Reading and writing meshes in the Gmsh format. More...

#include <gmsh_io.h>

Inheritance diagram for libMesh::GmshIO:

Classes
struct	ElementDefinition
	Defines mapping from libMesh element types to Gmsh element types or vice-versa. More...

struct	ElementMaps
	struct which holds a map from Gmsh to libMesh element numberings and vice-versa. More...

Public Member Functions
	GmshIO (MeshBase &mesh)
	Constructor. More...

	GmshIO (const MeshBase &mesh)
	Constructor. More...

virtual void	read (const std::string &name) override
	Reads in a mesh in the Gmsh *.msh format from the ASCII file given by name. More...

virtual void	write (const std::string &name) override
	This method implements writing a mesh to a specified file in the Gmsh *.msh format. More...

virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided. More...

bool &	binary ()
	Flag indicating whether or not to write a binary file. More...

bool &	write_lower_dimensional_elements ()
	Access to the flag which controls whether boundary elements are written to the Mesh file. More...

virtual void	write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with data to a specified file where the data is taken from the `EquationSystems` object. More...

virtual void	write_discontinuous_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the `EquationSystems` object. More...

virtual void	write_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
	This method should be overridden by "parallel" output formats for writing nodal data. More...

virtual void	write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
	This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided. More...

unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files. More...

Protected Member Functions
MeshBase &	mesh ()

void	set_n_partitions (unsigned int n_parts)
	Sets the number of partitions in the mesh. More...

void	skip_comment_lines (std::istream &in, const char comment_start)
	Reads input from `in`, skipping all the lines that start with the character `comment_start`. More...

const MeshBase &	mesh () const

Protected Attributes
std::vector< bool >	elems_of_dimension
	A vector of bools describing what dimension elements have been encountered when reading a mesh. More...

const bool	_is_parallel_format
	Flag specifying whether this format is parallel-capable. More...

const bool	_serial_only_needed_on_proc_0
	Flag specifying whether this format can be written by only serializing the mesh to processor zero. More...

Private Member Functions
void	read_mesh (std::istream &in)
	Implementation of the read() function. More...

void	write_mesh (std::ostream &out)
	This method implements writing a mesh to a specified file. More...

void	write_post (const std::string &, const std::vector< Number > =nullptr, const std::vector< std::string > =nullptr)
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are optionally provided. More...

Static Private Member Functions
static ElementMaps	build_element_maps ()
	A static function used to construct the _element_maps struct, statically. More...

Private Attributes
bool	_binary
	Flag to write binary data. More...

bool	_write_lower_dimensional_elements
	If true, lower-dimensional elements based on the boundary conditions get written to the output file. More...

Static Private Attributes
static ElementMaps	_element_maps
	A static ElementMaps object that is built statically and used by all instances of this class. More...

Detailed Description

Reading and writing meshes in the Gmsh format.

For a full description of the Gmsh format and to obtain the GMSH software see the Gmsh home page

Author: John W. Peterson

Date: 2004, 2014

Author: Martin Luthi

Date: 2005

Definition at line 51 of file gmsh_io.h.

Constructor & Destructor Documentation

◆ GmshIO() [1/2]

libMesh::GmshIO::GmshIO ( MeshBase & mesh )

explicit

Constructor.

Takes a non-const Mesh reference which it will fill up with elements via the read() command.

◆ GmshIO() [2/2]

libMesh::GmshIO::GmshIO ( const MeshBase & mesh )

explicit

Constructor.

Takes a reference to a constant mesh object. This constructor will only allow us to write the mesh.

Member Function Documentation

◆ ascii_precision()

unsigned int & libMesh::MeshOutput< MeshBase >::ascii_precision ( )

inherited

Return/set the precision to use when writing ASCII files.

By default we use numeric_limits<Real>::digits10 + 2, which should be enough to write out to ASCII and get the exact same Real back when reading in.

Definition at line 244 of file mesh_output.h.

 {
   return _ascii_precision;
 }

◆ binary()

bool& libMesh::GmshIO::binary ( )

Flag indicating whether or not to write a binary file.

While binary files may end up being smaller than equivalent ASCII files, they will almost certainly take longer to write. The reason for this is that the ostream::write() function which is used to write "binary" data to streams, only takes a pointer to char as its first argument. This means if you want to write anything other than a buffer of chars, you first have to use a strange memcpy hack to get the data into the desired format. See the templated to_binary_stream() function below.

◆ build_element_maps()

static ElementMaps libMesh::GmshIO::build_element_maps ( )

staticprivate

A static function used to construct the _element_maps struct, statically.

◆ mesh() [1/2]

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )

protectedinherited

Returns: The object as a writable reference.

Definition at line 169 of file mesh_input.h.

Referenced by libMesh::XdrIO::write_parallel().

 {
   if (_obj == nullptr)
     libmesh_error_msg("ERROR: _obj should not be nullptr!");
   return *_obj;
 }

◆ mesh() [2/2]

const MeshBase & libMesh::MeshOutput< MeshBase >::mesh ( ) const

protectedinherited

Returns: The object as a read-only reference.

Definition at line 234 of file mesh_output.h.

 {
   libmesh_assert(_obj);
   return *_obj;
 }

◆ read()

virtual void libMesh::GmshIO::read ( const std::string & name )

overridevirtual

Reads in a mesh in the Gmsh *.msh format from the ASCII file given by name.

Note: The user is responsible for calling Mesh::prepare_for_use() after reading the mesh and before using it.

The physical group names defined in the Gmsh-file are stored, depending on the element dimension, as either subdomain name or as side name. The IDs of the former can be retrieved by using the MeshBase::get_id_by_name method; the IDs of the latter can be retrieved by using the MeshBase::get_boundary_info and the BoundaryInfo::get_id_by_name methods.

Implements libMesh::MeshInput< MeshBase >.

◆ read_mesh()

void libMesh::GmshIO::read_mesh ( std::istream & in )

private

Implementation of the read() function.

This function is called by the public interface function and implements reading the file.

◆ set_n_partitions()

void libMesh::MeshInput< MeshBase >::set_n_partitions ( unsigned int n_parts )

protectedinherited

Sets the number of partitions in the mesh.

Typically this gets done by the partitioner, but some parallel file formats begin "pre-partitioned".

Definition at line 91 of file mesh_input.h.

References libMesh::MeshInput< MT >::mesh().

91 { this->mesh().set_n_partitions() = n_parts; }

libMesh::MeshInput< MeshBase >::mesh

MeshBase & mesh()

Definition: mesh_input.h:169

libMesh::MeshBase::set_n_partitions

unsigned int & set_n_partitions()

Definition: mesh_base.h:1412

◆ skip_comment_lines()

void libMesh::MeshInput< MeshBase >::skip_comment_lines	(	std::istream &	in,
		const char	comment_start
	)

protectedinherited

Reads input from in, skipping all the lines that start with the character comment_start.

Definition at line 179 of file mesh_input.h.

 {
   char c, line[256];
 
   while (in.get(c), c==comment_start)
     in.getline (line, 255);
 
   // put back first character of
   // first non-comment line
   in.putback (c);
 }

◆ write()

virtual void libMesh::GmshIO::write ( const std::string & name )

overridevirtual

This method implements writing a mesh to a specified file in the Gmsh *.msh format.

Implements libMesh::MeshOutput< MeshBase >.

◆ write_discontinuous_equation_systems()

virtual void libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems	(	const std::string &	,
		const EquationSystems &	,
		const std::set< std::string > *	system_names = `nullptr`
	)

virtualinherited

This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the EquationSystems object.

◆ write_equation_systems()

virtual void libMesh::MeshOutput< MeshBase >::write_equation_systems	(	const std::string &	,
		const EquationSystems &	,
		const std::set< std::string > *	system_names = `nullptr`
	)

virtualinherited

This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems object.

Reimplemented in libMesh::NameBasedIO.

◆ write_lower_dimensional_elements()

bool& libMesh::GmshIO::write_lower_dimensional_elements ( )

Access to the flag which controls whether boundary elements are written to the Mesh file.

◆ write_mesh()

void libMesh::GmshIO::write_mesh ( std::ostream & out )

private

This method implements writing a mesh to a specified file.

This will write an ASCII *.msh file.

◆ write_nodal_data() [1/2]

virtual void libMesh::GmshIO::write_nodal_data	(	const std::string &	,
		const std::vector< Number > &	,
		const std::vector< std::string > &
	)

overridevirtual

This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided.

Reimplemented from libMesh::MeshOutput< MeshBase >.

◆ write_nodal_data() [2/2]

virtual void libMesh::MeshOutput< MeshBase >::write_nodal_data	(	const std::string &	,
		const NumericVector< Number > &	,
		const std::vector< std::string > &
	)

virtualinherited

This method should be overridden by "parallel" output formats for writing nodal data.

Instead of getting a localized copy of the nodal solution vector, it is passed a NumericVector of type=PARALLEL which is in node-major order i.e. (u0,v0,w0, u1,v1,w1, u2,v2,w2, u3,v3,w3, ...) and contains n_nodes*n_vars total entries. Then, it is up to the individual I/O class to extract the required solution values from this vector and write them in parallel.

If not implemented, localizes the parallel vector into a std::vector and calls the other version of this function.

Reimplemented in libMesh::Nemesis_IO.

◆ write_nodal_data_discontinuous()

virtual void libMesh::MeshOutput< MeshBase >::write_nodal_data_discontinuous	(	const std::string &	,
		const std::vector< Number > &	,
		const std::vector< std::string > &
	)

virtualinherited

This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided.

Reimplemented in libMesh::ExodusII_IO.

Definition at line 114 of file mesh_output.h.

117 { libmesh_not_implemented(); }

◆ write_post()

void libMesh::GmshIO::write_post	(	const std::string &	,
		const std::vector< Number > *	= `nullptr`,
		const std::vector< std::string > *	= `nullptr`
	)

private

This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are optionally provided.

This will write an ASCII or binary *.pos file, depending on the binary flag.

Member Data Documentation

◆ _binary

bool libMesh::GmshIO::_binary

private

Flag to write binary data.

Definition at line 149 of file gmsh_io.h.

◆ _element_maps

ElementMaps libMesh::GmshIO::_element_maps

staticprivate

A static ElementMaps object that is built statically and used by all instances of this class.

Definition at line 200 of file gmsh_io.h.

◆ _is_parallel_format

const bool libMesh::MeshOutput< MeshBase >::_is_parallel_format

protectedinherited

Flag specifying whether this format is parallel-capable.

If this is false (default) I/O is only permitted when the mesh has been serialized.

Definition at line 159 of file mesh_output.h.

◆ _serial_only_needed_on_proc_0

const bool libMesh::MeshOutput< MeshBase >::_serial_only_needed_on_proc_0

protectedinherited

Flag specifying whether this format can be written by only serializing the mesh to processor zero.

If this is false (default) the mesh will be serialized to all processors

Definition at line 168 of file mesh_output.h.

◆ _write_lower_dimensional_elements

bool libMesh::GmshIO::_write_lower_dimensional_elements

private

If true, lower-dimensional elements based on the boundary conditions get written to the output file.

Definition at line 155 of file gmsh_io.h.

◆ elems_of_dimension

std::vector<bool> libMesh::MeshInput< MeshBase >::elems_of_dimension

protectedinherited

A vector of bools describing what dimension elements have been encountered when reading a mesh.

Definition at line 97 of file mesh_input.h.

The documentation for this class was generated from the following file:

include/mesh/gmsh_io.h

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GmshIO() [1/2]

◆ GmshIO() [2/2]

Member Function Documentation

◆ ascii_precision()

◆ binary()

◆ build_element_maps()

◆ mesh() [1/2]

◆ mesh() [2/2]

◆ read()

◆ read_mesh()

◆ set_n_partitions()

◆ skip_comment_lines()

◆ write()

◆ write_discontinuous_equation_systems()

◆ write_equation_systems()

◆ write_lower_dimensional_elements()

◆ write_mesh()

◆ write_nodal_data() [1/2]

◆ write_nodal_data() [2/2]

◆ write_nodal_data_discontinuous()

◆ write_post()

Member Data Documentation

◆ _binary

◆ _element_maps

◆ _is_parallel_format

◆ _serial_only_needed_on_proc_0

◆ _write_lower_dimensional_elements

◆ elems_of_dimension