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// $Id: grid_in.h 31163 2013-10-07 13:43:08Z bangerth $
//
// Copyright (C) 1999 - 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.
//
// ---------------------------------------------------------------------
#ifndef __deal2__grid_in_h
#define __deal2__grid_in_h
#include <deal.II/base/config.h>
#include <deal.II/base/exceptions.h>
#include <deal.II/base/smartpointer.h>
#include <deal.II/base/point.h>
#include <iostream>
#include <vector>
#include <string>
DEAL_II_NAMESPACE_OPEN
template <int dim, int space_dim> class Triangulation;
template <int dim> struct CellData;
struct SubCellData;
/**
* 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, 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.
*
* @note Since deal.II only supports line, quadrilateral and hexahedral meshes,
* the functions in this class can only read meshes that consist exclusively
* of such cells. If you absolutely need to work with a mesh that uses triangles
* or tetrahedra, then your only option is to convert the mesh to quadrilaterals
* and hexahedra. A tool that can do this is tethex, see
* http://code.google.com/p/tethex/wiki/Tethex .
*
* The mesh you read will form the coarsest level of a @p Triangulation object.
* As such, it must not contain hanging nodes or other forms or adaptive
* refinement and 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.
*
* @note It is not uncommon to experience unexpected problems when reading
* generated meshes for the first time using this class. If this applies to
* you, be sure to read the documentation right until the end, and
* also read the documentation of the GridReordering class.
*
* To read grid data, the triangulation to be fed with has to be empty.
* When giving a file which does not contain the assumed information or
* which does not keep to the right format, the state of the triangulation
* will be undefined afterwards. Upon input, only lines in one dimension
* and line and quads in two dimensions are accepted. All other cell types
* (e.g. triangles in two dimensions, quads and hexes in 3d) are rejected.
* The vertex and cell numbering in the input file, which
* need not be consecutively, is lost upon transfer to the triangulation
* object, since this one needs consecutively numbered elements.
*
* Material indicators are accepted to denote the material ID of cells and
* to denote boundary part indication for lines in 2D. Read the according
* sections in the documentation of the Triangulation class for
* further details.
*
*
* <h3>Supported input formats</h3>
*
* At present, the following input formats are supported:
* <ul>
* <li> @p 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
* @verbatim
* 3-----2
* | |
* | |
* | |
* 0-----1
* @endverbatim
* and in 3d
* @verbatim
* 7-------6 7-------6
* /| | / /|
* / | | / / |
* / | | / / |
* 3 | | 3-------2 |
* | 4-------5 | | 5
* | / / | | /
* | / / | | /
* |/ / | |/
* 0-------1 0-------1
* @endverbatim
* 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 @p UCD format can be read by the
* read_ucd() function.
*
* <li> <tt>DB mesh</tt> format: this format is used by the @p BAMG mesh
* generator (see
* http://www-rocq.inria.fr/gamma/cdrom/www/bamg/eng.htm. The
* documentation of the format in the @p 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.
*
* <li> @p 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.
*
* <li> <tt>Gmsh 1.0 mesh</tt> format: this format is used by the @p
* GMSH mesh generator (see http://www.geuz.org/gmsh/ ). The
* documentation in the @p 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.
*
* <li> <tt>Gmsh 2.0 mesh</tt> 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.
*
* <li> <tt>Tecplot</tt> format: this format is used by @p 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.
*
* <li> <tt>UNV</tt> 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:
* <ul>
* <li> section 2411: http://www.sdrl.uc.edu/universal-file-formats-for-modal-analysis-testing-1/file-format-storehouse/unv_2411.htm
* <li> section 2412: http://www.sdrl.uc.edu/universal-file-formats-for-modal-analysis-testing-1/file-format-storehouse/unv_2412.htm
* <li> section 2467: http://www.sdrl.uc.edu/universal-file-formats-for-modal-analysis-testing-1/file-format-storehouse/unv_2467.htm
* <li> all sections of this format, even if they may not be supported in
* our reader, can be found here:
* http://www.sdrl.uc.edu/universal-file-formats-for-modal-analysis-testing-1/file-format-storehouse/file-formats
* </ul>
* 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.
*
* <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
* plug-in script can be found on the deal.II wiki page,
* http://code.google.com/p/dealii/wiki/MeshInputAndOutput .
*
* There is also a little program <code>bin/mesh_conversion</code> (in the directory
* where deal.II was installed), written by Jean-Paul Pelteret, that can
* convert Cubit ABAQUS files into the UCD format that can be read in as
* discussed above. The program was designed with the intention of
* exporting geometries with complex boundary condition surfaces and
* multiple materials from Cubit - information which is currently not
* easily obtained through Cubit's python interface. Using the the
* program is simple: to use it, it needs to be built and run with the
* command
* @code
* /path/to/deal.II/bin/mesh_conversion <spatial_dimension> /path/to/input_file.inp /path/to/output_file.ucd
* @endcode.
* More information is available in the readme file included with the
* program and located in the <code>contrib/mesh_conversion/README.txt</code> file in
* the deal.II source directory tree. Note that the program's copyright remains with its author
* and that it is under a separate license than the rest of the
* library.
*
* To build the program, see the <code>doc/readmes.html</code> and
* <code>doc/development/cmake.html</code> files.
* </ul>
*
*
* <h3>Structure of input grid data. The GridReordering class</h3>
*
* 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 @p 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 per definitionem as follows:
* @verbatim
* 3-->--2
* | |
* ^ ^
* | |
* 0-->--1
* @endverbatim
* 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
* @verbatim
* 3---4---5
* | | |
* 0---1---2
* @endverbatim
* may be characterised by the vertex numbers <tt>(0 1 4 3)</tt> and
* <tt>(1 2 5 4)</tt>, since the middle line would get the direction <tt>1->4</tt>
* when viewed from both cells. The numbering <tt>(0 1 4 3)</tt> and
* <tt>(5 4 1 2)</tt> would not be allowed, since the left quad would give the
* common line the direction <tt>1->4</tt>, while the right one would want
* to use <tt>4->1</tt>, 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 <tt>(4 1 2 5)</tt>, 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 <tt>read_*</tt> 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 requiremenets of the
* Triangulation class. Be sure to read the documentation of
* that class if you experience unexpected problems when reading grids
* through this class.
*
*
* <h3>Dealing with distorted mesh cells</h3>
*
* 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 @ref GlossDistorted "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.
*
*
* @ingroup grid
* @ingroup input
* @author Wolfgang Bangerth, 1998, 2000, Luca Heltai, 2004, 2007
*/
template <int dim, int spacedim=dim>
class GridIn
{
public:
/**
* 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.
*/
enum Format
{
/// Use GridIn::default_format stored in this object
Default,
/// Use read_unv()
unv,
/// Use read_ucd()
ucd,
/// Use read_dbmesh()
dbmesh,
/// Use read_xda()
xda,
/// Use read_msh()
msh,
/// Use read_netcdf()
netcdf,
/// Use read_tecplot()
tecplot,
/// Use read_vtk()
vtk
};
/**
* Constructor.
*/
GridIn ();
/**
* Attach this triangulation
* to be fed with the grid data.
*/
void attach_triangulation (Triangulation<dim,spacedim> &tria);
/**
* Read from the given stream. If
* no format is given,
* GridIn::Format::Default is
* used.
*/
void read (std::istream &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 <code>MESH</code>.
*/
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.
*/
void read_unv(std::istream &in);
/**
* Read grid data from an ucd file.
* Numerical data is ignored.
*/
void read_ucd (std::istream &in);
/**
* Read grid data from a file
* containing data in the DB mesh
* format.
*/
void read_dbmesh (std::istream &in);
/**
* Read grid data from a file
* containing data in the XDA
* format.
*/
void read_xda (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/ .
*
* @note The input function of
* deal.II does not distinguish
* between newline and other
* whitespace. Therefore, deal.II
* will be able to read files in
* a slightly more general format
* than Gmsh.
*/
void read_msh (std::istream &in);
/**
* Read grid data from a NetCDF
* file. The only data format
* currently supported is the
* <tt>TAU grid format</tt>.
*
* This function requires the
* library to be linked with the
* NetCDF library.
*/
void read_netcdf (const std::string &filename);
/**
* Read grid data from a file containing
* tecplot ASCII data. This also works in
* the absence of any tecplot
* installation.
*/
void read_tecplot (std::istream &in);
/**
* Returns the standard suffix
* for a file in this format.
*/
static std::string default_suffix (const Format format);
/**
* Return the enum Format for the
* format name.
*/
static Format parse_format (const std::string &format_name);
/**
* Return a list of implemented input
* formats. The different names are
* separated by vertical bar signs (<tt>`|'</tt>)
* as used by the ParameterHandler
* classes.
*/
static std::string get_format_names ();
/**
* Exception
*/
DeclException1(ExcUnknownSectionType,
int,
<< "The section type <" << arg1 << "> in an UNV "
<< "input file is not implemented.");
/**
* Exception
*/
DeclException1(ExcUnknownElementType,
int,
<< "The element type <" << arg1 << "> in an UNV "
<< "input file is not implemented.");
/**
* Exception
*/
DeclException1 (ExcUnknownIdentifier,
std::string,
<< "The identifier <" << arg1 << "> as name of a "
<< "part in an UCD input file is unknown or the "
<< "respective input routine is not implemented."
<< "(Maybe the space dimension of triangulation and "
<< "input file do not match?");
/**
* Exception
*/
DeclException0 (ExcNoTriangulationSelected);
/**
* Exception
*/
DeclException2 (ExcInvalidVertexIndex,
int, int,
<< "Trying to access invalid vertex index " << arg2
<< " while creating cell " << arg1);
/**
* Exception
*/
DeclException0 (ExcInvalidDBMeshFormat);
/**
* Exception
*/
DeclException1 (ExcInvalidDBMESHInput,
std::string,
<< "The string <" << arg1 << "> is not recognized at the present"
<< " position of a DB Mesh file.");
/**
* Exception
*/
DeclException1 (ExcDBMESHWrongDimension,
int,
<< "The specified dimension " << arg1
<< " is not the same as that of the triangulation to be created.");
DeclException1 (ExcInvalidGMSHInput,
std::string,
<< "The string <" << arg1 << "> is not recognized at the present"
<< " position of a Gmsh Mesh file.");
DeclException1 (ExcGmshUnsupportedGeometry,
int,
<< "The Element Identifier <" << arg1 << "> is not "
<< "supported in the Deal.II Library.\n"
<< "Supported elements are: \n"
<< "ELM-TYPE\n"
<< "1 Line (2 nodes, 1 edge).\n"
<< "3 Quadrilateral (4 nodes, 4 edges).\n"
<< "5 Hexahedron (8 nodes, 12 edges, 6 faces).\n"
<< "15 Point (1 node, ignored when read)");
DeclException0 (ExcGmshNoCellInformation);
protected:
/**
* Store address of the triangulation to
* be fed with the data read in.
*/
SmartPointer<Triangulation<dim,spacedim>,GridIn<dim,spacedim> > tria;
/**
* This function can write the
* raw cell data objects created
* by the <tt>read_*</tt> 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.
*/
static void debug_output_grid (const std::vector<CellData<dim> > &cells,
const std::vector<Point<spacedim> > &vertices,
std::ostream &out);
private:
/**
* Skip empty lines in the input
* stream, i.e. lines that
* contain either nothing or only
* whitespace.
*/
static void skip_empty_lines (std::istream &in);
/**
* Skip lines of comment that
* start with the indicated
* character (e.g. <tt>#</tt>)
* 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.
*/
static void skip_comment_lines (std::istream &in,
const char comment_start);
/**
* 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 @p header. The other variables
* are output variables, their value has no
* influence on the function execution..
*/
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);
/**
* Input format used by read() if
* no format is given.
*/
Format default_format;
};
/* -------------- declaration of explicit specializations ------------- */
#ifndef DOXYGEN
template <>
void
GridIn<2>::debug_output_grid (const std::vector<CellData<2> > &cells,
const std::vector<Point<2> > &vertices,
std::ostream &out);
template <>
void
GridIn<2,3>::debug_output_grid (const std::vector<CellData<2> > &cells,
const std::vector<Point<3> > &vertices,
std::ostream &out);
template <>
void
GridIn<3>::debug_output_grid (const std::vector<CellData<3> > &cells,
const std::vector<Point<3> > &vertices,
std::ostream &out);
#endif // DOXYGEN
DEAL_II_NAMESPACE_CLOSE
#endif
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