This class implements reading and writing meshes in the VTK format. More...

#include <vtk_io.h>

Inheritance diagram for libMesh::VTKIO:

Classes
struct	ElementMaps
	Helper object that holds a map from VTK to libMesh element types and vice-versa. More...

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

	VTKIO (const MeshBase &mesh)
	Constructor. 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...

virtual void	read (const std::string &) override
	This method implements reading a mesh from a specified file in VTK format. More...

virtual void	write (const std::string &) override
	Output the mesh without solutions to a .pvtu file. More...

void	set_compression (bool b)
	Setter for compression flag. More...

vtkUnstructuredGrid *	get_vtk_grid ()
	Get a pointer to the VTK unstructured grid data structure. 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	nodes_to_vtk ()
	write the nodes from the mesh into a vtkUnstructuredGrid and update the local_node_map. More...

void	cells_to_vtk ()
	write the cells from the mesh into a vtkUnstructuredGrid More...

void	node_values_to_vtk (const std::string &name, const std::vector< Real > &local_values)
	write the nodal values of soln to a vtkUnstructuredGrid More...

void	get_local_node_values (std::vector< Number > &local_values, std::size_t variable, const std::vector< Number > &soln, const std::vector< std::string > &names)
	Extract the values of soln that correspond to the nodes. More...

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

Private Attributes
vtkSmartPointer< vtkUnstructuredGrid >	_vtk_grid
	Write the system vectors to vtk. More...

bool	_compress
	Flag to indicate whether the output should be compressed. More...

std::map< dof_id_type, dof_id_type >	_local_node_map
	maps global node id to node id of partition More...

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

Detailed Description

This class implements reading and writing meshes in the VTK format.

Format description: cf. VTK home page.

This class will not have any functionality unless VTK is detected during configure and hence LIBMESH_HAVE_VTK is defined.

Author: Wout Ruijter; John W. Peterson

Date: 2007

Definition at line 59 of file vtk_io.h.

Constructor & Destructor Documentation

◆ VTKIO() [1/2]

libMesh::VTKIO::VTKIO ( MeshBase & mesh )

explicit

Constructor.

Takes a writable reference to a mesh object. This is the constructor required to read a mesh.

◆ VTKIO() [2/2]

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

explicit

Constructor.

Takes a read-only reference to a mesh object. This is the constructor required to write a 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;
 }

◆ build_element_maps()

static ElementMaps libMesh::VTKIO::build_element_maps ( )

staticprivate

Static function used to construct the _element_maps struct.

◆ cells_to_vtk()

void libMesh::VTKIO::cells_to_vtk ( )

private

write the cells from the mesh into a vtkUnstructuredGrid

◆ get_local_node_values()

void libMesh::VTKIO::get_local_node_values	(	std::vector< Number > &	local_values,
		std::size_t	variable,
		const std::vector< Number > &	soln,
		const std::vector< std::string > &	names
	)

private

Extract the values of soln that correspond to the nodes.

This method overwrites all values in local_values

◆ get_vtk_grid()

vtkUnstructuredGrid* libMesh::VTKIO::get_vtk_grid ( )

Get a pointer to the VTK unstructured grid data structure.

◆ 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;
 }

◆ node_values_to_vtk()

void libMesh::VTKIO::node_values_to_vtk	(	const std::string &	name,
		const std::vector< Real > &	local_values
	)

private

write the nodal values of soln to a vtkUnstructuredGrid

◆ nodes_to_vtk()

void libMesh::VTKIO::nodes_to_vtk ( )

private

write the nodes from the mesh into a vtkUnstructuredGrid and update the local_node_map.

◆ read()

virtual void libMesh::VTKIO::read ( const std::string & )

overridevirtual

This method implements reading a mesh from a specified file in VTK format.

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

Implements libMesh::MeshInput< MeshBase >.

◆ set_compression()

void libMesh::VTKIO::set_compression ( bool b )

Setter for compression flag.

◆ 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::VTKIO::write ( const std::string & )

overridevirtual

Output the mesh without solutions to a .pvtu file.

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

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_nodal_data() [1/2]

virtual void libMesh::VTKIO::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.

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

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(); }

Member Data Documentation

◆ _compress

bool libMesh::VTKIO::_compress

private

Flag to indicate whether the output should be compressed.

Definition at line 173 of file vtk_io.h.

◆ _element_maps

ElementMaps libMesh::VTKIO::_element_maps

staticprivate

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

Definition at line 224 of file vtk_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.

◆ _local_node_map

std::map<dof_id_type, dof_id_type> libMesh::VTKIO::_local_node_map

private

maps global node id to node id of partition

Definition at line 178 of file vtk_io.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.

◆ _vtk_grid

vtkSmartPointer<vtkUnstructuredGrid> libMesh::VTKIO::_vtk_grid

private

Write the system vectors to vtk.

This function is not currently used by anything, so it is commented out, and may eventually be removed entirely. pointer to the VTK grid. the vtkSmartPointer will automatically initialize the value to null and keep track of reference counting.

Definition at line 168 of file vtk_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/vtk_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

◆ VTKIO() [1/2]

◆ VTKIO() [2/2]

Member Function Documentation

◆ ascii_precision()

◆ build_element_maps()

◆ cells_to_vtk()

◆ get_local_node_values()

◆ get_vtk_grid()

◆ mesh() [1/2]

◆ mesh() [2/2]

◆ node_values_to_vtk()

◆ nodes_to_vtk()

◆ read()

◆ set_compression()

◆ set_n_partitions()

◆ skip_comment_lines()

◆ write()

◆ write_discontinuous_equation_systems()

◆ write_equation_systems()

◆ write_nodal_data() [1/2]

◆ write_nodal_data() [2/2]

◆ write_nodal_data_discontinuous()

Member Data Documentation

◆ _compress

◆ _element_maps

◆ _is_parallel_format

◆ _local_node_map

◆ _serial_only_needed_on_proc_0

◆ _vtk_grid

◆ elems_of_dimension