Mercurial > fem-fenics-eugenio
view src/Mesh.cc @ 257:fb67b636616f
Distribute mesh after creating it
* Subdomain markers are not supported by DOLFIN in parallel execution!
author | Eugenio Gianniti <eugenio.gianniti@mail.polimi.it> |
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date | Wed, 30 Jul 2014 21:09:52 +0200 |
parents | 5e9b5bbdc56b |
children | ab35a8b0deef |
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/* Copyright (C) 2013 Marco Vassallo <gedeone-octave@users.sourceforge.net> This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, see <http://www.gnu.org/licenses/>. */ #include "mesh.h" #include "dolfin_compat.h" #ifdef LATEST_DOLFIN #include <dolfin/mesh/MeshPartitioning.h> #endif DEFUN_DLD (Mesh, args, ,"-*- texinfo -*-\n\ @deftypefn {Function File} {[@var{mesh_out}]} = \ Mesh (@var{mesh_in}) \n\ Construct a mesh from file or from (p, e, t) format.\n\ The @var{mesh_in} should be either\n\ @itemize @bullet \n\ @item a string containing the name of the file where the mesh \ is stored in .xml file\n\ If the file is not a .xml file you can try to use the command\ dolfin-convert directly from the terminal. \n\ @item a a PDE-tool like structure with matrix fields (p,e,t)\ @end itemize\n\ The output @var{mesh_out} is a representation of the\ @var{mesh_in} which is compatible with fem-fenics.\n\ The easiest way for dealing with meshes is using the msh pkg. \n\ @seealso{FunctionSpace}\n\ @end deftypefn") { int nargin = args.length (); octave_value retval = 0; if (nargin < 1 || nargin > 1) print_usage (); else { if (!error_state) { if (! mesh_type_loaded) { mesh::register_type (); mesh_type_loaded = true; mlock (); } if (args(0).is_string () == true) { std::string filename = args(0).string_value (); //if the filename is not valid, dolfin takes care of it retval = new mesh (filename); } else if (args(0).is_map () == true) { octave_scalar_map a = args(0).scalar_map_value (); Array<double> p = a.contents ("p").matrix_value (); Array<octave_idx_type> t = a.contents ("t").matrix_value (); Array<octave_idx_type> e = a.contents ("e").matrix_value (); if (! error_state) { retval = new mesh (p, e, t); } } else error ("Mesh: the argument you provide is invalid"); } } return retval; } mesh::mesh (Array<double>& p, Array<octave_idx_type>& e, Array<octave_idx_type>& t) { std::size_t D = p.rows (); if (D < 2 || D > 3) error ("Mesh constructor: only 2D or 3D meshes are supported"); else { dolfin::MeshEditor editor; SHARED_PTR <dolfin::Mesh> msh (new dolfin::Mesh ()); editor.open (*msh, D, D); editor.init_vertices (p.cols ()); editor.init_cells (t.cols ()); if (D == 2) { for (uint i = 0; i < p.cols (); ++i) editor.add_vertex (i, p.xelem (0, i), p.xelem (1, i)); for (uint i = 0; i < t.cols (); ++i) editor.add_cell (i, t.xelem (0, i) - 1, t.xelem (1, i) - 1, t.xelem (2, i) - 1); } if (D == 3) { for (uint i = 0; i < p.cols (); ++i) editor.add_vertex (i, p.xelem (0, i), p.xelem (1, i), p.xelem (2, i)); for (uint i = 0; i < t.cols (); ++i) editor.add_cell (i, t.xelem (0, i) - 1, t.xelem (1, i) - 1, t.xelem (2, i) - 1, t.xelem (3, i) - 1); } editor.close (); // store information associated with e msh->init (D - 1); dolfin::MeshValueCollection<std::size_t> facet(*msh, D - 1); std::size_t num_side_edges = e.cols (); unsigned const num_procs = #ifdef LATEST_DOLFIN dolfin::MPI::size (MPI_COMM_WORLD); #else dolfin::MPI::num_processes (); #endif if (num_procs == 1) { if (D == 2) { for (uint i = 0; i < num_side_edges; ++i) { dolfin::Vertex v (*msh, e.xelem (0, i) - 1); for (dolfin::FacetIterator f (v); ! f.end (); ++f) { if ((*f).entities(0)[0] == e.xelem (0, i) - 1 && (*f).entities(0)[1] == e.xelem (1, i) - 1 || (*f).entities(0)[0] == e.xelem (1, i) - 1 && (*f).entities(0)[1] == e.xelem (0, i) - 1) { std::pair <std::size_t, std::size_t> idxvl ((*f).index (), e.xelem (4, i)); msh->domains ().set_marker (idxvl, D - 1); break; } } } } if (D == 3) { for (uint i = 0; i < num_side_edges; ++i) { dolfin::Vertex v (*msh, e.xelem (0, i) - 1); for (dolfin::FacetIterator f (v); ! f.end (); ++f) { if ((*f).entities(0)[0] == e(0, i) - 1 && (*f).entities(0)[1] == e.xelem (1, i) - 1 && (*f).entities(0)[2] == e.xelem (2, i) - 1 || (*f).entities(0)[0] == e.xelem (0, i) - 1 && (*f).entities(0)[1] == e.xelem (2, i) - 1 && (*f).entities(0)[2] == e.xelem (1, i) - 1 || (*f).entities(0)[0] == e.xelem (1, i) - 1 && (*f).entities(0)[1] == e.xelem (0, i) - 1 && (*f).entities(0)[2] == e.xelem (2, i) - 1 || (*f).entities(0)[0] == e.xelem (1, i) - 1 && (*f).entities(0)[1] == e.xelem (2, i) - 1 && (*f).entities(0)[2] == e.xelem (0, i) - 1 || (*f).entities(0)[0] == e.xelem (2, i) - 1 && (*f).entities(0)[1] == e.xelem (0, i) - 1 && (*f).entities(0)[2] == e.xelem (1, i) - 1 || (*f).entities(0)[0] == e.xelem (2, i) - 1 && (*f).entities(0)[1] == e.xelem (1, i) - 1 && (*f).entities(0)[2] == e.xelem (0, i) - 1) { std::pair <std::size_t, std::size_t> idxvl ((*f).index (), e.xelem (9, i)); msh->domains ().set_marker (idxvl, D - 1); break; } } } } } dolfin::MeshValueCollection<std::size_t> cell (*msh, D); std::size_t num_cells = t.cols (); if (num_procs == 1) { if (D == 2) { for (uint i = 0; i < num_cells; ++i) { dolfin::Vertex v (*msh, t.xelem (0, i) - 1); for (dolfin::CellIterator f (v); ! f.end (); ++f) { if ((*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1) { std::pair <std::size_t, std::size_t> idxvl ((*f).index (), t.xelem (3, i)); msh->domains ().set_marker (idxvl, D); break; } } } } if (D == 3) { for (uint i = 0; i < num_cells; ++i) { dolfin::Vertex v (*msh, t.xelem (0, i) - 1); for (dolfin::CellIterator f (v); ! f.end (); ++f) { if ((*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (0, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (1, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (3, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (3, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (2, i) - 1 && (*f).entities(0)[1] == t.xelem (3, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (0, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (2, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (1, i) - 1 && (*f).entities(0)[2] == t.xelem (2, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (0, i) - 1 && (*f).entities(0)[3] == t.xelem (1, i) - 1 || (*f).entities(0)[0] == t.xelem (3, i) - 1 && (*f).entities(0)[1] == t.xelem (2, i) - 1 && (*f).entities(0)[2] == t.xelem (1, i) - 1 && (*f).entities(0)[3] == t.xelem (0, i) - 1) { std::pair <std::size_t, std::size_t> idxvl ((*f).index (), t.xelem (4, i)); msh->domains ().set_marker (idxvl, D); break; } } } } } dolfin::MeshPartitioning::build_distributed_mesh (*msh); pmsh = msh; } }