CylindricalHoneycombMeshGenerator.cpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 
00029 #include "CylindricalHoneycombMeshGenerator.hpp"
00030 #include "RandomNumberGenerator.hpp"
00031 #include "UblasCustomFunctions.hpp"
00032 
00033 CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(unsigned numNodesAlongWidth, unsigned numNodesAlongLength, unsigned ghosts, double scaleFactor)
00034 {
00035     mpMesh = NULL;
00036     mDomainWidth = numNodesAlongWidth*scaleFactor;
00037     mNumCellWidth = numNodesAlongWidth; //*1 because cells are considered to be size one
00038     mNumCellLength = numNodesAlongLength;
00039 
00040     // The getpid code below won't work in parallel
00041     assert(PetscTools::IsSequential());
00042 
00043     // Get a unique mesh filename
00044     std::stringstream pid;
00045     pid << getpid();
00046     mMeshFilename = "2D_temporary_honeycomb_mesh_" + pid.str();
00047 
00048     mGhostNodeIndices.empty();
00049 
00050     OutputFileHandler output_file_handler("");
00051     std::string output_dir = output_file_handler.GetOutputDirectoryFullPath();
00052 
00053     if (PetscTools::AmMaster())
00054     {
00055         unsigned numNodesAlongWidth = mNumCellWidth;
00056         unsigned numNodesAlongLength = mNumCellLength;
00057         double horizontal_spacing = mDomainWidth / (double)numNodesAlongWidth;
00058         double vertical_spacing = (sqrt(3)/2)*horizontal_spacing;
00059 
00060         // This line is needed to define ghost nodes later
00061         mDomainDepth = (double)(numNodesAlongLength) * vertical_spacing;
00062 
00063         // Take account of ghost nodes
00064         numNodesAlongLength = numNodesAlongLength + 2*ghosts;
00065 
00066         unsigned num_nodes            = numNodesAlongWidth*numNodesAlongLength;
00067         unsigned num_elem_along_width = numNodesAlongWidth-1;
00068         unsigned num_elem_along_length = numNodesAlongLength-1;
00069         unsigned num_elem             = 2*num_elem_along_width*num_elem_along_length;
00070         unsigned num_edges            = 3*num_elem_along_width*num_elem_along_length + num_elem_along_width + num_elem_along_length;
00071 
00072         double x0 = 0;
00073         double y0 = -vertical_spacing*ghosts;
00074 
00075         mBottom = -vertical_spacing*ghosts;
00076         mTop = mBottom + vertical_spacing*(numNodesAlongLength-1);
00077 
00078         // Write node file
00079         out_stream p_node_file = output_file_handler.OpenOutputFile(mMeshFilename+".node");
00080         (*p_node_file) << std::scientific;
00081         (*p_node_file) << num_nodes << "\t2\t0\t1" << std::endl;
00082 
00083         unsigned node = 0;
00084         for (unsigned i=0; i<numNodesAlongLength; i++)
00085         {
00086             for (unsigned j=0; j<numNodesAlongWidth; j++)
00087             {
00088                 if (i<ghosts || i>=(ghosts+mNumCellLength))
00089                 {
00090                     mGhostNodeIndices.insert(node);
00091                 }
00092                 unsigned boundary = 0;
00093                 if ((i==0) || (i==numNodesAlongLength-1))
00094                 {
00095                     boundary = 1;
00096                 }
00097 
00098                 double x = x0 + horizontal_spacing*((double)j + 0.25*(1.0+ SmallPow(-1,i+1)));
00099                 double y = y0 + vertical_spacing*(double)i;
00100 
00101                 // Avoid floating point errors which upset CellBasedSimulation
00102                 if ( (y<0.0) && (y>-1e-12) )
00103                 {
00104                     // Difficult to cover - just corrects floating point errors that have occurred from time to time!
00105                     #define COVERAGE_IGNORE
00106                     y = 0.0;
00107                     #undef COVERAGE_IGNORE
00108                 }
00109 
00110                 (*p_node_file) << node++ << "\t" << x << "\t" << y << "\t" << boundary << std::endl;
00111             }
00112         }
00113         p_node_file->close();
00114 
00115         // Write element file and edge file
00116         out_stream p_elem_file = output_file_handler.OpenOutputFile(mMeshFilename+".ele");
00117         (*p_elem_file) << std::scientific;
00118 
00119         out_stream p_edge_file = output_file_handler.OpenOutputFile(mMeshFilename+".edge");
00120         (*p_node_file) << std::scientific;
00121 
00122         (*p_elem_file) << num_elem << "\t3\t0" << std::endl;
00123         (*p_edge_file) << num_edges << "\t1" << std::endl;
00124 
00125         unsigned elem = 0;
00126         unsigned edge = 0;
00127         for (unsigned i=0; i<num_elem_along_length; i++)
00128         {
00129             for (unsigned j=0; j < num_elem_along_width; j++)
00130             {
00131                 unsigned node0 =     i*numNodesAlongWidth + j;
00132                 unsigned node1 =     i*numNodesAlongWidth + j+1;
00133                 unsigned node2 = (i+1)*numNodesAlongWidth + j;
00134 
00135                 if (i%2 != 0)
00136                 {
00137                     node2 = node2 + 1;
00138                 }
00139 
00140                 (*p_elem_file) << elem++ << "\t" << node0 << "\t" << node1 << "\t" << node2 << std::endl;
00141 
00142                 unsigned horizontal_edge_is_boundary_edge = 0;
00143                 unsigned vertical_edge_is_boundary_edge = 0;
00144                 if (i==0)
00145                 {
00146                     horizontal_edge_is_boundary_edge = 1;
00147                 }
00148 
00149                 (*p_edge_file) << edge++ << "\t" << node0 << "\t" << node1 << "\t" << horizontal_edge_is_boundary_edge << std::endl;
00150                 (*p_edge_file) << edge++ << "\t" << node1 << "\t" << node2 << "\t" << 0 << std::endl;
00151                 (*p_edge_file) << edge++ << "\t" << node2 << "\t" << node0 << "\t" << vertical_edge_is_boundary_edge << std::endl;
00152 
00153                 node0 = i*numNodesAlongWidth + j + 1;
00154 
00155                 if (i%2 != 0)
00156                 {
00157                     node0 = node0 - 1;
00158                 }
00159                 node1 = (i+1)*numNodesAlongWidth + j+1;
00160                 node2 = (i+1)*numNodesAlongWidth + j;
00161 
00162                 (*p_elem_file) << elem++ << "\t" << node0 << "\t" << node1 << "\t" << node2 << std::endl;
00163             }
00164         }
00165 
00166         for (unsigned i=0; i<num_elem_along_length; i++)
00167         {
00168             unsigned node0, node1;
00169 
00170             if (i%2==0)
00171             {
00172                  node0 = (i+1)*numNodesAlongWidth - 1;
00173                  node1 = (i+2)*numNodesAlongWidth - 1;
00174             }
00175             else
00176             {
00177                 node0 = (i+1)*numNodesAlongWidth;
00178                 node1 = (i)*numNodesAlongWidth;
00179             }
00180             (*p_edge_file) << edge++ << "\t" << node0 << "\t" << node1 << "\t" << 1 << std::endl;
00181         }
00182 
00183         for (unsigned j=0; j<num_elem_along_width; j++)
00184         {
00185             unsigned node0 = numNodesAlongWidth*(numNodesAlongLength-1) + j;
00186             unsigned node1 = numNodesAlongWidth*(numNodesAlongLength-1) + j+1;
00187             (*p_edge_file) << edge++ << "\t" << node1 << "\t" << node0 << "\t" << 1 << std::endl;
00188         }
00189 
00190         p_elem_file->close();
00191         p_edge_file->close();
00192     }
00193 
00194     // Wait for the new mesh to be available
00195     PetscTools::Barrier();
00196 
00197     // Having written the mesh to file, now construct it using TrianglesMeshReader
00198     TrianglesMeshReader<2,2> mesh_reader(output_dir + mMeshFilename);
00199     mpMesh = new Cylindrical2dMesh(mDomainWidth);
00200     mpMesh->ConstructFromMeshReader(mesh_reader);
00201     NodeMap map(mpMesh->GetNumNodes());
00202 
00203     // Make the mesh cylindrical (we use Triangle library mode inside this ReMesh call)
00204     mpMesh->ReMesh(map);
00205 
00206     // Delete the temporary files
00207     std::string command = "rm " + output_dir + mMeshFilename + ".*";
00208     int return_value = system(command.c_str());
00209     if (return_value != 0)
00210     {
00211         // Can't figure out how to make this throw but seems as if it should be here?
00212         #define COVERAGE_IGNORE
00213         EXCEPTION("HoneycombMeshGenerator cannot delete temporary files\n");
00214         #undef COVERAGE_IGNORE
00215     }
00216 
00217     // The original files have been deleted, it is better if the mesh object forgets about them
00218     mpMesh->SetMeshHasChangedSinceLoading();
00219 }
00220 
00221 MutableMesh<2,2>* CylindricalHoneycombMeshGenerator::GetMesh()
00222 {
00223     EXCEPTION("A cylindrical mesh was created but a normal mesh is being requested.");
00224     return mpMesh; // Not really
00225 }
00226 
00227 Cylindrical2dMesh* CylindricalHoneycombMeshGenerator::GetCylindricalMesh()
00228 {
00229     return (Cylindrical2dMesh*) mpMesh;
00230 }

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