HoneycombMeshGenerator.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2010
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 #ifndef HONEYCOMBMESHGENERATOR_HPP_
00029 #define HONEYCOMBMESHGENERATOR_HPP_
00030 
00031 #include <cmath>
00032 #include <vector>
00033 
00034 #include "Cylindrical2dMesh.hpp"
00035 #include "TrianglesMeshReader.hpp"
00036 #include "OutputFileHandler.hpp"
00037 #include "TissueConfig.hpp"
00038 
00039 #include "PetscTools.hpp"
00040 
00041 
00051 class HoneycombMeshGenerator
00052 {
00053 private:
00054 
00056     MutableMesh<2,2>* mpMesh;
00057 
00059     std::set<unsigned> mGhostNodeIndices;
00060 
00062     std::string mMeshFilename;
00063 
00065     double mCryptWidth;
00066 
00068     double mCryptDepth;
00069 
00071     double mBottom;
00072 
00074     double mTop;
00075 
00077     unsigned mNumCellWidth;
00078 
00080     unsigned mNumCellLength;
00081 
00083     bool mCylindrical;
00084 
00091     void Make2dPeriodicCryptMesh(double width, unsigned ghosts);
00092 
00093 public:
00094 
00109     HoneycombMeshGenerator(unsigned numNodesAlongWidth, unsigned numNodesAlongLength, unsigned ghosts=3, bool cylindrical=true, double scaleFactor=1.0);
00110 
00114     ~HoneycombMeshGenerator();
00115 
00119     MutableMesh<2,2>* GetMesh();
00120 
00124     Cylindrical2dMesh* GetCylindricalMesh();
00125 
00133     std::vector<unsigned> GetCellLocationIndices();
00134 
00139     MutableMesh<2,2>* GetCircularMesh(double radius);
00140 
00141 };
00142 #endif /*HONEYCOMBMESHGENERATOR_HPP_*/

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