libMesh::Nemesis_IO Class Reference

The Nemesis_IO class implements reading parallel meshes in the Nemesis file format from Sandia National Labs. More...

#include <nemesis_io.h>

Inheritance diagram for libMesh::Nemesis_IO:

Public Member Functions
	Nemesis_IO (MeshBase &mesh, bool single_precision=false)
	Constructor. More...
virtual	~Nemesis_IO ()
	Destructor. More...
virtual void	read (const std::string &base_filename) override
	Implements reading the mesh from several different files. More...
virtual void	write (const std::string &base_filename) override
	This method implements writing a mesh to a specified file. More...
void	write_timestep (const std::string &fname, const EquationSystems &es, const int timestep, const Real time)
	Write one timestep's worth of the solution. More...
void	set_output_variables (const std::vector< std::string > &output_variables, bool allow_empty=true)
	Specify the list of variables which should be included in the output (whitelist) If empty, then all variables will be present in the output. More...
virtual void	write_nodal_data (const std::string &fname, const std::vector< Number > &soln, const std::vector< std::string > &names) override
	Output a nodal solution. More...
virtual void	write_nodal_data (const std::string &fname, const NumericVector< Number > &parallel_soln, const std::vector< std::string > &names) override
	Output a nodal solution in parallel, without localizing the soln vector. More...
void	write_element_data (const EquationSystems &es)
	Write out element solution in parallel, without localizing the solution vector. More...
void	verbose (bool set_verbosity)
	Set the flag indicating if we should be verbose. 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	append (bool val)
	If true, this flag will cause the Nemesis_IO object to attempt to open an existing file for writing, rather than creating a new 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_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...
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 Member Functions
void	prepare_to_write_nodal_data (const std::string &fname, const std::vector< std::string > &names)
	Helper function containing code shared between the two different versions of write_nodal_data which take std::vector and NumericVector, respectively. More...

Private Attributes
std::unique_ptr< Nemesis_IO_Helper >	nemhelper
int	_timestep
	Keeps track of the current timestep index being written. More...
bool	_verbose
	Controls whether extra debugging information is printed to the screen or not. 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 Nemesis_IO class implements reading parallel meshes in the Nemesis file format from Sandia National Labs.

Nemesis files are essentially in the Exodus format plus some additional information. All the Nemesis files for a single mesh have the same basename, e.g. cylinder.e, followed by ".size.rank", where size is the total number of files the Mesh is split into and rank is the ID of the processor's elements that were written to the file.

Author

John Peterson

Date

2008

Definition at line 50 of file nemesis_io.h.

Constructor & Destructor Documentation

Nemesis_IO()

libMesh::Nemesis_IO::Nemesis_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.

~Nemesis_IO()

virtual libMesh::Nemesis_IO::~Nemesis_IO ( )

virtual

Destructor.

Member Function Documentation

append()

void libMesh::Nemesis_IO::append

(

bool

val

)

If true, this flag will cause the Nemesis_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; }

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()); }

prepare_to_write_nodal_data()

void libMesh::Nemesis_IO::prepare_to_write_nodal_data ( const std::string &  fname, const std::vector< std::string > &  names  )

private

Helper function containing code shared between the two different versions of write_nodal_data which take std::vector and NumericVector, respectively.

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::Nemesis_IO::read ( const std::string &  base_filename )

overridevirtual

Implements reading the mesh from several different files.

You provide the basename, then LibMesh appends the ".size.rank" depending on this->n_processors() and this->processor_id().

Implements libMesh::MeshInput< MeshBase >.

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

Specify the list of variables which should be included in the output (whitelist) If empty, then all variables will be present in the output.

This interface is copied from ExodusII_IO since it was found to be useful there, but perhaps eventually these implementations could somehow be combined.

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);
}

verbose()

void libMesh::Nemesis_IO::verbose

(

bool

set_verbosity

)

Set the flag indicating if we should be verbose.

write()

virtual void libMesh::Nemesis_IO::write ( const std::string &  base_filename )

overridevirtual

This method implements writing a mesh to a specified file.

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_element_data()

void libMesh::Nemesis_IO::write_element_data

(

const EquationSystems &

es

)

Write out element solution in parallel, without localizing the solution vector.

Note

Unlike write_nodal_data(), this function is not virtual and it does not override anything from the base class. This design is similar to the function by the same name in ExodusII_IO.

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::Nemesis_IO::write_global_data	(	const std::vector< Number > &	,
		const std::vector< std::string > &
	)

Write out global variables.

write_information_records()

void libMesh::Nemesis_IO::write_information_records

(

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

)

Write out information records.

write_nodal_data() [1/2]

virtual void libMesh::Nemesis_IO::write_nodal_data ( const std::string &  fname, const std::vector< Number > &  soln, const std::vector< std::string > &  names  )

overridevirtual

Output a nodal solution.

Reimplemented from libMesh::MeshOutput< MeshBase >.

write_nodal_data() [2/2]

virtual void libMesh::Nemesis_IO::write_nodal_data ( const std::string &  fname, const NumericVector< Number > &  parallel_soln, const std::vector< std::string > &  names  )

overridevirtual

Output a nodal solution in parallel, without localizing the soln vector.

Reimplemented from libMesh::MeshOutput< MeshBase >.

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.

  { libmesh_not_implemented(); }

write_timestep()

void libMesh::Nemesis_IO::write_timestep	(	const std::string &	fname,
		const EquationSystems &	es,
		const int	timestep,
		const Real	time
	)

Write one timestep's worth of the solution.

Member Data Documentation

_allow_empty_variables

bool libMesh::Nemesis_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 188 of file nemesis_io.h.

_append

bool libMesh::Nemesis_IO::_append

private

Default false.

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

Definition at line 167 of file nemesis_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::Nemesis_IO::_output_variables

private

The names of the variables to be output.

If this is empty then all variables are output.

Definition at line 181 of file nemesis_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::Nemesis_IO::_timestep

private

Keeps track of the current timestep index being written.

Used when calling write_nodal_data() and other functions.

Definition at line 155 of file nemesis_io.h.

_verbose

bool libMesh::Nemesis_IO::_verbose

private

Controls whether extra debugging information is printed to the screen or not.

Definition at line 161 of file nemesis_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.

nemhelper

std::unique_ptr<Nemesis_IO_Helper> libMesh::Nemesis_IO::nemhelper

private

Definition at line 149 of file nemesis_io.h.

---

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

• include/mesh/nemesis_io.h