<h3>Specific improvements</h3>
<ol>
+ <li>
+ New: GridIn::read_vtk() reads 2d and 3d meshes in VTK format.
+ <br>
+ (Mayank Sabharwal, Andreas Putz, 2013/10/07)
+ </li>
+
<li>
Fixed: ConstraintMatrix would not compress() the IndexSet in the constructor
leading to crashes that only happen in release mode. This is now fixed.
/**
* This class implements an input mechanism for grid data. It allows to read a
* grid structure into a triangulation object. At present, UCD (unstructured
- * cell data), DB Mesh, XDA, Gmsh, Tecplot, NetCDF, UNV, and Cubit are supported as
+ * cell data), DB Mesh, XDA, Gmsh, Tecplot, NetCDF, UNV, VTK, and Cubit are supported as
* input format for grid data. Any numerical data other than geometric
* (vertex locations) and topological (how vertices form cells) information is
* ignored.
* mesh is built up, and 4) all numbers that might be associated with some of
* the internal faces of this compound mesh are removed.
*
+ * <li> <tt>VTK</tt> format: VTK Unstructured Grid Legacy file reader
+ * generator. The reader can handle only Unstructured Grid format of data
+ * at present for 2D & 3D geometries.
+ * The documentation for the general legacy vtk file, including Unstructured Grid format
+ * can be found here:
+ * http://www.cacr.caltech.edu/~slombey/asci/vtk/vtk_formats.simple.html
+ *
+ * The VTK format requires the vertices to be
+ * in following ordering: in 2d
+ * @verbatim
+ * 3-----2
+ * | |
+ * | |
+ * | |
+ * 0-----1
+ * @endverbatim
+ * and in 3d
+ * @verbatim
+ * 7-------6 7-------6
+ * /| | / /|
+ * / | | / / |
+ * / | | / / |
+ * 4 | | 4-------5 |
+ * | 3-------2 | | 2
+ * | / / | | /
+ * | / / | | /
+ * |/ / | |/
+ * 0-------1 0-------1
+ * @endverbatim
+ *
+ *
* <li> <tt>Cubit</tt> format: deal.II doesn't directly support importing from
* Cubit at this time. However, Cubit can export in UCD format using a simple
* plug-in, and the resulting UCD file can then be read by this class. The
/// Use read_netcdf()
netcdf,
/// Use read_tecplot()
- tecplot
+ tecplot,
+ /// Use read_vtk()
+ vtk
};
/**
*/
void read (const std::string &in, Format format=Default);
+ /**
+ * Read grid data from an vtk file.
+ * Numerical data is ignored.
+ *
+ * @author Mayank Sabharwal, Andreas Putz, 2013
+ */
+ void read_vtk(std::istream &in);
+
/**
* Read grid data from an unv
* file as generated by the
* Salome mesh generator.
* Numerical data is ignored.
- *
- * Note the comments on
- * generating this file format in
- * the general documentation of
- * this class.
+ *
+ * Note the comments on
+ * generating this file format in
+ * the general documentation of
+ * this class.
*/
void read_unv(std::istream &in);
#include <deal.II/base/path_search.h>
#include <deal.II/base/utilities.h>
+#include <deal.II/base/exceptions.h>
#include <deal.II/grid/grid_in.h>
#include <deal.II/grid/tria.h>
-// --- ---
-// --- read_unv ---
-// --- ---
+template<int dim, int spacedim>
+void GridIn<dim, spacedim>::read_vtk(std::istream &in)
+{
+ Assert((dim == 2)||(dim == 3), ExcNotImplemented());
+ std::string line;
+ std::string text[4];
+ text[0] = "# vtk DataFile Version 3.0";
+ text[1] = "vtk output";
+ text[2] = "ASCII";
+ text[3] = "DATASET UNSTRUCTURED_GRID";
+
+ for(unsigned int i = 0;i < 4;i++)//Checking for the match between initial strings/text in the file.
+ {
+ getline(in,line);
+
+ AssertThrow (line.compare(text[i]) == 0,
+ ExcMessage(std::string("While reading VTK file, failed to find <") +
+ text[i] + ">"));
+ }
+
+ ///////////////////Declaring storage and mappings//////////////////
+
+ std::vector< Point<spacedim> > vertices;//vector of vertices
+ std::vector< CellData<dim> > cells;//vector of cells
+ SubCellData subcelldata;//subcell data that includes bounds and material IDs.
+ std::map<int, int> vertex_indices; // # vert in unv (key) ---> # vert in deal.II (value)
+ std::map<int, int> cell_indices; // # cell in unv (key) ---> # cell in deal.II (value)
+ std::map<int, int> quad_indices; // # quad in unv (key) ---> # quad in deal.II (value)
+ std::map<int, int> line_indices; // # line in unv(key) ---> # line in deal.II (value)
+
+ unsigned int no_vertices, no_quads=0,no_lines=0;
+
+ char keyword_1[7],keyword_2[6],keyword_3[10] ;//keywords for the three types of data
+
+ in.get(keyword_1, 7);
+
+ //////////////////Processing the POINTS section///////////////
+
+ if (std::strcmp(keyword_1,"POINTS") == 0)//comparing the keyword points
+ {
+ in>>no_vertices;// taking the no. of vertices
+ in.ignore(256, '\n');//ignoring the number beside the total no. of points.
+
+ for(unsigned int count = 0; count < no_vertices; count++)//loop to read three values till the no . vertices is satisfied
+ {
+ // VTK format always specifies vertex coordinates with 3 components
+ Point<3> x;
+ in >> x(0) >> x(1) >> x(2);
+
+ vertices.push_back(Point<spacedim>());
+ for (unsigned int d=0; d<spacedim; ++d)
+ vertices.back()(d) = x(d);
+
+ vertex_indices[count] = count;
+ }
+ }
+
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, failed to find POINTS section"));
+
+
+ //////////////////ignoring space between points and cells sections////////////////////
+ std::string checkline;
+ int no;
+ in.ignore(256, '\n');//this move pointer to the next line ignoring unwanted no.
+ no = in.tellg();
+ getline(in,checkline);
+ if (checkline.compare("") == 0)
+ {
+ in.get(keyword_2, 6);
+ }
+ else
+ {
+ in.seekg(no);
+ in.get(keyword_2, 6);
+ }
+
+
+ unsigned int total_cells, no_cells = 0, type, j = 0;// declaring counters, refer to the order of declaring variables for an idea of what is what!
+
+ ///////////////////Processing the CELLS section that contains cells(cells) and bound_quads(subcelldata)///////////////////////
+
+ if (std::strcmp(keyword_2,"CELLS") == 0)//comparing the keyword cells.
+ {
+
+ in>>total_cells;
+ in.ignore(256,'\n');
+
+ if (dim == 3)
+ {
+ for(unsigned int count = 0; count < total_cells; count++)
+ {
+ in>>type;
+
+ if(type == 8)
+ {
+
+ cells.push_back(CellData<dim>());
+
+ for(j = 0; j < type; j++)//loop to feed data
+ in >> cells.back().vertices[j];
+
+ cells.back().material_id = 0;
+
+ for(j = 0; j < type; j++)//loop to feed the data of the vertices to the cell
+ {
+ cells.back().vertices[j] = vertex_indices[cells.back().vertices[j]];
+ }
+ cell_indices[count] = count;
+ no_cells++;
+ }
+
+ else if ( type == 4)
+ {
+
+ subcelldata.boundary_quads.push_back(CellData<2>());
+ int no_quads = 0;
+
+ for(j = 0; j < type; j++)//loop to feed the data to the boundary
+ {
+ in >> subcelldata.boundary_quads.back().vertices[j];
+ }
+ subcelldata.boundary_quads.back().material_id = 0;
+ for(unsigned int j = 0; j < type; j++)
+ {
+ subcelldata.boundary_quads.back().vertices[j] = vertex_indices[subcelldata.boundary_quads.back().vertices[j]];
+ }
+ quad_indices[count] = count + 1;
+ no_quads++;
+ }
+
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, unknown file type encountered"));
+ }
+ }
+
+ else if (dim == 2)
+ {
+ for(unsigned int count = 0; count < total_cells; count++)
+ {
+ in>>type;
+
+ if(type == 4)
+ {
+ cells.push_back(CellData<dim>());
+
+ for(j = 0; j < type; j++)//loop to feed data
+ in >> cells.back().vertices[j];
+
+ cells.back().material_id = 0;
+
+ for(j = 0; j < type; j++)//loop to feed the data of the vertices to the cell
+ {
+ cells.back().vertices[j] = vertex_indices[cells.back().vertices[j]];
+ }
+ cell_indices[count] = count;
+ no_cells++;
+ }
+
+ else if(type == 2)
+ {
+ //If this is encountered, the pointer comes out of the loop
+ //and starts processing boundaries.
+ subcelldata.boundary_lines.push_back(CellData<1>());
+ int no_lines = 0;
+
+ for(j = 0; j < type; j++)//loop to feed the data to the boundary
+ {
+ in >> subcelldata.boundary_lines.back().vertices[j];
+ }
+ subcelldata.boundary_lines.back().material_id = 0;
+ for(unsigned int j = 0; j < type; j++)
+ {
+ subcelldata.boundary_lines.back().vertices[j] = vertex_indices[subcelldata.boundary_lines.back().vertices[j]];
+ }
+ line_indices[count] = count + 1;
+ no_lines++;
+ }
+
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, unknown file type encountered"));
+ }
+ }
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, failed to find CELLS section"));
+
+ /////////////////////Processing the CELL_TYPES section////////////////////////
+
+ in>>keyword_3;
+
+ if (std::strcmp(keyword_3,"CELL_TYPES") == 0)//Entering the cell_types section and ignoring data.
+ {
+ in.ignore(256, '\n');
+
+ while(!in.eof())
+ {
+ in>>keyword_3;
+ if(std::strcmp(keyword_3,"12") && std::strcmp(keyword_3,"9"))
+ {
+ break;
+ }
+ }
+ }
+
+ ////////////////////////Processing the CELL_DATA section/////////////////////////////
+
+ if (std::strcmp(keyword_3,"CELL_DATA") == 0)
+ {
+ int no_ids;
+ in>>no_ids;
+
+ std::string linenew;
+ std::string textnew[2];
+ textnew[0] = "SCALARS MaterialID double";
+ textnew[1] = "LOOKUP_TABLE default";
+
+ in.ignore(256, '\n');
+
+ for(unsigned int i = 0;i < 2;i++)
+ {
+ getline(in,linenew);
+
+ if(linenew.compare(textnew[i]) == 0)
+ {}
+ else
+ AssertThrow (false,
+ ExcMessage (std::string("While reading VTK file, failed to find <") +
+ textnew[i] + "> section"));
+ }
+
+ for(unsigned int i = 0; i < no_cells; i++)//assigning IDs to cells.
+ {
+ int id;
+ in>>id;
+ cells[cell_indices[i]].material_id = id;
+ }
+
+ if (dim == 3)
+ {
+ for(unsigned int i = 0; i < no_quads; i++)//assigning IDs to bounds.
+ {
+ int id;
+ in>>id;
+ subcelldata.boundary_quads[quad_indices[i]].material_id = id;
+ }
+ }
+ else if (dim == 2)
+ {
+ for(unsigned int i = 0; i < no_lines; i++)//assigning IDs to bounds.
+ {
+ int id;
+ in>>id;
+ subcelldata.boundary_lines[line_indices[i]].material_id = id;
+ }
+ }
+ }
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, failed to find CELL_DATA section"));
+
+
+ Assert(subcelldata.check_consistency(dim), ExcInternalError());
+
+ GridTools::delete_unused_vertices(vertices,
+ cells,
+ subcelldata);
+
+ if(dim == spacedim)
+ GridReordering<dim, spacedim>::invert_all_cells_of_negative_grid(vertices,
+ cells);
+
+ GridReordering<dim, spacedim>::reorder_cells(cells);
+ tria->create_triangulation_compatibility(vertices,
+ cells,
+ subcelldata);
+
+ return;
+ }
+ else
+ AssertThrow (false,
+ ExcMessage ("While reading VTK file, failed to find CELLS section"));
+}
+
+
template<int dim, int spacedim>
void GridIn<dim, spacedim>::read_unv(std::istream &in)
AssertThrow(in, ExcIO());
in >> id;
- int n_lines = (n_entities%2 == 0)?(n_entities/2):((n_entities+1)/2);
+ const unsigned int n_lines = (n_entities%2 == 0)?(n_entities/2):((n_entities+1)/2);
- for (int no_line = 0; no_line < n_lines; no_line++)
+ for (unsigned int no_line = 0; no_line < n_lines; no_line++)
{
- int n_fragments;
+ unsigned int n_fragments;
if (no_line == n_lines-1)
n_fragments = (n_entities%2 == 0)?(2):(1);
else
n_fragments = 2;
- for (int no_fragment = 0; no_fragment < n_fragments; no_fragment++)
+ for (unsigned int no_fragment = 0; no_fragment < n_fragments; no_fragment++)
{
AssertThrow(in, ExcIO());
in >> dummy >> no >> dummy >> dummy;
read_msh (in);
return;
+ case vtk:
+ read_vtk (in);
+ return;
+
case unv:
read_unv (in);
return;
return ".dbmesh";
case msh:
return ".msh";
+ case vtk:
+ return ".vtk";
case unv:
return ".unv";
case ucd:
if (format_name == "unv")
return unv;
+ if (format_name == "vtk")
+ return vtk;
+
if (format_name == "inp")
return ucd;
template <int dim, int spacedim>
std::string GridIn<dim, spacedim>::get_format_names ()
{
- return "dbmesh|msh|unv|ucd|xda|netcdf|tecplot";
+ return "dbmesh|msh|unv|vtk|ucd|xda|netcdf|tecplot";
}
--- /dev/null
+// ---------------------------------------------------------------------
+// $Id$
+//
+// Copyright (C) 2002 - 2013 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// read a 2d file in the VTK format
+
+#include "../tests.h"
+#include <deal.II/dofs/dof_handler.h>
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/tria_boundary.h>
+#include <deal.II/grid/tria_boundary_lib.h>
+#include <deal.II/grid/tria_accessor.h>
+#include <deal.II/grid/tria_iterator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_in.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/base/logstream.h>
+
+#include <fstream>
+#include <iomanip>
+#include <string>
+
+std::ofstream logfile("grid_in_vtk_2d/output");
+
+
+template<int dim>
+void check_file (const std::string name,
+ typename GridIn<dim>::Format format)
+{
+ Triangulation<dim> tria;
+ GridIn<dim> gi;
+ gi.attach_triangulation (tria);
+ gi.read(name, format);
+ deallog << name
+ << '\t' << tria.n_vertices()
+ << '\t' << tria.n_cells()
+ << std::endl;
+
+ GridOut grid_out;
+ grid_out.write_gnuplot (tria, deallog.get_file_stream());
+}
+
+void filename_resolution()
+{
+ check_file<2> (std::string("grid_in_vtk_2d/mesh"), GridIn<2>::vtk);
+}
+
+
+int main ()
+{
+ deallog << std::setprecision (2);
+ logfile << std::setprecision (2);
+ deallog.attach(logfile);
+ deallog.depth_console(0);
+ deallog.threshold_double(1.e-10);
+
+ filename_resolution();
+}
+
--- /dev/null
+
+DEAL::grid_in_vtk_2d/mesh 4 1
+-0.50 -0.50 0 1
+0.50 -0.50 0 1
+0.50 0.50 0 1
+-0.50 0.50 0 1
+-0.50 -0.50 0 1
+
+
--- /dev/null
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET UNSTRUCTURED_GRID
+POINTS 4 float
+-0.5 -0.5 0 0.5 -0.5 0 -0.5 0.5 0
+0.5 0.5 0
+CELLS 1 5
+4 0 1 3 2
+CELL_DATA 1
+SCALARS MaterialID double
+LOOKUP_TABLE default
+1
\ No newline at end of file
--- /dev/null
+$NOD
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--- /dev/null
+// ---------------------------------------------------------------------
+// $Id$
+//
+// Copyright (C) 2002 - 2013 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// read a 3d file in the VTK format
+
+#include "../tests.h"
+#include <deal.II/dofs/dof_handler.h>
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/tria_boundary.h>
+#include <deal.II/grid/tria_boundary_lib.h>
+#include <deal.II/grid/tria_accessor.h>
+#include <deal.II/grid/tria_iterator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_in.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/base/logstream.h>
+
+#include <fstream>
+#include <iomanip>
+#include <string>
+
+std::ofstream logfile("grid_in_vtk_3d/output");
+
+
+template<int dim>
+void check_file (const std::string name,
+ typename GridIn<dim>::Format format)
+{
+ Triangulation<dim> tria;
+ GridIn<dim> gi;
+ gi.attach_triangulation (tria);
+ gi.read(name, format);
+ deallog << name
+ << '\t' << tria.n_vertices()
+ << '\t' << tria.n_cells()
+ << std::endl;
+
+ GridOut grid_out;
+ grid_out.write_gnuplot (tria, deallog.get_file_stream());
+}
+
+void filename_resolution()
+{
+ check_file<3> (std::string("grid_in_vtk_3d/mesh"), GridIn<3>::vtk);
+}
+
+
+int main ()
+{
+ deallog << std::setprecision (2);
+ logfile << std::setprecision (2);
+ deallog.attach(logfile);
+ deallog.depth_console(0);
+ deallog.threshold_double(1.e-10);
+
+ filename_resolution();
+}
+
--- /dev/null
+
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--- /dev/null
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projects / dealii-svn.git / commitdiff