libMesh::ExodusII_IO Class Reference

The ExodusII_IO class implements reading meshes in the ExodusII file format from Sandia National Labs. More...

#include <exodusII_io.h>

Inheritance diagram for libMesh::ExodusII_IO:

Public Member Functions
	ExodusII_IO (MeshBase &mesh, bool single_precision=false)
	Constructor. More...
virtual	~ExodusII_IO ()
	Destructor. More...
virtual void	read (const std::string &name) override
	This method implements reading a mesh from a specified file. More...
virtual void	write (const std::string &fname) override
	This method implements writing a mesh to a specified file. More...
void	verbose (bool set_verbosity)
	Set the flag indicating if we should be verbose. More...
const std::vector< Real > &	get_time_steps ()
int	get_num_time_steps ()
void	copy_nodal_solution (System &system, std::string var_name, unsigned int timestep=1)
	Backward compatibility version of function that takes a single variable name. More...
void	copy_nodal_solution (System &system, std::string system_var_name, std::string exodus_var_name, unsigned int timestep=1)
	If we read in a nodal solution while reading in a mesh, we can attempt to copy that nodal solution into an EquationSystems object. More...
void	copy_elemental_solution (System &system, std::string system_var_name, std::string exodus_var_name, unsigned int timestep=1)
	If we read in a elemental solution while reading in a mesh, we can attempt to copy that elemental solution into an EquationSystems object. More...
void	read_elemental_variable (std::string elemental_var_name, unsigned int timestep, std::map< unsigned int, Real > &unique_id_to_value_map)
	Given an elemental variable and a time step, returns a mapping from the elements (top parent) unique IDs to the value of the elemental variable at the corresponding time step index. More...
void	read_global_variable (std::vector< std::string > global_var_names, unsigned int timestep, std::vector< Real > &global_values)
	Given a vector of global variables and a time step, returns the values of the global variable at the corresponding time step index. More...
void	write_discontinuous_exodusII (const std::string &name, const EquationSystems &es, const std::set< std::string > *system_names=nullptr)
	Writes a exodusII file with discontinuous data. More...
void	write_timestep_discontinuous (const std::string &fname, const EquationSystems &es, const int timestep, const Real time, const std::set< std::string > *system_names=nullptr)
	Writes a discontinuous solution at a specific timestep. More...
void	write_element_data (const EquationSystems &es)
	Write out element solution. More...
void	write_element_data_from_discontinuous_nodal_data (const EquationSystems &es, const std::set< std::string > *system_names=nullptr, const std::string &var_suffix="_elem_node_")
	Similar to the function above, but instead of only handling (CONSTANT, MONOMIAL) data, writes out a general discontinuous solution field, e.g. More...
virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	Write out a nodal solution. More...
void	write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	Write out a discontinuous nodal solution. More...
void	write_global_data (const std::vector< Number > &, const std::vector< std::string > &)
	Write out global variables. More...
void	write_information_records (const std::vector< std::string > &)
	Write out information records. More...
void	write_timestep (const std::string &fname, const EquationSystems &es, const int timestep, const Real time, const std::set< std::string > *system_names=nullptr)
	Writes out the solution at a specific timestep. More...
void	set_output_variables (const std::vector< std::string > &output_variables, bool allow_empty=true)
	Sets the list of variable names to be included in the output. More...
void	use_mesh_dimension_instead_of_spatial_dimension (bool val)
	In the general case, meshes containing 2D elements can be manifolds living in 3D space, thus by default we write all meshes with the Exodus dimension set to LIBMESH_DIM = mesh.spatial_dimension(). More...
void	write_as_dimension (unsigned dim)
	Directly control the num_dim which is written to the Exodus file. More...
void	set_coordinate_offset (Point p)
	Allows you to set a vector that is added to the coordinates of all of the nodes. More...
void	append (bool val)
	If true, this flag will cause the ExodusII_IO object to attempt to open an existing file for writing, rather than creating a new file. More...
const std::vector< std::string > &	get_elem_var_names ()
	Return list of the elemental variable names. More...
const std::vector< std::string > &	get_nodal_var_names ()
	Return list of the nodal variable names. More...
ExodusII_IO_Helper &	get_exio_helper ()
	Return a reference to the ExodusII_IO_Helper object. More...
void	write_nodal_data_common (std::string fname, const std::vector< std::string > &names, bool continuous=true)
	This function factors out a bunch of code which is common to the write_nodal_data() and write_nodal_data_discontinuous() functions. 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...
unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files. More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

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...
const Parallel::Communicator &	_communicator

Private Attributes
std::unique_ptr< ExodusII_IO_Helper >	exio_helper
	Only attempt to instantiate an ExodusII helper class if the Exodus API is defined. More...
int	_timestep
	Stores the current value of the timestep when calling ExodusII_IO::write_timestep(). More...
bool	_verbose
	should we be verbose? More...
bool	_append
	Default false. More...
std::vector< std::string >	_output_variables
	The names of the variables to be output. More...
bool	_allow_empty_variables
	If true, _output_variables is allowed to remain empty. More...

Detailed Description

The ExodusII_IO class implements reading meshes in the ExodusII file format from Sandia National Labs.

By default, LibMesh expects ExodusII files to have a ".exd" or ".e" file extension.

Author

Benjamin Kirk

John Peterson

Date

2004 Handles reading and writing of Exodus binary files.

Definition at line 52 of file exodusII_io.h.

Constructor & Destructor Documentation

ExodusII_IO()

libMesh::ExodusII_IO::ExodusII_IO ( MeshBase &  mesh, bool  single_precision = false  )

explicit

Constructor.

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

~ExodusII_IO()

virtual libMesh::ExodusII_IO::~ExodusII_IO ( )

virtual

Destructor.

Member Function Documentation

append()

void libMesh::ExodusII_IO::append

(

bool

val

)

If true, this flag will cause the ExodusII_IO object to attempt to open an existing file for writing, rather than creating a new file.

Obviously this will only work if the file already exists.

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;
}

comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inherited

Returns

A reference to the Parallel::Communicator object used by this mesh.

Definition at line 89 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::EpetraVector< T >::EpetraVector(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), and libMesh::Parallel::sync_node_data_by_element_id_once().

  { return _communicator; }

copy_elemental_solution()

void libMesh::ExodusII_IO::copy_elemental_solution	(	System &	system,
		std::string	system_var_name,
		std::string	exodus_var_name,
		unsigned int	timestep = 1
	)

If we read in a elemental solution while reading in a mesh, we can attempt to copy that elemental solution into an EquationSystems object.

copy_nodal_solution() [1/2]

void libMesh::ExodusII_IO::copy_nodal_solution	(	System &	system,
		std::string	var_name,
		unsigned int	timestep = 1
	)

Backward compatibility version of function that takes a single variable name.

Deprecated:

Use the version of copy_nodal_solution() that takes two names.

copy_nodal_solution() [2/2]

void libMesh::ExodusII_IO::copy_nodal_solution	(	System &	system,
		std::string	system_var_name,
		std::string	exodus_var_name,
		unsigned int	timestep = 1
	)

If we read in a nodal solution while reading in a mesh, we can attempt to copy that nodal solution into an EquationSystems object.

get_elem_var_names()

const std::vector<std::string>& libMesh::ExodusII_IO::get_elem_var_names

(

)

Return list of the elemental variable names.

get_exio_helper()

ExodusII_IO_Helper& libMesh::ExodusII_IO::get_exio_helper

(

)

Return a reference to the ExodusII_IO_Helper object.

get_nodal_var_names()

const std::vector<std::string>& libMesh::ExodusII_IO::get_nodal_var_names

(

)

Return list of the nodal variable names.

get_num_time_steps()

int libMesh::ExodusII_IO::get_num_time_steps

(

)

Returns

The number of timesteps currently stored in the Exodus file.

Knowing the number of time steps currently stored in the file is sometimes necessary when appending, so we can know where to start writing new data. Throws an error if the file is not currently open for reading or writing.

get_time_steps()

const std::vector<Real>& libMesh::ExodusII_IO::get_time_steps

(

)

Returns

An array containing the timesteps in the file.

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;
}

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inherited

Returns

The number of processors in the group.

Definition at line 95 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::size().

Referenced by libMesh::MeshBase::partition().

  { return cast_int<processor_id_type>(_communicator.size()); }

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inherited

Returns

The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::Communicator::rank().

Referenced by libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::DofMap::last_dof(), libMesh::MeshBase::n_active_local_elem(), libMesh::DofMap::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), and libMesh::MeshTools::weight().

  { return cast_int<processor_id_type>(_communicator.rank()); }

read()

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

overridevirtual

This method implements reading a mesh from a specified file.

Open the file named name and read the mesh in Sandia National Lab's ExodusII format. This is the method to use for reading in meshes generated by cubit. Works in 2D for TRIs, TRI6s, QUAD s, and QUAD9s. Works in 3D for TET4s, TET10s, HEX8s, and HEX27s.

Implements libMesh::MeshInput< MeshBase >.

read_elemental_variable()

void libMesh::ExodusII_IO::read_elemental_variable	(	std::string	elemental_var_name,
		unsigned int	timestep,
		std::map< unsigned int, Real > &	unique_id_to_value_map
	)

Given an elemental variable and a time step, returns a mapping from the elements (top parent) unique IDs to the value of the elemental variable at the corresponding time step index.

Note that this function MUST only be called before renumbering! This function is essentially a wrapper for read_elemental_var_values from the exodus helper (which is not accessible outside this class).

Parameters

elemental_var_name	Name of an elemental variable
timestep	The corresponding time step index
unique_id_to_value_map	The map to be filled

read_global_variable()

void libMesh::ExodusII_IO::read_global_variable	(	std::vector< std::string >	global_var_names,
		unsigned int	timestep,
		std::vector< Real > &	global_values
	)

Given a vector of global variables and a time step, returns the values of the global variable at the corresponding time step index.

Parameters

global_var_names	Vector of names of global variables
timestep	The corresponding time step index
global_values	The vector to be filled

set_coordinate_offset()

void libMesh::ExodusII_IO::set_coordinate_offset

(

Point

p

)

Allows you to set a vector that is added to the coordinates of all of the nodes.

Effectively, this "moves" the mesh to a particular position.

Deprecated:

As requested by Roy in libmesh PR #90, this function was "deprecated on arrival". There is not really a suitable replacement for it in the works, however. The same effect could be achieved by calling MeshTools::Modification::translate() twice, but that approach seems inefficient in the case of very large problems with millions of nodes. That said, this should probably become a base class API so that it works for all the different IO subclasses.

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().

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

set_output_variables()

void libMesh::ExodusII_IO::set_output_variables	(	const std::vector< std::string > &	output_variables,
		bool	allow_empty = true
	)

Sets the list of variable names to be included in the output.

This is optional. If this is never called then all variables will be present. If this is called and an empty vector is supplied no variables will be output. Setting the allow_empty = false will result in empty vectors supplied here to also be populated with all variables.

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);
}

use_mesh_dimension_instead_of_spatial_dimension()

void libMesh::ExodusII_IO::use_mesh_dimension_instead_of_spatial_dimension

(

bool

val

)

In the general case, meshes containing 2D elements can be manifolds living in 3D space, thus by default we write all meshes with the Exodus dimension set to LIBMESH_DIM = mesh.spatial_dimension().

In certain cases, however, the user may know his 2D mesh actually lives in the z=0 plane, and therefore wants to write a truly 2D Exodus mesh. In such a case, he should call this function with val=true.

verbose()

void libMesh::ExodusII_IO::verbose

(

bool

set_verbosity

)

Set the flag indicating if we should be verbose.

write()

virtual void libMesh::ExodusII_IO::write ( const std::string &  fname )

overridevirtual

This method implements writing a mesh to a specified file.

Implements libMesh::MeshOutput< MeshBase >.

write_as_dimension()

void libMesh::ExodusII_IO::write_as_dimension

(

unsigned

dim

)

Directly control the num_dim which is written to the Exodus file.

If non-zero, this value supersedes all other dimensions, including: 1.) MeshBase::spatial_dimension() 2.) MeshBase::mesh_dimension() 3.) Any value passed to use_mesh_dimension_instead_of_spatial_dimension() This is useful/necessary for working around a bug in Paraview which prevents the "Plot Over Line" filter from working on 1D meshes.

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_discontinuous_exodusII()

void libMesh::ExodusII_IO::write_discontinuous_exodusII	(	const std::string &	name,
		const EquationSystems &	es,
		const std::set< std::string > *	system_names = nullptr
	)

Writes a exodusII file with discontinuous data.

write_element_data()

void libMesh::ExodusII_IO::write_element_data

(

const EquationSystems &

es

)

Write out element solution.

write_element_data_from_discontinuous_nodal_data()

void libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data	(	const EquationSystems &	es,
		const std::set< std::string > *	system_names = nullptr,
		const std::string &	var_suffix = "_elem_node_"
	)

Similar to the function above, but instead of only handling (CONSTANT, MONOMIAL) data, writes out a general discontinuous solution field, e.g.

(FIRST, L2_LAGRANGE) or (SECOND, MONOMIAL) as a number of elemental fields equal to the number of vertices in each element. For example, if you have a (FIRST, L2_LAGRANGE) variable "u" defined on HEX8 elements, calling this function would by default write 8 elemental fields named u_elem_node_0, u_elem_node_1, u_elem_node_2, etc.

This may be useful if you have a viz tool which is capable of interpreting this element data as a discontinuous solution field. Note that (CONSTANT, MONOMIAL) data is still written as a single value per element, as it makes no sense to write n_vertices copies of the same value.

The 'var_suffix' parameter, which defaults to "_elem_node_", is used to generate the elemental variable names, and is inserted between the base variable name and the node id which the variable applies to, e.g. "u_elem_node_0", "u_elem_node_1", etc.

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_global_data()

void libMesh::ExodusII_IO::write_global_data	(	const std::vector< Number > &	,
		const std::vector< std::string > &
	)

Write out global variables.

write_information_records()

void libMesh::ExodusII_IO::write_information_records

(

const std::vector< std::string > &

)

Write out information records.

write_nodal_data() [1/2]

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() [2/2]

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

overridevirtual

Write out a nodal solution.

Reimplemented from libMesh::MeshOutput< MeshBase >.

write_nodal_data_common()

void libMesh::ExodusII_IO::write_nodal_data_common	(	std::string	fname,
		const std::vector< std::string > &	names,
		bool	continuous = true
	)

This function factors out a bunch of code which is common to the write_nodal_data() and write_nodal_data_discontinuous() functions.

write_nodal_data_discontinuous()

void libMesh::ExodusII_IO::write_nodal_data_discontinuous ( const std::string &  , const std::vector< Number > &  , const std::vector< std::string > &    )

overridevirtual

Write out a discontinuous nodal solution.

Reimplemented from libMesh::MeshOutput< MeshBase >.

write_timestep()

void libMesh::ExodusII_IO::write_timestep	(	const std::string &	fname,
		const EquationSystems &	es,
		const int	timestep,
		const Real	time,
		const std::set< std::string > *	system_names = nullptr
	)

Writes out the solution at a specific timestep.

Parameters

fname	Name of the file to write to
es	EquationSystems object which contains the solution vector.
timestep	The timestep to write out, should be 1 indexed.
time	The current simulation time.
system_names	Optional list of systems to write solutions for.

write_timestep_discontinuous()

void libMesh::ExodusII_IO::write_timestep_discontinuous	(	const std::string &	fname,
		const EquationSystems &	es,
		const int	timestep,
		const Real	time,
		const std::set< std::string > *	system_names = nullptr
	)

Writes a discontinuous solution at a specific timestep.

Parameters

fname	Name of the file to be written
es	EquationSystems object which contains the solution vector
timestep	The timestep to write out. (should be 1 indexed)
time	The current simulation time
system_names	Optional list of systems to write solutions for.

Member Data Documentation

_allow_empty_variables

bool libMesh::ExodusII_IO::_allow_empty_variables

private

If true, _output_variables is allowed to remain empty.

If false, if _output_variables is empty it will be populated with a complete list of all variables By default, calling set_output_variables() sets this flag to true, but it provides an override.

Definition at line 381 of file exodusII_io.h.

_append

bool libMesh::ExodusII_IO::_append

private

Default false.

If true, files will be opened with EX_WRITE rather than created from scratch when writing.

Definition at line 367 of file exodusII_io.h.

_communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 107 of file parallel_object.h.

Referenced by libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

_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.

_output_variables

std::vector<std::string> libMesh::ExodusII_IO::_output_variables

private

The names of the variables to be output.

If this is empty then all variables are output.

Definition at line 374 of file exodusII_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.

_timestep

int libMesh::ExodusII_IO::_timestep

private

Stores the current value of the timestep when calling ExodusII_IO::write_timestep().

Definition at line 356 of file exodusII_io.h.

_verbose

bool libMesh::ExodusII_IO::_verbose

private

should we be verbose?

Definition at line 361 of file exodusII_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.

exio_helper

std::unique_ptr<ExodusII_IO_Helper> libMesh::ExodusII_IO::exio_helper

private

Only attempt to instantiate an ExodusII helper class if the Exodus API is defined.

This class will have no functionality when LIBMESH_HAVE_EXODUS_API is not defined.

Definition at line 350 of file exodusII_io.h.

---

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

• include/mesh/exodusII_io.h