This is the Nemesis_IO_Helper class. More...

#include <nemesis_io_helper.h>

Inheritance diagram for libMesh::Nemesis_IO_Helper:

Public Types
enum	ExodusVarType { NODAL =0, ELEMENTAL =1, GLOBAL =2 }
	Wraps calls to exII::ex_get_var_names() and exII::ex_get_var_param(). More...

Public Member Functions
	Nemesis_IO_Helper (const ParallelObject &parent, bool verbose=false, bool single_precision=false)
	Constructor. More...

virtual	~Nemesis_IO_Helper ()
	Destructor. More...

void	get_init_global ()
	Reading functions. More...

void	get_ss_param_global ()
	Fills: global_sideset_ids, num_global_side_counts, num_global_side_df_counts Call after: get_init_global() More...

void	get_ns_param_global ()

void	get_eb_info_global ()

void	get_init_info ()

void	get_loadbal_param ()

void	get_elem_map ()

void	get_node_map ()

void	get_cmap_params ()

void	get_node_cmap ()

void	get_elem_cmap ()

void	put_init_info (unsigned num_proc, unsigned num_proc_in_file, const char *ftype)
	Writing functions. More...

void	put_init_global (dof_id_type num_nodes_global, dof_id_type num_elems_global, unsigned num_elem_blks_global, unsigned num_node_sets_global, unsigned num_side_sets_global)
	Writes global information including: .) global number of nodes .) global number of elems .) global number of element blocks .) global number of node sets .) global number of side sets. More...

void	put_eb_info_global (std::vector< int > &global_elem_blk_ids, std::vector< int > &global_elem_blk_cnts)
	Writes global block information to the file .) global_elem_blk_ids - list of block IDs for all blocks present in the mesh .) global_elem_blk_cnts - number of elements in each block for the global mesh. More...

void	put_ns_param_global (std::vector< int > &global_nodeset_ids, std::vector< int > &num_global_node_counts, std::vector< int > &num_global_node_df_counts)
	This function writes information about global node sets. More...

void	put_ss_param_global (std::vector< int > &global_sideset_ids, std::vector< int > &num_global_side_counts, std::vector< int > &num_global_side_df_counts)
	This function writes information about global side sets. More...

void	put_loadbal_param (unsigned num_internal_nodes, unsigned num_border_nodes, unsigned num_external_nodes, unsigned num_internal_elems, unsigned num_border_elems, unsigned num_node_cmaps, unsigned num_elem_cmaps)
	Writes load balance parameters, some of which are described below: .) num_internal_nodes - nodes "wholly" owned by the current processor .) num_border_nodes - nodes local to a processor but residing in an element which also has nodes on other processors .) num_external_nodes - nodes that reside on other processors but whose element "partially" resides on the current processor – we assert this should be zero on reading! .) num_border_elems - elements local to this processor but whose nodes reside on other processors as well. More...

void	put_cmap_params (std::vector< int > &node_cmap_ids, std::vector< int > &node_cmap_node_cnts, std::vector< int > &elem_cmap_ids, std::vector< int > &elem_cmap_elem_cnts)
	Outputs initial information for communication maps. More...

void	put_node_cmap (std::vector< std::vector< int >> &node_cmap_node_ids, std::vector< std::vector< int >> &node_cmap_proc_ids)
	Outputs all of the nodal communication maps for this processor. More...

void	put_node_map (std::vector< int > &node_mapi, std::vector< int > &node_mapb, std::vector< int > &node_mape)
	Outputs IDs of internal, border, and external nodes. More...

void	put_elem_cmap (std::vector< std::vector< int >> &elem_cmap_elem_ids, std::vector< std::vector< int >> &elem_cmap_side_ids, std::vector< std::vector< int >> &elem_cmap_proc_ids)
	Writes information about elemental communication map. More...

void	put_elem_map (std::vector< int > &elem_mapi, std::vector< int > &elem_mapb)
	Outputs IDs of internal and border elements. More...

void	put_n_coord (unsigned start_node_num, unsigned num_nodes, std::vector< Real > &x_coor, std::vector< Real > &y_coor, std::vector< Real > &z_coor)
	Writes the specified number of coordinate values starting at the specified index. More...

virtual void	write_nodal_coordinates (const MeshBase &mesh, bool use_discontinuous=false) override
	This function is specialized from ExodusII_IO_Helper to write only the nodal coordinates stored on the local piece of the Mesh. More...

virtual void	write_elements (const MeshBase &mesh, bool use_discontinuous=false) override
	This function is specialized to write the connectivity. More...

virtual void	write_sidesets (const MeshBase &mesh) override
	Writes the sidesets for this processor. More...

virtual void	write_nodesets (const MeshBase &mesh) override
	Writes the nodesets for this processor. More...

virtual void	create (std::string filename) override
	This function is specialized from ExodusII_IO_Helper to create the nodal coordinates stored on the local piece of the Mesh. More...

virtual void	initialize (std::string title, const MeshBase &mesh, bool use_discontinuous=false) override
	Specialization of the initialize function from ExodusII_IO_Helper that also writes global initial data to file. More...

void	write_nodal_solution (const NumericVector< Number > &parallel_soln, const std::vector< std::string > &names, int timestep, const std::vector< std::string > &output_names)
	Takes a parallel solution vector containing the node-major solution vector for all variables and outputs it to the files. More...

void	write_nodal_solution (const std::vector< Number > &values, const std::vector< std::string > &names, int timestep)
	Takes a solution vector containing the solution for all variables and outputs it to the files. More...

virtual void	initialize_element_variables (std::vector< std::string > names, const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains) override
	Override the Exodus Helper's implementation of this function so that it works correctly in parallel. More...

void	write_element_values (const MeshBase &mesh, const NumericVector< Number > &parallel_soln, const std::vector< std::string > &names, int timestep, const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains)
	Writes the vector of elemental variable values, one variable and one subdomain at a time. More...

std::string	construct_nemesis_filename (const std::string &base_filename)
	Given base_filename, foo.e, constructs the Nemesis filename foo.e.X.Y, where X=n. More...

const char *	get_elem_type () const

void	open (const char *filename, bool read_only)
	Opens an `ExodusII` mesh file named `filename`. More...

void	read_header ()
	Reads an `ExodusII` mesh file header. More...

void	read_qa_records ()
	Reads the QA records from an ExodusII file. More...

void	print_header ()
	Prints the `ExodusII` mesh file header, which includes the mesh title, the number of nodes, number of elements, mesh dimension, number of sidesets, and number of nodesets. More...

void	read_nodes ()
	Reads the nodal data (x,y,z coordinates) from the `ExodusII` mesh file. More...

void	read_node_num_map ()
	Reads the optional `node_num_map` from the `ExodusII` mesh file. More...

void	print_nodes (std::ostream &out=libMesh::out)
	Prints the nodal information, by default to `libMesh::out`. More...

void	read_block_info ()
	Reads information for all of the blocks in the `ExodusII` mesh file. More...

int	get_block_id (int index)
	Get the block number for the given block index. More...

std::string	get_block_name (int index)
	Get the block name for the given block index if supplied in the mesh file. More...

int	get_side_set_id (int index)
	Get the side set id for the given side set index. More...

std::string	get_side_set_name (int index)
	Get the side set name for the given side set index if supplied in the mesh file. More...

int	get_node_set_id (int index)
	Get the node set id for the given node set index. More...

std::string	get_node_set_name (int index)
	Get the node set name for the given node set index if supplied in the mesh file. More...

void	read_elem_in_block (int block)
	Reads all of the element connectivity for block `block` in the `ExodusII` mesh file. More...

void	read_elem_num_map ()
	Reads the optional `node_num_map` from the `ExodusII` mesh file. More...

void	read_sideset_info ()
	Reads information about all of the sidesets in the `ExodusII` mesh file. More...

void	read_nodeset_info ()
	Reads information about all of the nodesets in the `ExodusII` mesh file. More...

void	read_sideset (int id, int offset)
	Reads information about sideset `id` and inserts it into the global sideset array at the position `offset`. More...

void	read_nodeset (int id)
	Reads information about nodeset `id` and inserts it into the global nodeset array at the position `offset`. More...

void	close ()
	Closes the `ExodusII` mesh file. More...

int	inquire (int req_info, std::string error_msg="")

void	read_time_steps ()
	Reads and stores the timesteps in the 'time_steps' array. More...

void	read_num_time_steps ()
	Reads the number of timesteps currently stored in the Exodus file and stores it in the num_time_steps variable. More...

void	read_nodal_var_values (std::string nodal_var_name, int time_step)
	Reads the nodal values for the variable 'nodal_var_name' at the specified time into the 'nodal_var_values' array. More...

void	read_elemental_var_values (std::string elemental_var_name, int time_step, std::map< dof_id_type, Real > &elem_var_value_map)
	Reads elemental values for the variable 'elemental_var_name' at the specified timestep into the 'elem_var_value_map' which is passed in. More...

void	initialize_nodal_variables (std::vector< std::string > names)
	Sets up the nodal variables. More...

void	initialize_global_variables (std::vector< std::string > names)
	Sets up the global variables. More...

void	write_timestep (int timestep, Real time)
	Writes the time for the timestep. More...

void	write_element_values (const MeshBase &mesh, const std::vector< Real > &values, int timestep, const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains)
	Writes the vector of values to the element variables. More...

void	write_element_values_element_major (const MeshBase &mesh, const std::vector< Real > &values, int timestep, const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains, const std::vector< std::string > &derived_var_names, const std::map< subdomain_id_type, std::vector< std::string >> &subdomain_to_var_names)
	Same as the function above, but assume the input 'values' vector is in element-major order, i.e. More...

void	write_nodal_values (int var_id, const std::vector< Real > &values, int timestep)
	Writes the vector of values to a nodal variable. More...

void	write_information_records (const std::vector< std::string > &records)
	Writes the vector of information records. More...

void	write_global_values (const std::vector< Real > &values, int timestep)
	Writes the vector of global variables. More...

void	read_global_values (std::vector< Real > &values, int timestep)
	Reads the vector of global variables. More...

void	use_mesh_dimension_instead_of_spatial_dimension (bool val)
	Sets the underlying value of the boolean flag _use_mesh_dimension_instead_of_spatial_dimension. More...

void	write_as_dimension (unsigned dim)
	Sets the value of _write_as_dimension. 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...

std::vector< std::string >	get_complex_names (const std::vector< std::string > &names) const

std::vector< std::set< subdomain_id_type > >	get_complex_vars_active_subdomains (const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains) const
	returns a "tripled" copy of `vars_active_subdomains`, which is necessary in the complex-valued case. More...

void	message (const std::string &msg)
	Prints the message defined in `msg`. More...

void	message (const std::string &msg, int i)
	Prints the message defined in `msg`, and appends the number `i` to the end of the message. More...

void	read_var_names (ExodusVarType type)

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Public Attributes
int	nemesis_err_flag
	Member data. More...

int	num_nodes_global
	Global initial information. More...

int	num_elems_global

int	num_elem_blks_global

int	num_node_sets_global

int	num_side_sets_global

int	num_proc
	The number of processors for which the NEMESIS I file was created. More...

int	num_proc_in_file
	The number of processors for which the NEMESIS I file stores information. More...

char	ftype
	The type of file to be written. More...

std::vector< int >	global_sideset_ids
	Containers for reading global sideset (boundary conditions) information. More...

std::vector< int >	num_global_side_counts

std::vector< int >	num_global_side_df_counts

std::vector< int >	global_nodeset_ids
	Containers for reading global nodeset information. More...

std::vector< int >	num_global_node_counts

std::vector< int >	num_global_node_df_counts

std::vector< int >	global_elem_blk_ids
	Read the global element block IDs and counts. More...

std::vector< int >	global_elem_blk_cnts

std::set< int >	nodes_attached_to_local_elems
	libMesh numbered node ids attached to local elems. More...

std::map< subdomain_id_type, std::vector< dof_id_type > >	subdomain_map
	Map of subdomains to element numbers. More...

std::map< int, std::vector< int > >	block_id_to_elem_connectivity
	This is the block connectivity, i.e. More...

int	num_internal_nodes
	To be used with the Nemesis::ne_get_loadbal_param() routine. More...

int	num_border_nodes
	The number of FEM nodes local to a processor but residing in an element which also has FEM nodes on other processors. More...

int	num_external_nodes
	The number of FEM nodes that reside on another processor but whose element partially resides on the current processor. More...

int	num_internal_elems
	The number of internal FEM elements. More...

int	num_border_elems
	The number of border FEM elements. More...

int	num_node_cmaps
	The number of nodal communication maps for this processor. More...

int	num_elem_cmaps
	The number of elemental communication maps for this processor. More...

std::vector< int >	elem_mapi
	Vector which stores internal element IDs. More...

std::vector< int >	elem_mapb
	Vector which stores border element IDs. More...

std::vector< int >	node_mapi
	Vector which stores internal node IDs. More...

std::vector< int >	node_mapb
	Vector which stores border node IDs. More...

std::vector< int >	node_mape
	Vector which stores external node IDs. More...

std::vector< int >	node_cmap_ids
	Vectors for storing the communication map parameters. More...

std::vector< int >	node_cmap_node_cnts

std::vector< int >	elem_cmap_ids

std::vector< int >	elem_cmap_elem_cnts

std::vector< std::vector< int > >	node_cmap_node_ids
	2 vectors of vectors for storing the node communication IDs for this processor. More...

std::vector< std::vector< int > >	node_cmap_proc_ids

std::vector< std::vector< int > >	elem_cmap_elem_ids
	3 vectors of vectors for storing element communication IDs for this processor. More...

std::vector< std::vector< int > >	elem_cmap_side_ids

std::vector< std::vector< int > >	elem_cmap_proc_ids

int	ex_id

int	ex_err

int	num_dim

int	num_global_vars

int	num_nodes

int	num_elem

int	num_elem_blk

int	num_node_sets

int	num_side_sets

int	num_elem_this_blk

int	num_nodes_per_elem

int	num_attr

int	num_elem_all_sidesets

std::vector< int >	block_ids

std::vector< int >	connect

std::vector< int >	ss_ids

std::vector< int >	nodeset_ids

std::vector< int >	num_sides_per_set

std::vector< int >	num_nodes_per_set

std::vector< int >	num_df_per_set

std::vector< int >	num_node_df_per_set

std::vector< int >	elem_list

std::vector< int >	side_list

std::vector< int >	node_list

std::vector< int >	id_list

std::vector< int >	node_num_map

std::vector< int >	elem_num_map

std::vector< Real >	x

std::vector< Real >	y

std::vector< Real >	z

std::vector< char >	title

std::vector< char >	elem_type

std::map< int, int >	libmesh_elem_num_to_exodus

std::vector< int >	exodus_elem_num_to_libmesh

std::map< int, int >	libmesh_node_num_to_exodus

std::vector< int >	exodus_node_num_to_libmesh

int	num_time_steps

std::vector< Real >	time_steps

int	num_nodal_vars

std::vector< std::string >	nodal_var_names

std::vector< Real >	nodal_var_values

int	num_elem_vars

std::vector< std::string >	elem_var_names

std::vector< Real >	elem_var_values

std::vector< std::string >	global_var_names

std::map< int, std::string >	id_to_block_names

std::map< int, std::string >	id_to_ss_names

std::map< int, std::string >	id_to_ns_names

bool	verbose

bool	opened_for_writing

bool	opened_for_reading

std::string	current_filename

Protected Member Functions
void	check_existing_vars (ExodusVarType type, std::vector< std::string > &names, std::vector< std::string > &names_from_file)
	When appending: during initialization, check that variable names in the file match those you attempt to initialize with. More...

void	write_var_names (ExodusVarType type, std::vector< std::string > &names)
	Wraps calls to exII::ex_put_var_names() and exII::ex_put_var_param(). More...

Protected Attributes
bool	_run_only_on_proc0

bool	_elem_vars_initialized

bool	_global_vars_initialized

bool	_nodal_vars_initialized

bool	_use_mesh_dimension_instead_of_spatial_dimension

unsigned	_write_as_dimension

Point	_coordinate_offset

bool	_single_precision

const Parallel::Communicator &	_communicator

Private Types
typedef std::map< unsigned, std::set< unsigned > >::iterator	proc_nodes_touched_iterator
	Typedef for an iterator into the data structure above. More...

typedef std::map< unsigned, std::set< std::pair< unsigned, unsigned > > >::iterator	proc_border_elem_sets_iterator
	Typedef for an iterator into the data structure above. More...

Private Member Functions
void	compute_num_global_elem_blocks (const MeshBase &pmesh)
	This function uses global communication routines to determine the number of element blocks across the entire mesh. More...

void	compute_num_global_nodesets (const MeshBase &pmesh)
	This function uses global communication routines to determine the number of nodesets across the entire mesh. More...

void	compute_num_global_sidesets (const MeshBase &pmesh)
	This function uses global communication routines to determine the number of sidesets across the entire mesh. More...

void	build_element_and_node_maps (const MeshBase &pmesh)
	This function builds the libmesh -> exodus and exodus -> libmesh node and element maps. More...

void	compute_border_node_ids (const MeshBase &pmesh)
	This function constructs the set of border node IDs present on the current mesh. More...

void	compute_internal_and_border_elems_and_internal_nodes (const MeshBase &pmesh)
	This function constructs the set of border and internal element IDs and internal node IDs present on the current mesh. More...

void	compute_communication_map_parameters ()
	This function determines the communication map parameters which will eventually be written to file. More...

void	compute_node_communication_maps ()
	Compute the node communication maps (really just pack vectors) in preparation for writing them to file. More...

void	compute_node_maps ()
	Compute the node maps (really just pack vectors) which map the nodes to internal, border, and external nodes in the file. More...

void	compute_elem_communication_maps ()
	This function computes element communication maps (really just packs vectors) in preparation for writing them to file. More...

void	compute_element_maps ()
	This function computes element maps (really just packs vectors) which map the elements to internal and border elements. More...

void	write_exodus_initialization_info (const MeshBase &pmesh, const std::string &title)
	This function writes exodus-specific initialization information. More...

Private Attributes
std::map< subdomain_id_type, unsigned >	local_subdomain_counts
	This map keeps track of the number of elements in each subdomain (block) for this processor. More...

std::set< unsigned >	border_node_ids
	The set which will eventually contain the IDs of "border nodes". More...

std::map< unsigned, std::set< unsigned > >	proc_nodes_touched_intersections
	Another map to store sets of intersections with each other processor (other than ourself, of course). More...

std::map< unsigned, std::set< std::pair< unsigned, unsigned > > >	proc_border_elem_sets
	Map between processor ID and (element,side) pairs bordering that processor ID. More...

std::set< unsigned >	internal_node_ids
	A set of internal node IDs for this processor. More...

std::set< unsigned >	internal_elem_ids
	A set of internal elem IDs for this processor. More...

std::set< unsigned >	border_elem_ids
	A set of border elem IDs for this processor. More...

Detailed Description

This is the Nemesis_IO_Helper class.

Think of it as a big struct with storage for all the stuff one might want to pull from a Nemesis file. Derived from ExodusII_IO_Helper object, since Nemesis is based on the same file format.

Author: John W. Peterson

Date: 2008

Definition at line 64 of file nemesis_io_helper.h.

Member Typedef Documentation

◆ proc_border_elem_sets_iterator

typedef std::map<unsigned, std::set<std::pair<unsigned,unsigned> > >::iterator libMesh::Nemesis_IO_Helper::proc_border_elem_sets_iterator

private

Typedef for an iterator into the data structure above.

Definition at line 594 of file nemesis_io_helper.h.

◆ proc_nodes_touched_iterator

typedef std::map<unsigned, std::set<unsigned> >::iterator libMesh::Nemesis_IO_Helper::proc_nodes_touched_iterator

private

Typedef for an iterator into the data structure above.

Definition at line 584 of file nemesis_io_helper.h.

Member Enumeration Documentation

◆ ExodusVarType

enum libMesh::ExodusII_IO_Helper::ExodusVarType

inherited

Wraps calls to exII::ex_get_var_names() and exII::ex_get_var_param().

The enumeration controls whether nodal, elemental, or global variable names are read and which class members are filled in. NODAL: num_nodal_vars nodal_var_names ELEMENTAL: num_elem_vars elem_var_names GLOBAL: num_global_vars global_var_names

Enumerator
NODAL
ELEMENTAL
GLOBAL

Definition at line 632 of file exodusII_io_helper.h.

632 {NODAL=0, ELEMENTAL=1, GLOBAL=2};

libMesh::ExodusII_IO_Helper::GLOBAL

Definition: exodusII_io_helper.h:632

libMesh::ExodusII_IO_Helper::ELEMENTAL

Definition: exodusII_io_helper.h:632

libMesh::ExodusII_IO_Helper::NODAL

Definition: exodusII_io_helper.h:632

Constructor & Destructor Documentation

◆ Nemesis_IO_Helper()

libMesh::Nemesis_IO_Helper::Nemesis_IO_Helper	(	const ParallelObject &	parent,
		bool	verbose = `false`,
		bool	single_precision = `false`
	)

explicit

Constructor.

◆ ~Nemesis_IO_Helper()

virtual libMesh::Nemesis_IO_Helper::~Nemesis_IO_Helper ( )

virtual

Destructor.

Member Function Documentation

◆ build_element_and_node_maps()

void libMesh::Nemesis_IO_Helper::build_element_and_node_maps ( const MeshBase & pmesh )

private

This function builds the libmesh -> exodus and exodus -> libmesh node and element maps.

These maps allow us to have a consistent numbering scheme within an Exodus file, given an existing globally consistent numbering scheme from LibMesh.

◆ check_existing_vars()

void libMesh::ExodusII_IO_Helper::check_existing_vars	(	ExodusVarType	type,
		std::vector< std::string > &	names,
		std::vector< std::string > &	names_from_file
	)

protectedinherited

When appending: during initialization, check that variable names in the file match those you attempt to initialize with.

◆ close()

void libMesh::ExodusII_IO_Helper::close ( )

inherited

Closes the ExodusII mesh file.

◆ 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().

90 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ compute_border_node_ids()

void libMesh::Nemesis_IO_Helper::compute_border_node_ids ( const MeshBase & pmesh )

private

This function constructs the set of border node IDs present on the current mesh.

These are nodes which live on the "border" between elements which live on different processors.

◆ compute_communication_map_parameters()

void libMesh::Nemesis_IO_Helper::compute_communication_map_parameters ( )

private

This function determines the communication map parameters which will eventually be written to file.

◆ compute_elem_communication_maps()

void libMesh::Nemesis_IO_Helper::compute_elem_communication_maps ( )

private

This function computes element communication maps (really just packs vectors) in preparation for writing them to file.

◆ compute_element_maps()

void libMesh::Nemesis_IO_Helper::compute_element_maps ( )

private

This function computes element maps (really just packs vectors) which map the elements to internal and border elements.

◆ compute_internal_and_border_elems_and_internal_nodes()

void libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes ( const MeshBase & pmesh )

private

This function constructs the set of border and internal element IDs and internal node IDs present on the current mesh.

◆ compute_node_communication_maps()

void libMesh::Nemesis_IO_Helper::compute_node_communication_maps ( )

private

Compute the node communication maps (really just pack vectors) in preparation for writing them to file.

◆ compute_node_maps()

void libMesh::Nemesis_IO_Helper::compute_node_maps ( )

private

Compute the node maps (really just pack vectors) which map the nodes to internal, border, and external nodes in the file.

◆ compute_num_global_elem_blocks()

void libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks ( const MeshBase & pmesh )

private

This function uses global communication routines to determine the number of element blocks across the entire mesh.

◆ compute_num_global_nodesets()

void libMesh::Nemesis_IO_Helper::compute_num_global_nodesets ( const MeshBase & pmesh )

private

This function uses global communication routines to determine the number of nodesets across the entire mesh.

◆ compute_num_global_sidesets()

void libMesh::Nemesis_IO_Helper::compute_num_global_sidesets ( const MeshBase & pmesh )

private

This function uses global communication routines to determine the number of sidesets across the entire mesh.

◆ construct_nemesis_filename()

std::string libMesh::Nemesis_IO_Helper::construct_nemesis_filename ( const std::string & base_filename )

Given base_filename, foo.e, constructs the Nemesis filename foo.e.X.Y, where X=n.

CPUs and Y=processor ID

◆ create()

virtual void libMesh::Nemesis_IO_Helper::create ( std::string filename )

overridevirtual

This function is specialized from ExodusII_IO_Helper to create the nodal coordinates stored on the local piece of the Mesh.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ get_block_id()

int libMesh::ExodusII_IO_Helper::get_block_id ( int index )

inherited

Get the block number for the given block index.

◆ get_block_name()

std::string libMesh::ExodusII_IO_Helper::get_block_name ( int index )

inherited

Get the block name for the given block index if supplied in the mesh file.

Otherwise an empty string is returned.

◆ get_cmap_params()

void libMesh::Nemesis_IO_Helper::get_cmap_params ( )

◆ get_complex_names()

std::vector<std::string> libMesh::ExodusII_IO_Helper::get_complex_names ( const std::vector< std::string > & names ) const

inherited

Returns: A vector with three copies of each element in the provided name vector, starting with r_, i_ and a_ respectively.

◆ get_complex_vars_active_subdomains()

std::vector<std::set<subdomain_id_type> > libMesh::ExodusII_IO_Helper::get_complex_vars_active_subdomains ( const std::vector< std::set< subdomain_id_type >> & vars_active_subdomains ) const

inherited

returns a "tripled" copy of vars_active_subdomains, which is necessary in the complex-valued case.

◆ get_eb_info_global()

void libMesh::Nemesis_IO_Helper::get_eb_info_global ( )

◆ get_elem_cmap()

void libMesh::Nemesis_IO_Helper::get_elem_cmap ( )

◆ get_elem_map()

void libMesh::Nemesis_IO_Helper::get_elem_map ( )

◆ get_elem_type()

const char* libMesh::ExodusII_IO_Helper::get_elem_type ( ) const

inherited

Returns: The current element type.

Note: The default behavior is for this value to be in all capital letters, e.g. HEX27.

◆ get_init_global()

void libMesh::Nemesis_IO_Helper::get_init_global ( )

Reading functions.

These just allocate memory for you and call the Nemesis routines of the same name. They also handle error checking for the Nemesis return value. Be careful calling these at random, some depend on others being called first... Fills: num_nodes_global, num_elems_global, num_elem_blks_global, num_node_sets_global, num_side_sets_global Call after: read_header() Call before: Any other get_* function from this class

◆ get_init_info()

void libMesh::Nemesis_IO_Helper::get_init_info ( )

◆ get_loadbal_param()

void libMesh::Nemesis_IO_Helper::get_loadbal_param ( )

◆ get_node_cmap()

void libMesh::Nemesis_IO_Helper::get_node_cmap ( )

◆ get_node_map()

void libMesh::Nemesis_IO_Helper::get_node_map ( )

◆ get_node_set_id()

int libMesh::ExodusII_IO_Helper::get_node_set_id ( int index )

inherited

Get the node set id for the given node set index.

◆ get_node_set_name()

std::string libMesh::ExodusII_IO_Helper::get_node_set_name ( int index )

inherited

Get the node set name for the given node set index if supplied in the mesh file.

Otherwise an empty string is returned.

◆ get_ns_param_global()

void libMesh::Nemesis_IO_Helper::get_ns_param_global ( )

◆ get_side_set_id()

int libMesh::ExodusII_IO_Helper::get_side_set_id ( int index )

inherited

Get the side set id for the given side set index.

◆ get_side_set_name()

std::string libMesh::ExodusII_IO_Helper::get_side_set_name ( int index )

inherited

Get the side set name for the given side set index if supplied in the mesh file.

Otherwise an empty string is returned.

◆ get_ss_param_global()

void libMesh::Nemesis_IO_Helper::get_ss_param_global ( )

Fills: global_sideset_ids, num_global_side_counts, num_global_side_df_counts Call after: get_init_global()

◆ initialize()

virtual void libMesh::Nemesis_IO_Helper::initialize	(	std::string	title,
		const MeshBase &	mesh,
		bool	use_discontinuous = `false`
	)

overridevirtual

Specialization of the initialize function from ExodusII_IO_Helper that also writes global initial data to file.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ initialize_element_variables()

virtual void libMesh::Nemesis_IO_Helper::initialize_element_variables	(	std::vector< std::string >	names,
		const std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains
	)

overridevirtual

Override the Exodus Helper's implementation of this function so that it works correctly in parallel.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ initialize_global_variables()

void libMesh::ExodusII_IO_Helper::initialize_global_variables ( std::vector< std::string > names )

inherited

Sets up the global variables.

◆ initialize_nodal_variables()

void libMesh::ExodusII_IO_Helper::initialize_nodal_variables ( std::vector< std::string > names )

inherited

Sets up the nodal variables.

◆ inquire()

int libMesh::ExodusII_IO_Helper::inquire	(	int	req_info,
		std::string	error_msg = `""`
	)

inherited

Returns: The value obtained from a generic exII::ex_inquire() call.

◆ message() [1/2]

void libMesh::ExodusII_IO_Helper::message ( const std::string & msg )

inherited

Prints the message defined in msg.

Can be turned off if verbosity is set to 0.

◆ message() [2/2]

void libMesh::ExodusII_IO_Helper::message	(	const std::string &	msg,
		int	i
	)

inherited

Prints the message defined in msg, and appends the number i to the end of the message.

Useful for printing messages in loops. Can be turned off if verbosity is set to 0.

◆ 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().

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

libMesh::Parallel::Communicator::size

processor_id_type size() const

Definition: communicator.h:175

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ open()

void libMesh::ExodusII_IO_Helper::open	(	const char *	filename,
		bool	read_only
	)

inherited

Opens an ExodusII mesh file named filename.

If read_only==true, the file will be opened with the EX_READ flag, otherwise it will be opened with the EX_WRITE flag.

◆ print_header()

void libMesh::ExodusII_IO_Helper::print_header ( )

inherited

Prints the ExodusII mesh file header, which includes the mesh title, the number of nodes, number of elements, mesh dimension, number of sidesets, and number of nodesets.

◆ print_nodes()

void libMesh::ExodusII_IO_Helper::print_nodes ( std::ostream & out = libMesh::out )

inherited

Prints the nodal information, by default to libMesh::out.

◆ 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().

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

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

libMesh::Parallel::Communicator::rank

processor_id_type rank() const

Definition: communicator.h:173

◆ put_cmap_params()

void libMesh::Nemesis_IO_Helper::put_cmap_params	(	std::vector< int > &	node_cmap_ids,
		std::vector< int > &	node_cmap_node_cnts,
		std::vector< int > &	elem_cmap_ids,
		std::vector< int > &	elem_cmap_elem_cnts
	)

Outputs initial information for communication maps.

Note: The order of the arguments specified in the Nemesis User's Manual is wrong. The correct order is (ids, counts, ids, counts). Must be called after put_loadbal_param().

◆ put_eb_info_global()

void libMesh::Nemesis_IO_Helper::put_eb_info_global	(	std::vector< int > &	global_elem_blk_ids,
		std::vector< int > &	global_elem_blk_cnts
	)

Writes global block information to the file .) global_elem_blk_ids - list of block IDs for all blocks present in the mesh .) global_elem_blk_cnts - number of elements in each block for the global mesh.

Must be called after put_init_global().

◆ put_elem_cmap()

void libMesh::Nemesis_IO_Helper::put_elem_cmap	(	std::vector< std::vector< int >> &	elem_cmap_elem_ids,
		std::vector< std::vector< int >> &	elem_cmap_side_ids,
		std::vector< std::vector< int >> &	elem_cmap_proc_ids
	)

Writes information about elemental communication map.

Note: This class contains elem_cmap_elem_ids, elem_cmap_side_ids, abd elem_cmap_proc_ids which can be used when calling this function.

Must be called after put_cmap_params().

◆ put_elem_map()

void libMesh::Nemesis_IO_Helper::put_elem_map	(	std::vector< int > &	elem_mapi,
		std::vector< int > &	elem_mapb
	)

Outputs IDs of internal and border elements.

Must be called after ne_put_loadbal_param().

◆ put_init_global()

void libMesh::Nemesis_IO_Helper::put_init_global	(	dof_id_type	num_nodes_global,
		dof_id_type	num_elems_global,
		unsigned	num_elem_blks_global,
		unsigned	num_node_sets_global,
		unsigned	num_side_sets_global
	)

Writes global information including: .) global number of nodes .) global number of elems .) global number of element blocks .) global number of node sets .) global number of side sets.

◆ put_init_info()

void libMesh::Nemesis_IO_Helper::put_init_info	(	unsigned	num_proc,
		unsigned	num_proc_in_file,
		const char *	ftype
	)

Writing functions.

Writes basic info about the partitioning to file .) num_proc - number of processors .) num_proc_in_file - number of processors in the current file - generally equal to 1 .) ftype = "s" for scalar load-balance file, "p" for parallel file

◆ put_loadbal_param()

void libMesh::Nemesis_IO_Helper::put_loadbal_param	(	unsigned	num_internal_nodes,
		unsigned	num_border_nodes,
		unsigned	num_external_nodes,
		unsigned	num_internal_elems,
		unsigned	num_border_elems,
		unsigned	num_node_cmaps,
		unsigned	num_elem_cmaps
	)

Writes load balance parameters, some of which are described below: .) num_internal_nodes - nodes "wholly" owned by the current processor .) num_border_nodes - nodes local to a processor but residing in an element which also has nodes on other processors .) num_external_nodes - nodes that reside on other processors but whose element "partially" resides on the current processor – we assert this should be zero on reading! .) num_border_elems - elements local to this processor but whose nodes reside on other processors as well.

.) processor - ID of the processor for which information is to be written

◆ put_n_coord()

void libMesh::Nemesis_IO_Helper::put_n_coord	(	unsigned	start_node_num,
		unsigned	num_nodes,
		std::vector< Real > &	x_coor,
		std::vector< Real > &	y_coor,
		std::vector< Real > &	z_coor
	)

Writes the specified number of coordinate values starting at the specified index.

◆ put_node_cmap()

void libMesh::Nemesis_IO_Helper::put_node_cmap	(	std::vector< std::vector< int >> &	node_cmap_node_ids,
		std::vector< std::vector< int >> &	node_cmap_proc_ids
	)

Outputs all of the nodal communication maps for this processor.

Internally, this function loops over all communication maps and calls Nemesis::ne_put_node_cmap() for each one.

.) node_cmap_node_ids = Nodal IDs of the FEM nodes in this communication map .) node_cmap_proc_ids = processor IDs associated with each of the nodes in node_ids

In the Nemesis file, these all appear to be written to the same chunks of data: n_comm_nids and n_comm_proc, but don't rely on these names...

Note: This class contains node_cmap_node_ids and node_cmap_proc_ids which can be used when calling this function.

Must be called after put_cmap_params().

◆ put_node_map()

void libMesh::Nemesis_IO_Helper::put_node_map	(	std::vector< int > &	node_mapi,
		std::vector< int > &	node_mapb,
		std::vector< int > &	node_mape
	)

Outputs IDs of internal, border, and external nodes.

LibMesh asserts that the number of external nodes is zero in the Nemesis files it reads

◆ put_ns_param_global()

void libMesh::Nemesis_IO_Helper::put_ns_param_global	(	std::vector< int > &	global_nodeset_ids,
		std::vector< int > &	num_global_node_counts,
		std::vector< int > &	num_global_node_df_counts
	)

This function writes information about global node sets.

.) global_nodeset_ids - vector of global node set IDs .) num_global_node_counts - vector of global node counts contained in each global node set .) num_global_df_count - vector of global distribution factors in each global node set

Must be called after put_init_global()

◆ put_ss_param_global()

void libMesh::Nemesis_IO_Helper::put_ss_param_global	(	std::vector< int > &	global_sideset_ids,
		std::vector< int > &	num_global_side_counts,
		std::vector< int > &	num_global_side_df_counts
	)

This function writes information about global side sets.

.) global_sideset_ids - vector of global side set IDs .) num_global_side_counts - vector of global side counts contained in each global side set .) num_global_df_count - vector of global distribution factors in each global side set

Must be called after put_init_global()

◆ read_block_info()

void libMesh::ExodusII_IO_Helper::read_block_info ( )

inherited

Reads information for all of the blocks in the ExodusII mesh file.

◆ read_elem_in_block()

void libMesh::ExodusII_IO_Helper::read_elem_in_block ( int block )

inherited

Reads all of the element connectivity for block block in the ExodusII mesh file.

◆ read_elem_num_map()

void libMesh::ExodusII_IO_Helper::read_elem_num_map ( )

inherited

Reads the optional node_num_map from the ExodusII mesh file.

◆ read_elemental_var_values()

void libMesh::ExodusII_IO_Helper::read_elemental_var_values	(	std::string	elemental_var_name,
		int	time_step,
		std::map< dof_id_type, Real > &	elem_var_value_map
	)

inherited

Reads elemental values for the variable 'elemental_var_name' at the specified timestep into the 'elem_var_value_map' which is passed in.

◆ read_global_values()

void libMesh::ExodusII_IO_Helper::read_global_values	(	std::vector< Real > &	values,
		int	timestep
	)

inherited

Reads the vector of global variables.

◆ read_header()

void libMesh::ExodusII_IO_Helper::read_header ( )

inherited

Reads an ExodusII mesh file header.

◆ read_nodal_var_values()

void libMesh::ExodusII_IO_Helper::read_nodal_var_values	(	std::string	nodal_var_name,
		int	time_step
	)

inherited

Reads the nodal values for the variable 'nodal_var_name' at the specified time into the 'nodal_var_values' array.

◆ read_node_num_map()

void libMesh::ExodusII_IO_Helper::read_node_num_map ( )

inherited

Reads the optional node_num_map from the ExodusII mesh file.

◆ read_nodes()

void libMesh::ExodusII_IO_Helper::read_nodes ( )

inherited

Reads the nodal data (x,y,z coordinates) from the ExodusII mesh file.

◆ read_nodeset()

void libMesh::ExodusII_IO_Helper::read_nodeset ( int id )

inherited

Reads information about nodeset id and inserts it into the global nodeset array at the position offset.

◆ read_nodeset_info()

void libMesh::ExodusII_IO_Helper::read_nodeset_info ( )

inherited

Reads information about all of the nodesets in the ExodusII mesh file.

◆ read_num_time_steps()

void libMesh::ExodusII_IO_Helper::read_num_time_steps ( )

inherited

Reads the number of timesteps currently stored in the Exodus file and stores it in the num_time_steps variable.

◆ read_qa_records()

void libMesh::ExodusII_IO_Helper::read_qa_records ( )

inherited

Reads the QA records from an ExodusII file.

We can use this to detect when e.g. CUBIT 14+ was used to generate a Mesh file, and work around certain known bugs in that version.

◆ read_sideset()

void libMesh::ExodusII_IO_Helper::read_sideset	(	int	id,
		int	offset
	)

inherited

Reads information about sideset id and inserts it into the global sideset array at the position offset.

◆ read_sideset_info()

void libMesh::ExodusII_IO_Helper::read_sideset_info ( )

inherited

Reads information about all of the sidesets in the ExodusII mesh file.

◆ read_time_steps()

void libMesh::ExodusII_IO_Helper::read_time_steps ( )

inherited

Reads and stores the timesteps in the 'time_steps' array.

◆ read_var_names()

void libMesh::ExodusII_IO_Helper::read_var_names ( ExodusVarType type )

inherited

◆ set_coordinate_offset()

void libMesh::ExodusII_IO_Helper::set_coordinate_offset ( Point p )

inherited

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

◆ use_mesh_dimension_instead_of_spatial_dimension()

void libMesh::ExodusII_IO_Helper::use_mesh_dimension_instead_of_spatial_dimension ( bool val )

inherited

Sets the underlying value of the boolean flag _use_mesh_dimension_instead_of_spatial_dimension.

By default, the value of this flag is false.

See the ExodusII_IO class documentation for a detailed description of this flag.

◆ write_as_dimension()

void libMesh::ExodusII_IO_Helper::write_as_dimension ( unsigned dim )

inherited

Sets the value of _write_as_dimension.

This directly controls 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_element_values() [1/2]

void libMesh::Nemesis_IO_Helper::write_element_values	(	const MeshBase &	mesh,
		const NumericVector< Number > &	parallel_soln,
		const std::vector< std::string > &	names,
		int	timestep,
		const std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains
	)

Writes the vector of elemental variable values, one variable and one subdomain at a time.

◆ write_element_values() [2/2]

void libMesh::ExodusII_IO_Helper::write_element_values	(	const MeshBase &	mesh,
		const std::vector< Real > &	values,
		int	timestep,
		const std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains
	)

inherited

Writes the vector of values to the element variables.

The 'values' vector is assumed to be in the order: {(u1, u2, u3, ..., uN), (v1, v2, v3, ..., vN), (w1, w2, w3, ..., wN)} where N is the number of elements.

This ordering is produced by calls to ES::build_elemental_solution_vector(). ES::build_discontinuous_solution_vector(), on the other hand, produces an element-major ordering. See the function below for that case.

◆ write_element_values_element_major()

void libMesh::ExodusII_IO_Helper::write_element_values_element_major	(	const MeshBase &	mesh,
		const std::vector< Real > &	values,
		int	timestep,
		const std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains,
		const std::vector< std::string > &	derived_var_names,
		const std::map< subdomain_id_type, std::vector< std::string >> &	subdomain_to_var_names
	)

inherited

Same as the function above, but assume the input 'values' vector is in element-major order, i.e.

{(u1,v1,w1), (u2,v2,w2), ... (uN,vN,wN)} This function is called by ExodusII_IO::write_element_data_from_discontinuous_nodal_data() because ES::build_discontinuous_solution_vector() builds the solution vector in this order.

Note: If some variables are subdomain-restricted, then the tuples will be of different lengths for each element, i.e. {(u1,v1,w1), (u2,v2), ... (uN,vN,wN)} if variable w is not active on element 2.

◆ write_elements()

virtual void libMesh::Nemesis_IO_Helper::write_elements	(	const MeshBase &	mesh,
		bool	use_discontinuous = `false`
	)

overridevirtual

This function is specialized to write the connectivity.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ write_exodus_initialization_info()

void libMesh::Nemesis_IO_Helper::write_exodus_initialization_info	(	const MeshBase &	pmesh,
		const std::string &	title
	)

private

This function writes exodus-specific initialization information.

This information is slightly different when you are working with Nemesis, as it depends on some global information being known.

◆ write_global_values()

void libMesh::ExodusII_IO_Helper::write_global_values	(	const std::vector< Real > &	values,
		int	timestep
	)

inherited

Writes the vector of global variables.

◆ write_information_records()

void libMesh::ExodusII_IO_Helper::write_information_records ( const std::vector< std::string > & records )

inherited

Writes the vector of information records.

◆ write_nodal_coordinates()

virtual void libMesh::Nemesis_IO_Helper::write_nodal_coordinates	(	const MeshBase &	mesh,
		bool	use_discontinuous = `false`
	)

overridevirtual

This function is specialized from ExodusII_IO_Helper to write only the nodal coordinates stored on the local piece of the Mesh.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ write_nodal_solution() [1/2]

void libMesh::Nemesis_IO_Helper::write_nodal_solution	(	const NumericVector< Number > &	parallel_soln,
		const std::vector< std::string > &	names,
		int	timestep,
		const std::vector< std::string > &	output_names
	)

Takes a parallel solution vector containing the node-major solution vector for all variables and outputs it to the files.

Parameters

parallel_soln
names	A vector containing the names of all variables in parallel_soln.
timestep	To be passed to the ExodusII_IO_Helper::write_nodal_values() function.
output_names	A vector containing the names of variables in parallel_soln that should actually be written (whitelist).

Note: This version of write_nodal_solution() is called by the parallel version of Nemesis_IO::write_nodal_data(), which is called by MeshOutput::write_equation_systems() for parallel I/O formats like Nemesis. The other version is still available to continue supporting things like NamebasedIO::write_nodal_data(), but this version should be preferred when running in parallel.

◆ write_nodal_solution() [2/2]

void libMesh::Nemesis_IO_Helper::write_nodal_solution	(	const std::vector< Number > &	values,
		const std::vector< std::string > &	names,
		int	timestep
	)

Takes a solution vector containing the solution for all variables and outputs it to the files.

◆ write_nodal_values()

void libMesh::ExodusII_IO_Helper::write_nodal_values	(	int	var_id,
		const std::vector< Real > &	values,
		int	timestep
	)

inherited

Writes the vector of values to a nodal variable.

◆ write_nodesets()

virtual void libMesh::Nemesis_IO_Helper::write_nodesets ( const MeshBase & mesh )

overridevirtual

Writes the nodesets for this processor.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ write_sidesets()

virtual void libMesh::Nemesis_IO_Helper::write_sidesets ( const MeshBase & mesh )

overridevirtual

Writes the sidesets for this processor.

Reimplemented from libMesh::ExodusII_IO_Helper.

◆ write_timestep()

void libMesh::ExodusII_IO_Helper::write_timestep	(	int	timestep,
		Real	time
	)

inherited

Writes the time for the timestep.

◆ write_var_names()

void libMesh::ExodusII_IO_Helper::write_var_names	(	ExodusVarType	type,
		std::vector< std::string > &	names
	)

protectedinherited

Wraps calls to exII::ex_put_var_names() and exII::ex_put_var_param().

The enumeration controls whether nodal, elemental, or global variable names are read and which class members are filled in.

Member Data Documentation

◆ _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().

◆ _coordinate_offset

Point libMesh::ExodusII_IO_Helper::_coordinate_offset

protectedinherited

Definition at line 671 of file exodusII_io_helper.h.

◆ _elem_vars_initialized

bool libMesh::ExodusII_IO_Helper::_elem_vars_initialized

protectedinherited

Definition at line 653 of file exodusII_io_helper.h.

◆ _global_vars_initialized

bool libMesh::ExodusII_IO_Helper::_global_vars_initialized

protectedinherited

Definition at line 656 of file exodusII_io_helper.h.

◆ _nodal_vars_initialized

bool libMesh::ExodusII_IO_Helper::_nodal_vars_initialized

protectedinherited

Definition at line 659 of file exodusII_io_helper.h.

◆ _run_only_on_proc0

bool libMesh::ExodusII_IO_Helper::_run_only_on_proc0

protectedinherited

Definition at line 650 of file exodusII_io_helper.h.

◆ _single_precision

bool libMesh::ExodusII_IO_Helper::_single_precision

protectedinherited

Definition at line 674 of file exodusII_io_helper.h.

◆ _use_mesh_dimension_instead_of_spatial_dimension

bool libMesh::ExodusII_IO_Helper::_use_mesh_dimension_instead_of_spatial_dimension

protectedinherited

Definition at line 664 of file exodusII_io_helper.h.

◆ _write_as_dimension

unsigned libMesh::ExodusII_IO_Helper::_write_as_dimension

protectedinherited

Definition at line 668 of file exodusII_io_helper.h.

◆ block_id_to_elem_connectivity

std::map<int, std::vector<int> > libMesh::Nemesis_IO_Helper::block_id_to_elem_connectivity

This is the block connectivity, i.e.

for each subdomain (block) there is an element connectivity list. This map associates the block ID to that vector.

Definition at line 434 of file nemesis_io_helper.h.

◆ block_ids

std::vector<int> libMesh::ExodusII_IO_Helper::block_ids

inherited

Definition at line 505 of file exodusII_io_helper.h.

◆ border_elem_ids

std::set<unsigned> libMesh::Nemesis_IO_Helper::border_elem_ids

private

A set of border elem IDs for this processor.

Definition at line 609 of file nemesis_io_helper.h.

◆ border_node_ids

std::set<unsigned> libMesh::Nemesis_IO_Helper::border_node_ids

private

The set which will eventually contain the IDs of "border nodes".

These are nodes that lie on the boundary between one or more processors.

Definition at line 572 of file nemesis_io_helper.h.

◆ connect

std::vector<int> libMesh::ExodusII_IO_Helper::connect

inherited

Definition at line 508 of file exodusII_io_helper.h.

◆ current_filename

std::string libMesh::ExodusII_IO_Helper::current_filename

inherited

Definition at line 622 of file exodusII_io_helper.h.

◆ elem_cmap_elem_cnts

std::vector<int> libMesh::Nemesis_IO_Helper::elem_cmap_elem_cnts

Definition at line 536 of file nemesis_io_helper.h.

◆ elem_cmap_elem_ids

std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::elem_cmap_elem_ids

3 vectors of vectors for storing element communication IDs for this processor.

There will be num_elem_cmaps rows, row i will have elem_cmap_elem_cnts[i] entries. To be used with Nemesis::ne_get_elem_cmap().

Definition at line 556 of file nemesis_io_helper.h.

◆ elem_cmap_ids

std::vector<int> libMesh::Nemesis_IO_Helper::elem_cmap_ids

Definition at line 535 of file nemesis_io_helper.h.

◆ elem_cmap_proc_ids

std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::elem_cmap_proc_ids

Definition at line 558 of file nemesis_io_helper.h.

◆ elem_cmap_side_ids

std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::elem_cmap_side_ids

Definition at line 557 of file nemesis_io_helper.h.

◆ elem_list

std::vector<int> libMesh::ExodusII_IO_Helper::elem_list

inherited

Definition at line 529 of file exodusII_io_helper.h.

◆ elem_mapb

std::vector<int> libMesh::Nemesis_IO_Helper::elem_mapb

Vector which stores border element IDs.

Will have length num_border_elems. To be used with Nemesis::ne_get_elem_map().

Definition at line 501 of file nemesis_io_helper.h.

◆ elem_mapi

std::vector<int> libMesh::Nemesis_IO_Helper::elem_mapi

Vector which stores internal element IDs.

Will have length num_internal_elems. To be used with Nemesis::ne_get_elem_map().

Definition at line 494 of file nemesis_io_helper.h.

◆ elem_num_map

std::vector<int> libMesh::ExodusII_IO_Helper::elem_num_map

inherited

Definition at line 544 of file exodusII_io_helper.h.

◆ elem_type

std::vector<char> libMesh::ExodusII_IO_Helper::elem_type

inherited

Definition at line 559 of file exodusII_io_helper.h.

◆ elem_var_names

std::vector<std::string> libMesh::ExodusII_IO_Helper::elem_var_names

inherited

Definition at line 590 of file exodusII_io_helper.h.

◆ elem_var_values

std::vector<Real> libMesh::ExodusII_IO_Helper::elem_var_values

inherited

Definition at line 593 of file exodusII_io_helper.h.

◆ ex_err

int libMesh::ExodusII_IO_Helper::ex_err

inherited

Definition at line 469 of file exodusII_io_helper.h.

◆ ex_id

int libMesh::ExodusII_IO_Helper::ex_id

inherited

Definition at line 466 of file exodusII_io_helper.h.

◆ exodus_elem_num_to_libmesh

std::vector<int> libMesh::ExodusII_IO_Helper::exodus_elem_num_to_libmesh

inherited

Definition at line 564 of file exodusII_io_helper.h.

◆ exodus_node_num_to_libmesh

std::vector<int> libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh

inherited

Definition at line 569 of file exodusII_io_helper.h.

◆ ftype

char libMesh::Nemesis_IO_Helper::ftype

The type of file to be written.

Either 's', for a scalar load-balance file, or 'p' for a parallel file. To be used with Nemesis::ne_get_init_info().

Definition at line 386 of file nemesis_io_helper.h.

◆ global_elem_blk_cnts

std::vector<int> libMesh::Nemesis_IO_Helper::global_elem_blk_cnts

Definition at line 418 of file nemesis_io_helper.h.

◆ global_elem_blk_ids

std::vector<int> libMesh::Nemesis_IO_Helper::global_elem_blk_ids

Read the global element block IDs and counts.

These vectors will eventually have num_elem_blks_global entries. To be used with Nemesis::ne_get_eb_info_global().

Definition at line 417 of file nemesis_io_helper.h.

◆ global_nodeset_ids

std::vector<int> libMesh::Nemesis_IO_Helper::global_nodeset_ids

Containers for reading global nodeset information.

One vector entry per nodeset. Each vector will eventually have num_node_sets_global entries, and will be used in calls to Nemesis::ne_get_ns_param_global().

It's an error to call ne_get_ns_param_global when num_node_sets_global==0

Definition at line 407 of file nemesis_io_helper.h.

◆ global_sideset_ids

std::vector<int> libMesh::Nemesis_IO_Helper::global_sideset_ids

Containers for reading global sideset (boundary conditions) information.

Each vector will eventually have num_side_sets_global entries, and be used in calls to Nemesis::ne_get_ss_param_global().

It's an error to call ne_get_ss_param_global when num_side_sets_global==0

Definition at line 395 of file nemesis_io_helper.h.

◆ global_var_names

std::vector<std::string> libMesh::ExodusII_IO_Helper::global_var_names

inherited

Definition at line 596 of file exodusII_io_helper.h.

◆ id_list

std::vector<int> libMesh::ExodusII_IO_Helper::id_list

inherited

Definition at line 538 of file exodusII_io_helper.h.

◆ id_to_block_names

std::map<int, std::string> libMesh::ExodusII_IO_Helper::id_to_block_names

inherited

Definition at line 599 of file exodusII_io_helper.h.

◆ id_to_ns_names

std::map<int, std::string> libMesh::ExodusII_IO_Helper::id_to_ns_names

inherited

Definition at line 601 of file exodusII_io_helper.h.

◆ id_to_ss_names

std::map<int, std::string> libMesh::ExodusII_IO_Helper::id_to_ss_names

inherited

Definition at line 600 of file exodusII_io_helper.h.

◆ internal_elem_ids

std::set<unsigned> libMesh::Nemesis_IO_Helper::internal_elem_ids

private

A set of internal elem IDs for this processor.

Definition at line 604 of file nemesis_io_helper.h.

◆ internal_node_ids

std::set<unsigned> libMesh::Nemesis_IO_Helper::internal_node_ids

private

A set of internal node IDs for this processor.

Definition at line 599 of file nemesis_io_helper.h.

◆ libmesh_elem_num_to_exodus

std::map<int, int> libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus

inherited

Definition at line 563 of file exodusII_io_helper.h.

◆ libmesh_node_num_to_exodus

std::map<int, int> libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus

inherited

Definition at line 568 of file exodusII_io_helper.h.

◆ local_subdomain_counts

std::map<subdomain_id_type, unsigned> libMesh::Nemesis_IO_Helper::local_subdomain_counts

private

This map keeps track of the number of elements in each subdomain (block) for this processor.

Definition at line 566 of file nemesis_io_helper.h.

◆ nemesis_err_flag

int libMesh::Nemesis_IO_Helper::nemesis_err_flag

Member data.

All (?) Nemesis functions return an int. If it's negative that signals an error! Internally, we use the ExodusII_IO_Helper::check_err() function to check for errors.

Definition at line 356 of file nemesis_io_helper.h.

◆ nodal_var_names

std::vector<std::string> libMesh::ExodusII_IO_Helper::nodal_var_names

inherited

Definition at line 581 of file exodusII_io_helper.h.

◆ nodal_var_values

std::vector<Real> libMesh::ExodusII_IO_Helper::nodal_var_values

inherited

Definition at line 584 of file exodusII_io_helper.h.

◆ node_cmap_ids

std::vector<int> libMesh::Nemesis_IO_Helper::node_cmap_ids

Vectors for storing the communication map parameters.

Each will eventually have length num_node_cmaps OR num_elem_cmaps as appropriate. For use with Nemesis::ne_get_cmap_params().

Definition at line 533 of file nemesis_io_helper.h.

◆ node_cmap_node_cnts

std::vector<int> libMesh::Nemesis_IO_Helper::node_cmap_node_cnts

Definition at line 534 of file nemesis_io_helper.h.

◆ node_cmap_node_ids

std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::node_cmap_node_ids

2 vectors of vectors for storing the node communication IDs for this processor.

There will be num_node_cmaps rows, row i will have node_cmap_node_cnts[i] entries. To be used with Nemesis::ne_get_node_cmap().

Remark: node_cmap_proc_ids is a vector, all entries of which are = node_cmap_ids[i] Not sure what the point of that is...

Definition at line 547 of file nemesis_io_helper.h.

◆ node_cmap_proc_ids

std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::node_cmap_proc_ids

Definition at line 548 of file nemesis_io_helper.h.

◆ node_list

std::vector<int> libMesh::ExodusII_IO_Helper::node_list

inherited

Definition at line 535 of file exodusII_io_helper.h.

◆ node_mapb

std::vector<int> libMesh::Nemesis_IO_Helper::node_mapb

Vector which stores border node IDs.

Will have length num_border_nodes. To be used with Nemesis::ne_get_node_map().

Definition at line 517 of file nemesis_io_helper.h.

◆ node_mape

std::vector<int> libMesh::Nemesis_IO_Helper::node_mape

Vector which stores external node IDs.

Will have length num_external_nodes. To be used with Nemesis::ne_get_node_map().

Definition at line 524 of file nemesis_io_helper.h.

◆ node_mapi

std::vector<int> libMesh::Nemesis_IO_Helper::node_mapi

Vector which stores internal node IDs.

Will have length num_internal_nodes. To be used with Nemesis::ne_get_node_map().

Definition at line 510 of file nemesis_io_helper.h.

◆ node_num_map

std::vector<int> libMesh::ExodusII_IO_Helper::node_num_map

inherited

Definition at line 541 of file exodusII_io_helper.h.

◆ nodes_attached_to_local_elems

std::set<int> libMesh::Nemesis_IO_Helper::nodes_attached_to_local_elems

libMesh numbered node ids attached to local elems.

Definition at line 423 of file nemesis_io_helper.h.

◆ nodeset_ids

std::vector<int> libMesh::ExodusII_IO_Helper::nodeset_ids

inherited

Definition at line 514 of file exodusII_io_helper.h.

◆ num_attr

int libMesh::ExodusII_IO_Helper::num_attr

inherited

Definition at line 499 of file exodusII_io_helper.h.

◆ num_border_elems

int libMesh::Nemesis_IO_Helper::num_border_elems

The number of border FEM elements.

Elements local to this processor but whose FEM nodes reside on other processors as well. To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 471 of file nemesis_io_helper.h.

◆ num_border_nodes

int libMesh::Nemesis_IO_Helper::num_border_nodes

The number of FEM nodes local to a processor but residing in an element which also has FEM nodes on other processors.

To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 451 of file nemesis_io_helper.h.

◆ num_df_per_set

std::vector<int> libMesh::ExodusII_IO_Helper::num_df_per_set

inherited

Definition at line 523 of file exodusII_io_helper.h.

◆ num_dim

int libMesh::ExodusII_IO_Helper::num_dim

inherited

Definition at line 472 of file exodusII_io_helper.h.

◆ num_elem

int libMesh::ExodusII_IO_Helper::num_elem

inherited

Definition at line 481 of file exodusII_io_helper.h.

◆ num_elem_all_sidesets

int libMesh::ExodusII_IO_Helper::num_elem_all_sidesets

inherited

Definition at line 502 of file exodusII_io_helper.h.

◆ num_elem_blk

int libMesh::ExodusII_IO_Helper::num_elem_blk

inherited

Definition at line 484 of file exodusII_io_helper.h.

◆ num_elem_blks_global

int libMesh::Nemesis_IO_Helper::num_elem_blks_global

Definition at line 364 of file nemesis_io_helper.h.

◆ num_elem_cmaps

int libMesh::Nemesis_IO_Helper::num_elem_cmaps

The number of elemental communication maps for this processor.

(One per neighboring proc?) To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 485 of file nemesis_io_helper.h.

◆ num_elem_this_blk

int libMesh::ExodusII_IO_Helper::num_elem_this_blk

inherited

Definition at line 493 of file exodusII_io_helper.h.

◆ num_elem_vars

int libMesh::ExodusII_IO_Helper::num_elem_vars

inherited

Definition at line 587 of file exodusII_io_helper.h.

◆ num_elems_global

int libMesh::Nemesis_IO_Helper::num_elems_global

Definition at line 363 of file nemesis_io_helper.h.

◆ num_external_nodes

int libMesh::Nemesis_IO_Helper::num_external_nodes

The number of FEM nodes that reside on another processor but whose element partially resides on the current processor.

To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 458 of file nemesis_io_helper.h.

◆ num_global_node_counts

std::vector<int> libMesh::Nemesis_IO_Helper::num_global_node_counts

Definition at line 408 of file nemesis_io_helper.h.

◆ num_global_node_df_counts

std::vector<int> libMesh::Nemesis_IO_Helper::num_global_node_df_counts

Definition at line 409 of file nemesis_io_helper.h.

◆ num_global_side_counts

std::vector<int> libMesh::Nemesis_IO_Helper::num_global_side_counts

Definition at line 396 of file nemesis_io_helper.h.

◆ num_global_side_df_counts

std::vector<int> libMesh::Nemesis_IO_Helper::num_global_side_df_counts

Definition at line 397 of file nemesis_io_helper.h.

◆ num_global_vars

int libMesh::ExodusII_IO_Helper::num_global_vars

inherited

Definition at line 475 of file exodusII_io_helper.h.

◆ num_internal_elems

int libMesh::Nemesis_IO_Helper::num_internal_elems

The number of internal FEM elements.

Elements local to this processor. To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 464 of file nemesis_io_helper.h.

◆ num_internal_nodes

int libMesh::Nemesis_IO_Helper::num_internal_nodes

To be used with the Nemesis::ne_get_loadbal_param() routine.

The number of FEM nodes contained in FEM elements wholly owned by the current processor. To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 444 of file nemesis_io_helper.h.

◆ num_nodal_vars

int libMesh::ExodusII_IO_Helper::num_nodal_vars

inherited

Definition at line 578 of file exodusII_io_helper.h.

◆ num_node_cmaps

int libMesh::Nemesis_IO_Helper::num_node_cmaps

The number of nodal communication maps for this processor.

(One per neighboring proc?) To be used with the Nemesis::ne_get_loadbal_param() routine.

Definition at line 478 of file nemesis_io_helper.h.

◆ num_node_df_per_set

std::vector<int> libMesh::ExodusII_IO_Helper::num_node_df_per_set

inherited

Definition at line 526 of file exodusII_io_helper.h.

◆ num_node_sets

int libMesh::ExodusII_IO_Helper::num_node_sets

inherited

Definition at line 487 of file exodusII_io_helper.h.

◆ num_node_sets_global

int libMesh::Nemesis_IO_Helper::num_node_sets_global

Definition at line 365 of file nemesis_io_helper.h.

◆ num_nodes

int libMesh::ExodusII_IO_Helper::num_nodes

inherited

Definition at line 478 of file exodusII_io_helper.h.

◆ num_nodes_global

int libMesh::Nemesis_IO_Helper::num_nodes_global

Global initial information.

The names are self-explanatory for the most part. Used with Nemesis::ne_get_init_global().

Definition at line 362 of file nemesis_io_helper.h.

◆ num_nodes_per_elem

int libMesh::ExodusII_IO_Helper::num_nodes_per_elem

inherited

Definition at line 496 of file exodusII_io_helper.h.

◆ num_nodes_per_set

std::vector<int> libMesh::ExodusII_IO_Helper::num_nodes_per_set

inherited

Definition at line 520 of file exodusII_io_helper.h.

◆ num_proc

int libMesh::Nemesis_IO_Helper::num_proc

The number of processors for which the NEMESIS I file was created.

To be used with Nemesis::ne_get_init_info().

Definition at line 372 of file nemesis_io_helper.h.

◆ num_proc_in_file

int libMesh::Nemesis_IO_Helper::num_proc_in_file

The number of processors for which the NEMESIS I file stores information.

This is generally equal to 1 (1 CPU/file) at least for the splitting Derek gave us. To be used with Nemesis::ne_get_init_info().

Definition at line 379 of file nemesis_io_helper.h.

◆ num_side_sets

int libMesh::ExodusII_IO_Helper::num_side_sets

inherited

Definition at line 490 of file exodusII_io_helper.h.

◆ num_side_sets_global

int libMesh::Nemesis_IO_Helper::num_side_sets_global

Definition at line 366 of file nemesis_io_helper.h.

◆ num_sides_per_set

std::vector<int> libMesh::ExodusII_IO_Helper::num_sides_per_set

inherited

Definition at line 517 of file exodusII_io_helper.h.

◆ num_time_steps

int libMesh::ExodusII_IO_Helper::num_time_steps

inherited

Definition at line 572 of file exodusII_io_helper.h.

◆ opened_for_reading

bool libMesh::ExodusII_IO_Helper::opened_for_reading

inherited

Definition at line 612 of file exodusII_io_helper.h.

◆ opened_for_writing

bool libMesh::ExodusII_IO_Helper::opened_for_writing

inherited

Definition at line 608 of file exodusII_io_helper.h.

◆ proc_border_elem_sets

std::map<unsigned, std::set<std::pair<unsigned,unsigned> > > libMesh::Nemesis_IO_Helper::proc_border_elem_sets

private

Map between processor ID and (element,side) pairs bordering that processor ID.

Definition at line 589 of file nemesis_io_helper.h.

◆ proc_nodes_touched_intersections

std::map<unsigned, std::set<unsigned> > libMesh::Nemesis_IO_Helper::proc_nodes_touched_intersections

private

Another map to store sets of intersections with each other processor (other than ourself, of course).

A node which appears in one of these vectors belongs to element owned by at least this processor and one other.

Definition at line 579 of file nemesis_io_helper.h.

◆ side_list

std::vector<int> libMesh::ExodusII_IO_Helper::side_list

inherited

Definition at line 532 of file exodusII_io_helper.h.

◆ ss_ids

std::vector<int> libMesh::ExodusII_IO_Helper::ss_ids

inherited

Definition at line 511 of file exodusII_io_helper.h.

◆ subdomain_map

std::map<subdomain_id_type, std::vector<dof_id_type> > libMesh::Nemesis_IO_Helper::subdomain_map

Map of subdomains to element numbers.

Definition at line 428 of file nemesis_io_helper.h.

◆ time_steps

std::vector<Real> libMesh::ExodusII_IO_Helper::time_steps

inherited

Definition at line 575 of file exodusII_io_helper.h.

◆ title

std::vector<char> libMesh::ExodusII_IO_Helper::title

inherited

Definition at line 556 of file exodusII_io_helper.h.

◆ verbose

bool libMesh::ExodusII_IO_Helper::verbose

inherited

Definition at line 604 of file exodusII_io_helper.h.

◆ x

std::vector<Real> libMesh::ExodusII_IO_Helper::x

inherited

Definition at line 547 of file exodusII_io_helper.h.

◆ y

std::vector<Real> libMesh::ExodusII_IO_Helper::y

inherited

Definition at line 550 of file exodusII_io_helper.h.

◆ z

std::vector<Real> libMesh::ExodusII_IO_Helper::z

inherited

Definition at line 553 of file exodusII_io_helper.h.

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

include/mesh/nemesis_io_helper.h

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ proc_border_elem_sets_iterator

◆ proc_nodes_touched_iterator

Member Enumeration Documentation

◆ ExodusVarType

Constructor & Destructor Documentation

◆ Nemesis_IO_Helper()

◆ ~Nemesis_IO_Helper()

Member Function Documentation

◆ build_element_and_node_maps()

◆ check_existing_vars()

◆ close()

◆ comm()

◆ compute_border_node_ids()

◆ compute_communication_map_parameters()

◆ compute_elem_communication_maps()

◆ compute_element_maps()

◆ compute_internal_and_border_elems_and_internal_nodes()

◆ compute_node_communication_maps()

◆ compute_node_maps()

◆ compute_num_global_elem_blocks()

◆ compute_num_global_nodesets()

◆ compute_num_global_sidesets()

◆ construct_nemesis_filename()

◆ create()

◆ get_block_id()

◆ get_block_name()

◆ get_cmap_params()

◆ get_complex_names()

◆ get_complex_vars_active_subdomains()

◆ get_eb_info_global()

◆ get_elem_cmap()

◆ get_elem_map()

◆ get_elem_type()

◆ get_init_global()

◆ get_init_info()

◆ get_loadbal_param()

◆ get_node_cmap()

◆ get_node_map()

◆ get_node_set_id()

◆ get_node_set_name()

◆ get_ns_param_global()

◆ get_side_set_id()

◆ get_side_set_name()

◆ get_ss_param_global()

◆ initialize()

◆ initialize_element_variables()

◆ initialize_global_variables()

◆ initialize_nodal_variables()

◆ inquire()

◆ message() [1/2]

◆ message() [2/2]

◆ n_processors()

◆ open()

◆ print_header()

◆ print_nodes()

◆ processor_id()

◆ put_cmap_params()

◆ put_eb_info_global()

◆ put_elem_cmap()

◆ put_elem_map()

◆ put_init_global()

◆ put_init_info()

◆ put_loadbal_param()

◆ put_n_coord()

◆ put_node_cmap()

◆ put_node_map()

◆ put_ns_param_global()

◆ put_ss_param_global()

◆ read_block_info()

◆ read_elem_in_block()