    (*p_node_file) << std::scientific;
 
    (*p_elem_file) << num_elem << "\t3\t0" << std::endl;
    (*p_edge_file) << num_edges << "\t1" << std::endl;
 
    unsigned elem = 0;
    unsigned edge = 0;
    for (unsigned i=0; i<num_elem_along_length; i++)
    {
        for (unsigned j=0; j < num_elem_along_width; j++)
        {
            unsigned node0 =     i*num_nodes_along_width + j;
            unsigned node1 =     i*num_nodes_along_width + j+1;
            unsigned node2 = (i+1)*num_nodes_along_width + j;
 
            if (i%2 != 0)
            {
                node2 = node2 + 1;
            }
 
            (*p_elem_file) << elem++ << "\t" << node0 << "\t" << node1 << "\t" << node2 << std::endl;
 
            unsigned horizontal_edge_is_boundary_edge = 0;
            unsigned vertical_edge_is_boundary_edge = 0;
            if (i==0)
            {
                horizontal_edge_is_boundary_edge = 1;
            }
 
            (*p_edge_file) << edge++ << "\t" << node0 << "\t" << node1 << "\t" << horizontal_edge_is_boundary_edge << std::endl;
            (*p_edge_file) << edge++ << "\t" << node1 << "\t" << node2 << "\t" << 0 << std::endl;
            (*p_edge_file) << edge++ << "\t" << node2 << "\t" << node0 << "\t" << vertical_edge_is_boundary_edge << std::endl;
 
            node0 = i*num_nodes_along_width + j + 1;
 
            if (i%2 != 0)
            {
                node0 = node0 - 1;
            }
            node1 = (i+1)*num_nodes_along_width + j+1;
            node2 = (i+1)*num_nodes_along_width + j;
 
            (*p_elem_file) << elem++ << "\t" << node0 << "\t" << node1 << "\t" << node2 << std::endl;
        }
    }
 
    for (unsigned i=0; i<num_elem_along_length; i++)
    {
        unsigned node0, node1;
 
        if (i%2==0)
        {
             node0 = (i+1)*num_nodes_along_width - 1;
             node1 = (i+2)*num_nodes_along_width - 1;
        }
        else
        {
            node0 = (i+1)*num_nodes_along_width;
            node1 = (i)*num_nodes_along_width;
        }
        (*p_edge_file) << edge++ << "\t" << node0 << "\t" << node1 << "\t" << 1 << std::endl;
    }
 
    for (unsigned j=0; j<num_elem_along_width; j++)
    {
        unsigned node0 = num_nodes_along_width*(num_nodes_along_length-1) + j;
        unsigned node1 = num_nodes_along_width*(num_nodes_along_length-1) + j+1;
        (*p_edge_file) << edge++ << "\t" << node1 << "\t" << node0 << "\t" << 1 << std::endl;
    }
 
    p_elem_file->close();
    p_edge_file->close();
 
    // Having written the mesh to file, now construct it using TrianglesMeshReader.
    // Nested scope so the reader closes files before we delete them below.
    {
        TrianglesMeshReader<2,2> mesh_reader(output_file_handler.GetOutputDirectoryFullPath() + mMeshFilename);
        mpMesh = boost::make_shared<Cylindrical2dMesh>(mDomainWidth);
        mpMesh->ConstructFromMeshReader(mesh_reader);
    }
 
    // Make the mesh cylindrical (we use Triangle library mode inside this ReMesh call)
    mpMesh->ReMesh();
 
    // Delete the temporary files
    output_file_handler.FindFile("").Remove();
 
    // The original files have been deleted, it is better if the mesh object forgets about them
    mpMesh->SetMeshHasChangedSinceLoading();
}
 
boost::shared_ptr<MutableMesh<2,2> > CylindricalHoneycombMeshGenerator::GetMesh()
{
    EXCEPTION("A cylindrical mesh was created but a normal mesh is being requested.");
    return mpMesh; // Not really
}
 
boost::shared_ptr<Cylindrical2dMesh> CylindricalHoneycombMeshGenerator::GetCylindricalMesh()
{
    return boost::static_pointer_cast<Cylindrical2dMesh>(mpMesh);
}