 |
Reference documentation for deal.II version 9.1.0-pre
|
|
Reference documentation for deal.II version 9.1.0-pre
|
#include <deal.II/grid/grid_in.h>
Public Types |
Public Member Functions | |
| GridIn () | |
| void | attach_triangulation (Triangulation< dim, spacedim > &tria) |
| void | read (std::istream &in, Format format=Default) |
| void | read (const std::string &in, Format format=Default) |
| void | read_vtk (std::istream &in) |
| void | read_unv (std::istream &in) |
| void | read_ucd (std::istream &in, const bool apply_all_indicators_to_manifolds=false) |
| void | read_abaqus (std::istream &in, const bool apply_all_indicators_to_manifolds=false) |
| void | read_dbmesh (std::istream &in) |
| void | read_xda (std::istream &in) |
| void | read_msh (std::istream &in) |
| void | read_netcdf (const std::string &filename) |
| void | read_tecplot (std::istream &in) |
| void | read_assimp (const std::string &filename, const unsigned int mesh_index=numbers::invalid_unsigned_int, const bool remove_duplicates=true, const double tol=1e-12, const bool ignore_unsupported_element_types=true) |
Static Public Member Functions | |
| static std::string | default_suffix (const Format format) |
| static Format | parse_format (const std::string &format_name) |
| static std::string | get_format_names () |
| static::ExceptionBase & | ExcUnknownSectionType (int arg1) |
| static::ExceptionBase & | ExcUnknownElementType (int arg1) |
| static::ExceptionBase & | ExcUnknownIdentifier (std::string arg1) |
| static::ExceptionBase & | ExcNoTriangulationSelected () |
| static::ExceptionBase & | ExcInvalidVertexIndex (int arg1, int arg2) |
| static::ExceptionBase & | ExcInvalidVertexIndexGmsh (int arg1, int arg2, int arg3) |
| static::ExceptionBase & | ExcInvalidDBMeshFormat () |
| static::ExceptionBase & | ExcInvalidDBMESHInput (std::string arg1) |
| static::ExceptionBase & | ExcDBMESHWrongDimension (int arg1) |
| static::ExceptionBase & | ExcInvalidGMSHInput (std::string arg1) |
| static::ExceptionBase & | ExcGmshUnsupportedGeometry (int arg1) |
| static::ExceptionBase & | ExcGmshNoCellInformation () |
Static Protected Member Functions | |
| static void | debug_output_grid (const std::vector< CellData< dim >> &cells, const std::vector< Point< spacedim >> &vertices, std::ostream &out) |
Protected Attributes | |
| SmartPointer< Triangulation< dim, spacedim >, GridIn< dim, spacedim > > | tria |
Static Private Member Functions | |
| static void | skip_empty_lines (std::istream &in) |
| static void | skip_comment_lines (std::istream &in, const char comment_start) |
| static void | parse_tecplot_header (std::string &header, std::vector< unsigned int > &tecplot2deal, unsigned int &n_vars, unsigned int &n_vertices, unsigned int &n_cells, std::vector< unsigned int > &IJK, bool &structured, bool &blocked) |
Private Attributes | |
| Format | default_format |
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, VTK, ASSIMP, and Cubit are supported as input format for grid data. Any numerical data other than geometric (vertex locations) and topological (how vertices form cells, faces, and edges) information is ignored, but the readers for the various formats generally do read information that associates material ids or boundary ids to cells or faces (see this and this glossary entry for more information).
The mesh you read will form the coarsest level of a Triangulation object. As such, it must not contain hanging nodes or other forms of adaptive refinement, or strange things will happen if the mesh represented by the input file does in fact have them. This is due to the fact that most mesh description formats do not store neighborship information between cells, so the grid reading functions have to regenerate it. They do so by checking whether two cells have a common face. If there are hanging nodes in a triangulation, adjacent cells have no common (complete) face, so the grid reader concludes that the adjacent cells have no neighbors along these faces and must therefore be at the boundary. In effect, an internal crack of the domain is introduced this way. Since such cases are very hard to detect (how is GridIn supposed to decide whether a place where the faces of two small cells coincide with the face or a larger cell is in fact a hanging node associated with local refinement, or is indeed meant to be a crack in the domain?), the library does not make any attempt to catch such situations, and you will get a triangulation that probably does not do what you want. If your goal is to save and later read again a triangulation that has been adaptively refined, then this class is not your solution; rather take a look at the PersistentTriangulation class.
To read grid data, the triangulation to be filled has to be empty. Upon calling the functions of this class, the input file may contain only lines in one dimension; lines and quads in two dimensions; and lines, quads, and hexes in three dimensions. All other cell types (e.g. triangles in two dimensions, triangles or tetrahedra in 3d) are rejected. (Here, the "dimension" refers to the dimensionality of the mesh; it may be embedded in a higher dimensional space, such as a mesh on the two-dimensional surface of the sphere embedded in 3d, or a 1d mesh that discretizes a line in 3d.) The result will be a triangulation that consists of the cells described in the input file, and to the degree possible with material indicators and boundary indicators correctly set as described in the input file.
At present, the following input formats are supported:
UCD (unstructured cell data) format: this format is used for grid input as well as data output. If there are data vectors in the input file, they are ignored, as we are only interested in the grid in this class. The UCD format requires the vertices to be in following ordering: in 2d
* 3-----2 * | | * | | * | | * 0-----1 *
and in 3d
* 7-------6 7-------6 * /| | / /| * / | | / / | * / | | / / | * 3 | | 3-------2 | * | 4-------5 | | 5 * | / / | | / * | / / | | / * |/ / | |/ * 0-------1 0-------1 *
Note, that this ordering is different from the deal.II numbering scheme, see the Triangulation class. The exact description of the UCD format can be found in the AVS Explorer manual (see http://www.avs.com). The UCD format can be read by the read_ucd() function.
DB mesh format: this format is used by the BAMG mesh generator (see http://www-rocq.inria.fr/gamma/cdrom/www/bamg/eng.htm. The documentation of the format in the BAMG manual is very incomplete, so we don't actually parse many of the fields of the output since we don't know their meaning, but the data that is read is enough to build up the mesh as intended by the mesh generator. This format can be read by the read_dbmesh() function.
XDA format: this is a rather simple format used by the MGF code. We don't have an exact specification of the format, but the reader can read in several example files. If the reader does not grok your files, it should be fairly simple to extend it.
Gmsh 1.0 mesh format: this format is used by the Gmsh mesh generator (see http://www.geuz.org/gmsh/). The documentation in the Gmsh manual explains how to generate meshes compatible with the deal.II library (i.e. quads rather than triangles). In order to use this format, Gmsh has to output the file in the old format 1.0. This is done adding the line "Mesh.MshFileVersion = 1" to the input file.
Gmsh 2.0 mesh format: this is a variant of the above format. The read_msh() function automatically determines whether an input file is version 1 or version 2.
Tecplot format: this format is used by TECPLOT and often serves as a basis for data exchange between different applications. Note, that currently only the ASCII format is supported, binary data cannot be read.
UNV format: this format is generated by the Salome mesh generator, see http://www.salome-platform.org/ . The sections of the format that the GridIn::read_unv function supports are documented here:
Note that Salome, let's say in 2D, can only make a quad mesh on an object that has exactly 4 edges (or 4 pieces of the boundary). That means, that if you have a more complicated object and would like to mesh it with quads, you will need to decompose the object into >= 2 separate objects. Then 1) each of these separate objects is meshed, 2) the appropriate groups of cells and/or faces associated with each of these separate objects are created, 3) a compound mesh is built up, and 4) all numbers that might be associated with some of the internal faces of this compound mesh are removed.
VTK 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
* 3-----2 * | | * | | * | | * 0-----1 *
and in 3d
* 7-------6 7-------6 * /| | / /| * / | | / / | * / | | / / | * 4 | | 4-------5 | * | 3-------2 | | 2 * | / / | | / * | / / | | / * |/ / | |/ * 0-------1 0-------1 *
Cubit 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 plug-in script can be found on the deal.II wiki page under Mesh Input and Output.
Alternatively, Cubit can generate ABAQUS files that can be read in via the read_abaqus() function. This may be a better option for geometries with complex boundary condition surfaces and multiple materials - information which is currently not easily obtained through Cubit's python interface.
It is your duty to use a correct numbering of vertices in the cell list, i.e. for lines in 1d, you have to first give the vertex with the lower coordinate value, then that with the higher coordinate value. For quadrilaterals in two dimensions, the vertex indices in the quad list have to be such that the vertices are numbered in counter-clockwise sense.
In two dimensions, another difficulty occurs, which has to do with the sense of a quadrilateral. A quad consists of four lines which have a direction, which is by definition as follows:
* 3-->--2 * | | * ^ ^ * | | * 0-->--1 *
Now, two adjacent cells must have a vertex numbering such that the direction of the common side is the same. For example, the following two quads
* 3---4---5 * | | | * 0---1---2 *
may be characterised by the vertex numbers (0 1 4 3) and (1 2 5 4), since the middle line would get the direction 1->4 when viewed from both cells. The numbering (0 1 4 3) and (5 4 1 2) would not be allowed, since the left quad would give the common line the direction 1->4, while the right one would want to use 4->1, leading to an ambiguity. The Triangulation object is capable of detecting this special case, which can be eliminated by rotating the indices of the right quad by two. However, it would not know what to do if you gave the vertex indices (4 1 2 5), since then it would have to rotate by one element or three, the decision which to take is not yet implemented.
There are more ambiguous cases, where the triangulation may not know what to do at all without the use of sophisticated algorithms. Furthermore, similar problems exist in three space dimensions, where faces and lines have orientations that need to be taken care of.
For this reason, the read_* functions of this class that read in grids in various input formats call the GridReordering class to bring the order of vertices that define the cells into an ordering that satisfies the requirements of the Triangulation class. Be sure to read the documentation of that class if you experience unexpected problems when reading grids through this class.
For each of the mesh reading functions, the last call is always to Triangulation::create_triangulation(). That function checks whether all the cells it creates as part of the coarse mesh are distorted or not (where distortion here means that the Jacobian of the mapping from the reference cell to the real cell has a non-positive determinant, i.e. the cell is pinched or twisted; see the entry on distorted cells in the glossary). If it finds any such cells, it throws an exception. This exception is not caught in the grid reader functions of the current class, and so will propagate through to the function that called it. There, you can catch and ignore the exception if you are certain that there is no harm in dealing with such cells. If you were not aware that your mesh had such cells, your results will likely be of dubious quality at best if you ignore the exception.
| enum GridIn::Format |
List of possible mesh input formats. These values are used when calling the function read() in order to determine the actual reader to be called.
| Enumerator | |
|---|---|
| Default |
Use GridIn::default_format stored in this object. |
| unv |
Use read_unv() |
| ucd |
Use read_ucd() |
| abaqus |
Use read_abaqus() |
| dbmesh |
Use read_dbmesh() |
| xda |
Use read_xda() |
| msh |
Use read_msh() |
| netcdf |
Use read_netcdf() |
| tecplot |
Use read_tecplot() |
| vtk |
Use read_vtk() |
| assimp |
Use read_assimp() |
Constructor.
Definition at line 97 of file grid_in.cc.
| void GridIn< dim, spacedim >::attach_triangulation | ( | Triangulation< dim, spacedim > & | tria | ) |
Attach this triangulation to be fed with the grid data.
Definition at line 105 of file grid_in.cc.
| void GridIn< dim, spacedim >::read | ( | std::istream & | in, |
| Format | format = Default |
||
| ) |
Read from the given stream. If no format is given, GridIn::Format::Default is used.
Definition at line 3039 of file grid_in.cc.
| void GridIn< dim, spacedim >::read | ( | const std::string & | in, |
| Format | format = Default |
||
| ) |
Open the file given by the string and call the previous function read(). This function uses the PathSearch mechanism to find files. The file class used is MESH.
Definition at line 3006 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_vtk | ( | std::istream & | in | ) |
Read grid data from an vtk file. Numerical data is ignored.
ignoring space between points and cells sections////////////////////
Processing the CELLS section that contains cells(cells) and bound_quads(subcelldata)///////////////////////
Processing the CELL_TYPES section////////////////////////
Processing the CELL_DATA section/////////////////////////////
Definition at line 114 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_unv | ( | 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.
Definition at line 420 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_ucd | ( | std::istream & | in, |
| const bool | apply_all_indicators_to_manifolds = false |
||
| ) |
Read grid data from an ucd file. Numerical data is ignored. It is not possible to use a ucd file to set both boundary_id and manifold_id for the same cell. Yet it is possible to use the flag apply_all_indicators_to_manifolds to decide if the indicators in the file refer to manifolds (flag set to true) or boundaries (flag set to false).
Definition at line 669 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_abaqus | ( | std::istream & | in, |
| const bool | apply_all_indicators_to_manifolds = false |
||
| ) |
Read grid data from an Abaqus file. Numerical and constitutive data is ignored. As in the case of the ucd file format, it is possible to use the flag apply_all_indicators_to_manifolds to decide if the indicators in the file refer to manifolds (flag set to true) or boundaries (flag set to false).
Definition at line 928 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_dbmesh | ( | std::istream & | in | ) |
Read grid data from a file containing data in the DB mesh format.
Definition at line 978 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_xda | ( | std::istream & | in | ) |
Read grid data from a file containing data in the XDA format.
Definition at line 1145 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_msh | ( | std::istream & | in | ) |
Read grid data from an msh file, either version 1 or version 2 of that file format. The Gmsh formats are documented at http://www.geuz.org/gmsh/.
Definition at line 1303 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_netcdf | ( | const std::string & | filename | ) |
Read grid data from a NetCDF file. The only data format currently supported is the TAU grid format.
This function requires the library to be linked with the NetCDF library.
| void GridIn< dim, spacedim >::read_tecplot | ( | std::istream & | in | ) |
Read grid data from a file containing tecplot ASCII data. This also works in the absence of any tecplot installation.
Definition at line 2635 of file grid_in.cc.
| void GridIn< dim, spacedim >::read_assimp | ( | const std::string & | filename, |
| const unsigned int | mesh_index = numbers::invalid_unsigned_int, |
||
| const bool | remove_duplicates = true, |
||
| const double | tol = 1e-12, |
||
| const bool | ignore_unsupported_element_types = true |
||
| ) |
Read in a file supported by Assimp, and generate a Triangulation out of it. If you specify a mesh_index, only the mesh with the given index will be extracted, otherwise all meshes which are present in the file will be used to generate the Triangulation.
This function can only be used to read two-dimensional meshes (possibly embedded in three dimensions). This is the standard for graphical software such as blender, or 3D studio max, and that is what the original Assimp library was built for. We "bend" it to deal.II to support complex co-dimension one meshes and complex two-dimensional meshes.
If remove_duplicates is set to true (the default), then duplicated vertices will be removed if their distance is lower than tol.
Only the elements compatible with the given dimension and space dimension will be extracted from the mesh, and only those elements that are compatible with deal.II are supported. If you set ignore_unsupported_element_types, all the other element types are simply ignored by this algorithm. If your mesh contains a mixture of triangles and quadrilaterals, for example, only the quadrilaterals will be extracted. The resulting mesh (as represented in the Triangulation object) may not make any sense if you are mixing compatible and incompatible element types. If ignore_unsupported_element_types is set to false, then an exception is thrown when an unsupported type is encountered.
| filename | The file to read from |
| mesh_index | Index of the mesh within the file |
| remove_duplicates | Remove duplicated vertices |
| tol | Tolerance to use when removing vertices |
| ignore_unsupported_element_types | Don't throw exceptions if we encounter unsupported types during parsing |
Definition at line 2644 of file grid_in.cc.
|
static |
Return the standard suffix for a file in this format.
Definition at line 3102 of file grid_in.cc.
|
static |
Return the enum Format for the format name.
Definition at line 3135 of file grid_in.cc.
|
static |
Return a list of implemented input formats. The different names are separated by vertical bar signs (`|') as used by the ParameterHandler classes.
Definition at line 3192 of file grid_in.cc.
|
staticprotected |
This function can write the raw cell data objects created by the read_* functions in Gnuplot format to a stream. This is sometimes handy if one would like to see what actually was created, if it is known that the data is not correct in some way, but the Triangulation class refuses to generate a triangulation because of these errors. In particular, the output of this class writes out the cell numbers along with the direction of the faces of each cell. In particular the latter information is needed to verify whether the cell data objects follow the requirements of the ordering of cells and their faces, i.e. that all faces need to have unique directions and specified orientations with respect to neighboring cells (see the documentations to this class and the GridReordering class).
The output of this function consists of vectors for each line bounding the cells indicating the direction it has with respect to the orientation of this cell, and the cell number. The whole output is in a form such that it can be read in by Gnuplot and generate the full plot without further ado by the user.
Definition at line 2860 of file grid_in.cc.
|
staticprivate |
Skip empty lines in the input stream, i.e. lines that contain either nothing or only whitespace.
Definition at line 2802 of file grid_in.cc.
|
staticprivate |
Skip lines of comment that start with the indicated character (e.g. #) following the point where the given input stream presently is. After the call to this function, the stream is at the start of the first line after the comment lines, or at the same position as before if there were no lines of comments.
Definition at line 2834 of file grid_in.cc.
|
staticprivate |
This function does the nasty work (due to very lax conventions and different versions of the tecplot format) of extracting the important parameters from a tecplot header, contained in the string header. The other variables are output variables, their value has no influence on the function execution..
Definition at line 2159 of file grid_in.cc.
|
protected |
1.8.11
