libMesh
|
This is the Nemesis_IO_Helper
class.
More...
#include <nemesis_io_helper.h>
Public Types | |
enum | ExodusVarType { NODAL =0, ELEMENTAL =1, GLOBAL =2, SIDESET =3, NODESET =4, ELEMSET =5 } |
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 | write_complex_magnitude (bool val) |
Set the flag indicating whether the complex modulus should be written when complex numbers are enabled. More... | |
void | read_nodeset (int id) |
Reading functions. More... | |
void | get_init_global () |
Fills: num_nodes_global, num_elems_global, num_elem_blks_global, num_node_sets_global, num_side_sets_global Call after: read_and_store_header_info() Call before: Any other get_* function from this class. 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... | |
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 | 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 | 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 | build_element_and_node_maps (const MeshBase &pmesh) |
This function builds the libmesh -> exodus and exodus -> libmesh node and element maps. More... | |
void | write_nodal_solution (const NumericVector< Number > ¶llel_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 EquationSystems &es, const std::vector< std::pair< unsigned int, unsigned int >> &var_nums, int timestep, const std::vector< std::string > &output_names) |
Outputs EquationSystems current_local_solution nodal values. 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 EquationSystems &es, const std::vector< std::pair< unsigned int, unsigned int >> &var_nums, 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 (std::string_view 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 | set_add_sides (bool add_sides) |
Sets whether or not to write extra "side" elements. More... | |
bool | get_add_sides () |
void | open (const char *filename, bool read_only) |
Opens an ExodusII mesh file named filename . More... | |
ExodusHeaderInfo | read_header () const |
Reads an ExodusII mesh file header, leaving this object's internal data structures unchanged. More... | |
void | read_and_store_header_info () |
Reads an ExodusII mesh file header, and stores required information on this object. 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 | read_bex_cv_blocks () |
Reads the optional bex_cv_blocks from the ExodusII mesh file. More... | |
void | print_nodes (std::ostream &out_stream=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_edge_blocks (MeshBase &mesh) |
Read in edge blocks, storing information in the BoundaryInfo object. 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_elemset_info () |
Reads information about all of the elemsets 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_elemset (int id, int offset) |
Reads information about elemset id and inserts it into the global elemset array at the position offset . More... | |
void | read_all_nodesets () |
New API that reads all nodesets simultaneously. More... | |
void | close () noexcept |
Closes the ExodusII mesh file. More... | |
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... | |
virtual void | create (std::string filename) |
Opens an ExodusII mesh file named filename for writing. 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_elemsets (const MeshBase &mesh) |
Write elemsets stored on the Mesh to the exo file. More... | |
void | write_sideset_data (const MeshBase &mesh, int timestep, const std::vector< std::string > &var_names, const std::vector< std::set< boundary_id_type >> &side_ids, const std::vector< std::map< BoundaryInfo::BCTuple, Real >> &bc_vals) |
Write sideset data for the requested timestep. More... | |
void | read_sideset_data (const MeshBase &mesh, int timestep, std::vector< std::string > &var_names, std::vector< std::set< boundary_id_type >> &side_ids, std::vector< std::map< BoundaryInfo::BCTuple, Real >> &bc_vals) |
Read sideset variables, if any, into the provided data structures. More... | |
void | get_sideset_data_indices (const MeshBase &mesh, std::map< BoundaryInfo::BCTuple, unsigned int > &bc_array_indices) |
Similar to read_sideset_data(), but instead of creating one std::map per sideset per variable, creates a single map of (elem, side, boundary_id) tuples, and stores the exo file array indexing for any/all sideset variables on that sideset (they are all the same). More... | |
void | write_nodeset_data (int timestep, const std::vector< std::string > &var_names, const std::vector< std::set< boundary_id_type >> &node_boundary_ids, const std::vector< std::map< BoundaryInfo::NodeBCTuple, Real >> &bc_vals) |
Write nodeset data for the requested timestep. More... | |
void | read_nodeset_data (int timestep, std::vector< std::string > &var_names, std::vector< std::set< boundary_id_type >> &node_boundary_ids, std::vector< std::map< BoundaryInfo::NodeBCTuple, Real >> &bc_vals) |
Read nodeset variables, if any, into the provided data structures. More... | |
void | get_nodeset_data_indices (std::map< BoundaryInfo::NodeBCTuple, unsigned int > &bc_array_indices) |
Similar to read_nodeset_data(), but instead of creating one std::map per nodeset per variable, creates a single map of (node_id, boundary_id) tuples, and stores the exo file array indexing for any/all nodeset variables on that nodeset (they are all the same). More... | |
void | write_elemset_data (int timestep, const std::vector< std::string > &var_names, const std::vector< std::set< elemset_id_type >> &elemset_ids_in, const std::vector< std::map< std::pair< dof_id_type, elemset_id_type >, Real >> &elemset_vals) |
Write elemset data for the requested timestep. More... | |
void | read_elemset_data (int timestep, std::vector< std::string > &var_names, std::vector< std::set< elemset_id_type >> &elemset_ids_in, std::vector< std::map< std::pair< dof_id_type, elemset_id_type >, Real >> &elemset_vals) |
Read elemset variables, if any, into the provided data structures. More... | |
void | get_elemset_data_indices (std::map< std::pair< dof_id_type, elemset_id_type >, unsigned int > &elemset_array_indices) |
Similar to read_elemset_data(), but instead of creating one std::map per elemset per variable, creates a single map of (elem_id, elemset_id) tuples, and stores the exo file array indexing for any/all elemset variables on that elemset (they are all the same). 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 | update () |
Uses ex_update() to flush buffers to file. 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 | set_hdf5_writing (bool write_hdf5) |
Set to true (the default) to write files in an HDF5-based file format (when HDF5 is available), or to false to write files in the old NetCDF3-based format. 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, bool write_complex_abs) const |
std::vector< std::set< subdomain_id_type > > | get_complex_vars_active_subdomains (const std::vector< std::set< subdomain_id_type >> &vars_active_subdomains, bool write_complex_abs) const |
returns a "tripled" copy of vars_active_subdomains , which is necessary in the complex-valued case. More... | |
std::map< subdomain_id_type, std::vector< std::string > > | get_complex_subdomain_to_var_names (const std::map< subdomain_id_type, std::vector< std::string >> &subdomain_to_var_names, bool write_complex_abs) const |
Takes a map from subdomain id -> vector of active variable names as input and returns a corresponding map where the original variable names have been replaced by their complex counterparts. More... | |
void | message (std::string_view msg) |
Prints the message defined in msg . More... | |
void | message (std::string_view msg, int i) |
Prints the message defined in msg , and appends the number i to the end of the message. More... | |
int | end_elem_id () const |
void | read_var_names (ExodusVarType type) |
const ExodusII_IO_Helper::Conversion & | get_conversion (const ElemType type) const |
const ExodusII_IO_Helper::Conversion & | get_conversion (std::string type_str) const |
dof_id_type | node_id_to_vec_id (dof_id_type n) const |
dof_id_type | added_node_offset_on (processor_id_type p) const |
const Parallel::Communicator & | comm () const |
processor_id_type | n_processors () const |
processor_id_type | processor_id () const |
Static Public Member Functions | |
static int | get_exodus_version () |
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 > | node_list |
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 |
bool | write_complex_abs |
By default, when complex numbers are enabled, for each variable we write out three values: the real part, "r_u" the imaginary part, "i_u", and the complex modulus, a_u := sqrt(r_u*r_u + i_u*i_u), which is also the value returned by std::abs(std::complex). More... | |
int | ex_id |
int | ex_err |
ExodusHeaderInfo | header_info |
std::vector< char > & | title |
int & | num_dim |
int & | num_nodes |
int & | num_elem |
int & | num_elem_blk |
int & | num_edge |
int & | num_edge_blk |
int & | num_node_sets |
int & | num_side_sets |
int & | num_elem_sets |
int | num_global_vars |
int | num_sideset_vars |
int | num_nodeset_vars |
int | num_elemset_vars |
int | num_elem_this_blk |
int | num_nodes_per_elem |
int | num_attr |
int | num_elem_all_sidesets |
int | num_elem_all_elemsets |
std::vector< int > | block_ids |
std::vector< int > | edge_block_ids |
std::vector< int > | connect |
std::vector< int > | ss_ids |
std::vector< int > | nodeset_ids |
std::vector< int > | elemset_ids |
std::vector< int > | num_sides_per_set |
std::vector< int > | num_nodes_per_set |
std::vector< int > | num_elems_per_set |
std::vector< int > | num_df_per_set |
std::vector< int > | num_node_df_per_set |
std::vector< int > | num_elem_df_per_set |
std::vector< int > | node_sets_node_index |
std::vector< int > | node_sets_dist_index |
std::vector< int > | node_sets_node_list |
std::vector< Real > | node_sets_dist_fact |
std::vector< int > | elem_list |
std::vector< int > | side_list |
std::vector< int > | id_list |
std::vector< int > | elemset_list |
std::vector< int > | elemset_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< Real > | w |
unsigned int | bex_num_elem_cvs |
std::vector< std::vector< long unsigned int > > | bex_cv_conn |
std::vector< std::vector< std::vector< Real > > > | bex_dense_constraint_vecs |
std::vector< char > | elem_type |
std::map< dof_id_type, dof_id_type > | libmesh_elem_num_to_exodus |
std::vector< int > | exodus_elem_num_to_libmesh |
std::map< dof_id_type, dof_id_type > | 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::map< dof_id_type, 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::vector< std::string > | sideset_var_names |
std::vector< std::string > | nodeset_var_names |
std::vector< std::string > | elemset_var_names |
std::map< int, std::string > | id_to_block_names |
std::map< int, std::string > | id_to_edge_block_names |
std::map< int, std::string > | id_to_ss_names |
std::map< int, std::string > | id_to_ns_names |
std::map< int, std::string > | id_to_elemset_names |
bool | verbose |
bool | opened_for_writing |
bool | opened_for_reading |
std::string | current_filename |
Protected Member Functions | |
virtual void | read_var_names_impl (const char *var_type, int &count, std::vector< std::string > &result) override |
read_var_names() dispatches to this function. More... | |
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, const 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 | _opened_by_create |
bool | _elem_vars_initialized |
bool | _global_vars_initialized |
bool | _nodal_vars_initialized |
bool | _use_mesh_dimension_instead_of_spatial_dimension |
bool | _write_hdf5 |
int | _end_elem_id |
unsigned | _write_as_dimension |
Point | _coordinate_offset |
bool | _single_precision |
std::vector< dof_id_type > | _added_side_node_offsets |
If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS variables, _added_side_node_offsets[p] gives us the total solution vector offset to use on processor p+1 from the nodes on those previous ranks' sides. More... | |
std::vector< dof_id_type > | _true_node_offsets |
If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS variables, we also need to know how many real nodes from previous ranks are taking up space in a solution vector. More... | |
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_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 | 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... | |
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.
Definition at line 70 of file nemesis_io_helper.h.
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private |
Typedef for an iterator into the data structure above.
Definition at line 644 of file nemesis_io_helper.h.
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private |
Typedef for an iterator into the data structure above.
Definition at line 634 of file nemesis_io_helper.h.
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inherited |
Wraps calls to exII::ex_get_var_names() and exII::ex_get_var_param().
The enumeration controls whether nodal, elemental, global, etc. 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 SIDESET: num_sideset_vars sideset_var_names NODESET: num_nodeset_vars nodeset_var_names
Enumerator | |
---|---|
NODAL | |
ELEMENTAL | |
GLOBAL | |
SIDESET | |
NODESET | |
ELEMSET |
Definition at line 881 of file exodusII_io_helper.h.
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explicit |
Constructor.
Definition at line 58 of file nemesis_io_helper.C.
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virtual |
Destructor.
Definition at line 84 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, and libMesh::ExodusII_IO_Helper::opened_for_writing.
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inlineinherited |
Definition at line 915 of file exodusII_io_helper.h.
References libMesh::ExodusII_IO_Helper::_added_side_node_offsets, libMesh::ExodusII_IO_Helper::_true_node_offsets, and libMesh::libmesh_assert().
void libMesh::Nemesis_IO_Helper::build_element_and_node_maps | ( | const MeshBase & | pmesh | ) |
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.
Definition at line 1630 of file nemesis_io_helper.C.
References block_id_to_elem_connectivity, libMesh::ExodusII_IO_Helper::block_ids, libMesh::Elem::build(), libMesh::MeshBase::elem_ref(), libMesh::ExodusII_IO_Helper::exodus_elem_num_to_libmesh, libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh, libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::index_range(), libMesh::libmesh_assert(), libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus, libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus, local_subdomain_counts, libMesh::make_range(), n_nodes, libMesh::Elem::n_nodes(), libMesh::Elem::node_id(), nodes_attached_to_local_elems, libMesh::ExodusII_IO_Helper::num_nodes, libMesh::ExodusII_IO_Helper::num_nodes_per_elem, libMesh::out, libMesh::ParallelObject::processor_id(), subdomain_map, libMesh::Elem::type(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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protectedinherited |
When appending: during initialization, check that variable names in the file match those you attempt to initialize with.
Definition at line 3327 of file exodusII_io_helper.C.
References libMesh::err, libMesh::Quality::name(), and libMesh::ExodusII_IO_Helper::read_var_names().
Referenced by libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), and libMesh::ExodusII_IO_Helper::initialize_nodal_variables().
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noexceptinherited |
Closes the ExodusII
mesh file.
This function is called from the ExodusII_IO destructor, so it should not throw an exception.
Definition at line 1752 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_opened_by_create, libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::opened_for_reading, libMesh::ExodusII_IO_Helper::opened_for_writing, and libMesh::ParallelObject::processor_id().
Referenced by ~Nemesis_IO_Helper().
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inlineinherited |
Parallel::Communicator
object used by this mesh. Definition at line 97 of file parallel_object.h.
References libMesh::ParallelObject::_communicator.
Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), compute_num_global_elem_blocks(), compute_num_global_nodesets(), compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::PetscMatrix< libMesh::Number >::create_submatrix_nosort(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::MeshBase::get_info(), libMesh::System::get_info(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_bcids_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::DofMap::n_constrained_dofs(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::MeshBase::operator==(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), read_var_names_impl(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().
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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.
Definition at line 1793 of file nemesis_io_helper.C.
References border_node_ids, libMesh::ParallelObject::n_processors(), num_border_nodes, num_node_cmaps, libMesh::out, proc_nodes_touched_intersections, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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private |
This function determines the communication map parameters which will eventually be written to file.
Definition at line 1110 of file nemesis_io_helper.C.
References elem_cmap_elem_cnts, elem_cmap_ids, node_cmap_ids, node_cmap_node_cnts, num_elem_cmaps, num_node_cmaps, libMesh::out, proc_border_elem_sets, proc_nodes_touched_intersections, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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private |
This function computes element communication maps (really just packs vectors) in preparation for writing them to file.
Definition at line 958 of file nemesis_io_helper.C.
References elem_cmap_elem_ids, elem_cmap_ids, elem_cmap_proc_ids, elem_cmap_side_ids, libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus, num_elem_cmaps, and proc_border_elem_sets.
Referenced by initialize().
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private |
This function computes element maps (really just packs vectors) which map the elements to internal and border elements.
Definition at line 933 of file nemesis_io_helper.C.
References border_elem_ids, elem_mapb, elem_mapi, internal_elem_ids, and libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus.
Referenced by initialize().
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private |
This function constructs the set of border and internal element IDs and internal node IDs present on the current mesh.
Definition at line 1188 of file nemesis_io_helper.C.
References border_elem_ids, border_node_ids, libMesh::ExodusII_IO_Helper::get_conversion(), internal_elem_ids, internal_node_ids, nodes_attached_to_local_elems, num_border_elems, num_border_nodes, num_elem_cmaps, num_internal_elems, num_internal_nodes, libMesh::out, proc_border_elem_sets, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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Compute the node communication maps (really just pack vectors) in preparation for writing them to file.
Definition at line 1038 of file nemesis_io_helper.C.
References libMesh::index_range(), libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus, node_cmap_ids, node_cmap_node_ids, node_cmap_proc_ids, node_set, num_node_cmaps, libMesh::out, proc_nodes_touched_intersections, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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Compute the node maps (really just pack vectors) which map the nodes to internal, border, and external nodes in the file.
Definition at line 1009 of file nemesis_io_helper.C.
References border_node_ids, internal_node_ids, libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus, node_mapb, node_mape, and node_mapi.
Referenced by initialize().
void libMesh::Nemesis_IO_Helper::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.
Definition at line 1530 of file nemesis_io_helper.C.
References TIMPI::Communicator::allgather(), libMesh::ParallelObject::comm(), global_elem_blk_cnts, global_elem_blk_ids, local_subdomain_counts, num_elem_blks_global, libMesh::out, libMesh::ParallelObject::processor_id(), TIMPI::Communicator::sum(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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This function uses global communication routines to determine the number of nodesets across the entire mesh.
Definition at line 1419 of file nemesis_io_helper.C.
References libMesh::BoundaryInfo::build_node_list(), libMesh::ParallelObject::comm(), libMesh::MeshBase::get_boundary_info(), libMesh::BoundaryInfo::get_node_boundary_ids(), global_nodeset_ids, libMesh::index_range(), libMesh::MeshBase::node_ptr(), num_global_node_counts, num_node_sets_global, libMesh::out, libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), TIMPI::Communicator::set_union(), TIMPI::Communicator::sum(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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This function uses global communication routines to determine the number of sidesets across the entire mesh.
Definition at line 1326 of file nemesis_io_helper.C.
References libMesh::BoundaryInfo::build_side_list(), libMesh::ParallelObject::comm(), libMesh::MeshBase::elem_ref(), libMesh::MeshBase::get_boundary_info(), libMesh::BoundaryInfo::get_side_boundary_ids(), global_sideset_ids, libMesh::index_range(), num_global_side_counts, num_side_sets_global, libMesh::out, libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), TIMPI::Communicator::set_union(), TIMPI::Communicator::sum(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
std::string libMesh::Nemesis_IO_Helper::construct_nemesis_filename | ( | std::string_view | base_filename | ) |
Given base_filename, foo.e, constructs the Nemesis filename foo.e.X.Y, where X=n.
CPUs and Y=processor ID
Definition at line 2791 of file nemesis_io_helper.C.
References libMesh::ParallelObject::n_processors(), libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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virtualinherited |
Opens an ExodusII
mesh file named filename
for writing.
Definition at line 2125 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_opened_by_create, libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::_write_hdf5, libMesh::ExodusII_IO_Helper::current_filename, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::opened_for_writing, libMesh::out, libMesh::ParallelObject::processor_id(), libMesh::Real, and libMesh::ExodusII_IO_Helper::verbose.
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Definition at line 1301 of file exodusII_io_helper.h.
References libMesh::ExodusII_IO_Helper::_end_elem_id, libMesh::ExodusII_IO_Helper::elem_num_map, and libMesh::ExodusII_IO_Helper::num_elem.
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inlineinherited |
Definition at line 1295 of file exodusII_io_helper.h.
References libMesh::ExodusII_IO_Helper::_add_sides.
Get the block number for the given block index.
Definition at line 1070 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::block_ids.
Referenced by libMesh::ExodusII_IO_Helper::write_element_values(), and libMesh::ExodusII_IO_Helper::write_element_values_element_major().
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Get the block name for the given block index if supplied in the mesh file.
Otherwise an empty string is returned.
Definition at line 1079 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::block_ids, and libMesh::ExodusII_IO_Helper::id_to_block_names.
void libMesh::Nemesis_IO_Helper::get_cmap_params | ( | ) |
Definition at line 369 of file nemesis_io_helper.C.
References elem_cmap_elem_cnts, elem_cmap_ids, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), nemesis_err_flag, node_cmap_ids, node_cmap_node_cnts, num_elem_cmaps, num_node_cmaps, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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inherited |
Definition at line 4672 of file exodusII_io_helper.C.
References libMesh::Quality::name().
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inherited |
Takes a map from subdomain id -> vector of active variable names as input and returns a corresponding map where the original variable names have been replaced by their complex counterparts.
Used by the ExodusII_IO::write_element_data_from_discontinuous_nodal_data() function.
Definition at line 4718 of file exodusII_io_helper.C.
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inherited |
returns a "tripled" copy of vars_active_subdomains
, which is necessary in the complex-valued case.
Definition at line 4695 of file exodusII_io_helper.C.
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inherited |
Definition at line 536 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::conversion_map, and libMesh::ExodusII_IO_Helper::num_dim.
Referenced by build_element_and_node_maps(), compute_internal_and_border_elems_and_internal_nodes(), libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_sideset_data(), write_elements(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_sideset_data(), write_sidesets(), and libMesh::ExodusII_IO_Helper::write_sidesets().
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Definition at line 543 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::element_equivalence_map, and libMesh::ExodusII_IO_Helper::get_conversion().
void libMesh::Nemesis_IO_Helper::get_eb_info_global | ( | ) |
Definition at line 223 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, global_elem_blk_cnts, global_elem_blk_ids, libMesh::index_range(), nemesis_err_flag, num_elem_blks_global, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_elem_cmap | ( | ) |
Definition at line 454 of file nemesis_io_helper.C.
References elem_cmap_elem_cnts, elem_cmap_elem_ids, elem_cmap_ids, elem_cmap_proc_ids, elem_cmap_side_ids, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), nemesis_err_flag, num_elem_cmaps, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_elem_map | ( | ) |
Definition at line 301 of file nemesis_io_helper.C.
References elem_mapb, elem_mapi, libMesh::ExodusII_IO_Helper::ex_id, libMesh::make_range(), nemesis_err_flag, num_border_elems, num_internal_elems, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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HEX27
. Definition at line 550 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elem_type.
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Similar to read_elemset_data(), but instead of creating one std::map per elemset per variable, creates a single map of (elem_id, elemset_id) tuples, and stores the exo file array indexing for any/all elemset variables on that elemset (they are all the same).
Definition at line 4116 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elemset_ids, libMesh::ExodusII_IO_Helper::elemset_list, libMesh::ExodusII_IO_Helper::num_elem_sets, and libMesh::ExodusII_IO_Helper::num_elems_per_set.
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Definition at line 313 of file exodusII_io_helper.C.
Referenced by libMesh::ExodusII_IO::get_exodus_version().
void libMesh::Nemesis_IO_Helper::get_init_global | ( | ) |
Fills: num_nodes_global, num_elems_global, num_elem_blks_global, num_node_sets_global, num_side_sets_global Call after: read_and_store_header_info() Call before: Any other get_* function from this class.
Definition at line 132 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, num_elem_blks_global, num_elems_global, num_node_sets_global, num_nodes_global, num_side_sets_global, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_init_info | ( | ) |
Definition at line 252 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, ftype, nemesis_err_flag, num_proc, num_proc_in_file, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_loadbal_param | ( | ) |
Definition at line 271 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, num_border_elems, num_border_nodes, num_elem_cmaps, num_external_nodes, num_internal_elems, num_internal_nodes, num_node_cmaps, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_node_cmap | ( | ) |
Definition at line 412 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), nemesis_err_flag, node_cmap_ids, node_cmap_node_cnts, node_cmap_node_ids, node_cmap_proc_ids, num_node_cmaps, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
void libMesh::Nemesis_IO_Helper::get_node_map | ( | ) |
Definition at line 332 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, node_mapb, node_mape, node_mapi, num_border_nodes, num_external_nodes, num_internal_nodes, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Get the node set id for the given node set index.
Definition at line 1106 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::nodeset_ids.
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Get the node set name for the given node set index if supplied in the mesh file.
Otherwise an empty string is returned.
Definition at line 1115 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::id_to_ns_names, and libMesh::ExodusII_IO_Helper::nodeset_ids.
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inherited |
Similar to read_nodeset_data(), but instead of creating one std::map per nodeset per variable, creates a single map of (node_id, boundary_id) tuples, and stores the exo file array indexing for any/all nodeset variables on that nodeset (they are all the same).
Definition at line 4258 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::node_sets_node_list, libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::num_node_sets, and libMesh::ExodusII_IO_Helper::num_nodes_per_set.
void libMesh::Nemesis_IO_Helper::get_ns_param_global | ( | ) |
Definition at line 191 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, global_nodeset_ids, libMesh::index_range(), nemesis_err_flag, num_global_node_counts, num_global_node_df_counts, num_node_sets_global, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Get the side set id for the given side set index.
Definition at line 1088 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ss_ids.
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inherited |
Get the side set name for the given side set index if supplied in the mesh file.
Otherwise an empty string is returned.
Definition at line 1097 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::id_to_ss_names, and libMesh::ExodusII_IO_Helper::ss_ids.
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Similar to read_sideset_data(), but instead of creating one std::map per sideset per variable, creates a single map of (elem, side, boundary_id) tuples, and stores the exo file array indexing for any/all sideset variables on that sideset (they are all the same).
This function does not actually call exII::ex_get_sset_var() to get values, and can be useful if only the original ordering of (elem, side) pairs in the exo file is required in cases where a separate approach is used to read the sideset data arrays.
Definition at line 3731 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elem_list, libMesh::MeshBase::elem_ptr(), libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::ExodusII_IO_Helper::Conversion::get_side_map(), mesh, libMesh::ExodusII_IO_Helper::num_side_sets, libMesh::ExodusII_IO_Helper::num_sides_per_set, libMesh::ExodusII_IO_Helper::side_list, libMesh::ExodusII_IO_Helper::ss_ids, and libMesh::Elem::type().
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()
Definition at line 155 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, global_sideset_ids, libMesh::index_range(), nemesis_err_flag, num_global_side_counts, num_global_side_df_counts, num_side_sets_global, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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overridevirtual |
Specialization of the initialize function from ExodusII_IO_Helper that also writes global initial data to file.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 735 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::_use_mesh_dimension_instead_of_spatial_dimension, libMesh::ExodusII_IO_Helper::_write_as_dimension, build_element_and_node_maps(), 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(), elem_cmap_elem_cnts, elem_cmap_elem_ids, elem_cmap_ids, elem_cmap_proc_ids, elem_cmap_side_ids, elem_mapb, elem_mapi, global_elem_blk_cnts, global_elem_blk_ids, global_nodeset_ids, global_sideset_ids, mesh, libMesh::ParallelObject::n_processors(), node_cmap_ids, node_cmap_node_cnts, node_cmap_node_ids, node_cmap_proc_ids, node_mapb, node_mape, node_mapi, num_border_elems, num_border_nodes, libMesh::ExodusII_IO_Helper::num_dim, num_elem_blks_global, num_elem_cmaps, num_external_nodes, num_global_node_counts, num_global_node_df_counts, num_global_side_counts, num_global_side_df_counts, num_internal_elems, num_internal_nodes, num_node_cmaps, num_node_sets_global, num_side_sets_global, libMesh::MeshBase::parallel_n_elem(), libMesh::MeshBase::parallel_n_nodes(), put_cmap_params(), put_eb_info_global(), put_elem_cmap(), put_elem_map(), put_init_global(), put_init_info(), put_loadbal_param(), put_node_cmap(), put_node_map(), put_ns_param_global(), put_ss_param_global(), and write_exodus_initialization_info().
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overridevirtual |
Override the Exodus Helper's implementation of this function so that it works correctly in parallel.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 2584 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::_elem_vars_initialized, libMesh::ExodusII_IO_Helper::check_existing_vars(), libMesh::ExodusII_IO_Helper::elem_var_names, libMesh::ExodusII_IO_Helper::ELEMENTAL, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, global_elem_blk_ids, libMesh::index_range(), libMesh::ExodusII_IO_Helper::num_elem_vars, and libMesh::ExodusII_IO_Helper::write_var_names().
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inherited |
Sets up the global variables.
Definition at line 3301 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_global_vars_initialized, libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::check_existing_vars(), libMesh::ExodusII_IO_Helper::GLOBAL, libMesh::ExodusII_IO_Helper::global_var_names, libMesh::ExodusII_IO_Helper::num_global_vars, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::write_var_names().
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Sets up the nodal variables.
Definition at line 3273 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_nodal_vars_initialized, libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::check_existing_vars(), libMesh::ExodusII_IO_Helper::NODAL, libMesh::ExodusII_IO_Helper::nodal_var_names, libMesh::ExodusII_IO_Helper::num_nodal_vars, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::write_var_names().
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inherited |
Prints the message defined in msg
.
Can be turned off if verbosity is set to 0.
Definition at line 557 of file exodusII_io_helper.C.
References libMesh::out, and libMesh::ExodusII_IO_Helper::verbose.
Referenced by libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_info(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::ExodusII_IO_Helper::read_nodes(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), libMesh::ExodusII_IO_Helper::read_sideset(), and libMesh::ExodusII_IO_Helper::read_sideset_info().
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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.
Definition at line 564 of file exodusII_io_helper.C.
References libMesh::out, and libMesh::ExodusII_IO_Helper::verbose.
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Definition at line 103 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().
Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), compute_border_node_ids(), construct_nemesis_filename(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().
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Definition at line 896 of file exodusII_io_helper.h.
References libMesh::ExodusII_IO_Helper::_added_side_node_offsets, libMesh::ExodusII_IO_Helper::_true_node_offsets, and libMesh::libmesh_assert().
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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.
Definition at line 656 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::current_filename, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::opened_for_reading, libMesh::ExodusII_IO_Helper::opened_for_writing, libMesh::out, libMesh::Real, and libMesh::ExodusII_IO_Helper::verbose.
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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.
Definition at line 811 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::num_dim, libMesh::ExodusII_IO_Helper::num_elem, libMesh::ExodusII_IO_Helper::num_elem_blk, libMesh::ExodusII_IO_Helper::num_elem_sets, libMesh::ExodusII_IO_Helper::num_node_sets, libMesh::ExodusII_IO_Helper::num_nodes, libMesh::ExodusII_IO_Helper::num_side_sets, libMesh::out, libMesh::ExodusII_IO_Helper::title, and libMesh::ExodusII_IO_Helper::verbose.
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inherited |
Prints the nodal information, by default to libMesh::out
.
Definition at line 1012 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::num_nodes, libMesh::ExodusII_IO_Helper::x, libMesh::ExodusII_IO_Helper::y, and libMesh::ExodusII_IO_Helper::z.
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inlineinherited |
Definition at line 114 of file parallel_object.h.
References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().
Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::ExodusII_IO_Helper::close(), compute_border_node_ids(), compute_communication_map_parameters(), compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), compute_node_communication_maps(), compute_num_global_elem_blocks(), compute_num_global_nodesets(), compute_num_global_sidesets(), construct_nemesis_filename(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), get_cmap_params(), get_eb_info_global(), get_elem_cmap(), get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), get_init_global(), get_init_info(), get_loadbal_param(), libMesh::DofMap::get_local_constraints(), get_node_cmap(), get_node_map(), get_ns_param_global(), get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), put_cmap_params(), put_elem_cmap(), put_elem_map(), put_loadbal_param(), put_node_cmap(), put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), read_var_names_impl(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().
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.
Definition at line 620 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, and libMesh::ParallelObject::processor_id().
Referenced by initialize().
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().
Definition at line 540 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, and nemesis_err_flag.
Referenced by initialize().
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.
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().
Definition at line 700 of file nemesis_io_helper.C.
References elem_cmap_ids, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), nemesis_err_flag, and libMesh::ParallelObject::processor_id().
Referenced by initialize().
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().
Definition at line 721 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, and libMesh::ParallelObject::processor_id().
Referenced by initialize().
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.
Definition at line 521 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, and nemesis_err_flag.
Referenced by initialize().
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
Definition at line 505 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, and nemesis_err_flag.
Referenced by initialize().
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
Definition at line 594 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, and libMesh::ParallelObject::processor_id().
Referenced by initialize().
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...
node_cmap_node_ids
and node_cmap_proc_ids
which can be used when calling this function.Must be called after put_cmap_params().
Definition at line 639 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), nemesis_err_flag, node_cmap_ids, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
Referenced by initialize().
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
Definition at line 683 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, nemesis_err_flag, and libMesh::ParallelObject::processor_id().
Referenced by initialize().
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()
Definition at line 554 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, global_nodeset_ids, and nemesis_err_flag.
Referenced by initialize().
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()
Definition at line 574 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, global_sideset_ids, and nemesis_err_flag.
Referenced by initialize().
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New API that reads all nodesets simultaneously.
This may be slightly faster than reading them one at a time. Calls ex_get_concat_node_sets() under the hood.
Definition at line 1682 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::MappedInputVector::data(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_to_ns_names, libMesh::ExodusII_IO_Helper::node_sets_dist_fact, libMesh::ExodusII_IO_Helper::node_sets_dist_index, libMesh::ExodusII_IO_Helper::node_sets_node_index, libMesh::ExodusII_IO_Helper::node_sets_node_list, libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::num_node_df_per_set, libMesh::ExodusII_IO_Helper::num_node_sets, and libMesh::ExodusII_IO_Helper::num_nodes_per_set.
Referenced by libMesh::ExodusII_IO_Helper::write_nodeset_data().
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Reads an ExodusII
mesh file header, and stores required information on this object.
Definition at line 727 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::header_info, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_elem_vars, libMesh::ExodusII_IO_Helper::num_elemset_vars, libMesh::ExodusII_IO_Helper::num_global_vars, libMesh::ExodusII_IO_Helper::num_nodal_vars, libMesh::ExodusII_IO_Helper::num_nodeset_vars, libMesh::ExodusII_IO_Helper::num_sideset_vars, libMesh::ExodusII_IO_Helper::read_header(), and libMesh::ExodusII_IO_Helper::read_num_time_steps().
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Reads the optional bex_cv_blocks
from the ExodusII
mesh file.
Definition at line 901 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::bex_dense_constraint_vecs, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, and libMesh::make_range().
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inherited |
Reads information for all of the blocks in the ExodusII
mesh file.
Definition at line 1020 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::block_ids, libMesh::ExodusII_IO_Helper::edge_block_ids, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_to_block_names, libMesh::ExodusII_IO_Helper::id_to_edge_block_names, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_edge_blk, and libMesh::ExodusII_IO_Helper::num_elem_blk.
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Read in edge blocks, storing information in the BoundaryInfo object.
Definition at line 1283 of file exodusII_io_helper.C.
References libMesh::BoundaryInfo::add_edge(), libMesh::Elem::build(), libMesh::ExodusII_IO_Helper::connect, libMesh::ExodusII_IO_Helper::edge_block_ids, libMesh::BoundaryInfo::edgeset_name(), libMesh::MeshBase::elem_ptr(), libMesh::ExodusII_IO_Helper::elem_type, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::FIRST, libMesh::Elem::first_order_equivalent_type(), libMesh::MeshBase::get_boundary_info(), libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::ExodusII_IO_Helper::id_to_edge_block_names, mesh, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::node_num_map, libMesh::MeshBase::node_ptr(), and libMesh::ExodusII_IO_Helper::num_edge_blk.
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inherited |
Reads all of the element connectivity for block block
in the ExodusII
mesh file.
Definition at line 1125 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::bex_cv_conn, libMesh::ExodusII_IO_Helper::bex_num_elem_cvs, libMesh::ExodusII_IO_Helper::block_ids, libMesh::ExodusII_IO_Helper::connect, libMesh::ExodusII_IO_Helper::elem_type, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::libmesh_assert(), libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_attr, libMesh::ExodusII_IO_Helper::num_elem_this_blk, libMesh::ExodusII_IO_Helper::num_nodes_per_elem, libMesh::out, and libMesh::ExodusII_IO_Helper::verbose.
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Reads the optional node_num_map
from the ExodusII
mesh file.
Definition at line 1453 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_end_elem_id, libMesh::ExodusII_IO_Helper::elem_num_map, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_elem, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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Reads elemental values for the variable 'elemental_var_name' at the specified timestep into the 'elem_var_value_map' which is passed in.
Definition at line 2037 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::block_ids, libMesh::ExodusII_IO_Helper::elem_num_map, libMesh::ExodusII_IO_Helper::elem_var_names, libMesh::ExodusII_IO_Helper::ELEMENTAL, libMesh::err, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_elem_blk, libMesh::ExodusII_IO_Helper::num_elem_this_blk, and libMesh::ExodusII_IO_Helper::read_var_names().
Reads information about elemset id
and inserts it into the global elemset array at the position offset
.
Definition at line 1637 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elemset_id_list, libMesh::ExodusII_IO_Helper::elemset_ids, libMesh::ExodusII_IO_Helper::elemset_list, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_elem_df_per_set, and libMesh::ExodusII_IO_Helper::num_elems_per_set.
Referenced by libMesh::ExodusII_IO_Helper::write_elemset_data().
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Read elemset variables, if any, into the provided data structures.
Definition at line 4007 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ELEMSET, libMesh::ExodusII_IO_Helper::elemset_ids, libMesh::ExodusII_IO_Helper::elemset_list, libMesh::ExodusII_IO_Helper::elemset_var_names, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_elem_sets, libMesh::ExodusII_IO_Helper::num_elems_per_set, libMesh::ExodusII_IO_Helper::num_elemset_vars, and libMesh::ExodusII_IO_Helper::read_var_names().
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Reads information about all of the elemsets in the ExodusII
mesh file.
Definition at line 1550 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elemset_id_list, libMesh::ExodusII_IO_Helper::elemset_ids, libMesh::ExodusII_IO_Helper::elemset_list, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_to_elemset_names, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_elem_all_elemsets, libMesh::ExodusII_IO_Helper::num_elem_df_per_set, libMesh::ExodusII_IO_Helper::num_elem_sets, and libMesh::ExodusII_IO_Helper::num_elems_per_set.
Referenced by libMesh::ExodusII_IO_Helper::write_elemset_data().
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inherited |
Reads the vector of global variables.
Definition at line 4623 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_global_vars, and libMesh::ParallelObject::processor_id().
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inherited |
Reads an ExodusII
mesh file header, leaving this object's internal data structures unchanged.
Definition at line 697 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusHeaderInfo::num_dim, libMesh::ExodusHeaderInfo::num_edge, libMesh::ExodusHeaderInfo::num_edge_blk, libMesh::ExodusHeaderInfo::num_elem, libMesh::ExodusHeaderInfo::num_elem_blk, libMesh::ExodusHeaderInfo::num_elem_sets, libMesh::ExodusHeaderInfo::num_node_sets, libMesh::ExodusHeaderInfo::num_nodes, libMesh::ExodusHeaderInfo::num_side_sets, and libMesh::ExodusHeaderInfo::title.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info().
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inherited |
Reads the nodal values for the variable 'nodal_var_name' at the specified time into the 'nodal_var_values' array.
Definition at line 1816 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::err, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::NODAL, libMesh::ExodusII_IO_Helper::nodal_var_names, libMesh::ExodusII_IO_Helper::nodal_var_values, libMesh::ExodusII_IO_Helper::node_num_map, libMesh::ExodusII_IO_Helper::num_nodes, and libMesh::ExodusII_IO_Helper::read_var_names().
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inherited |
Reads the optional node_num_map
from the ExodusII
mesh file.
Definition at line 877 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::node_num_map, libMesh::ExodusII_IO_Helper::num_nodes, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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inherited |
Reads the nodal data (x,y,z coordinates) from the ExodusII
mesh file.
Definition at line 826 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_nodes, libMesh::ExodusII_IO_Helper::w, libMesh::ExodusII_IO_Helper::x, libMesh::ExodusII_IO_Helper::y, and libMesh::ExodusII_IO_Helper::z.
void libMesh::Nemesis_IO_Helper::read_nodeset | ( | int | id | ) |
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... Reads the node ids of nodeset id
and stores them in the node_list
member of this class.
Definition at line 99 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::message(), node_list, libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::num_node_df_per_set, and libMesh::ExodusII_IO_Helper::num_nodes_per_set.
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inherited |
Read nodeset variables, if any, into the provided data structures.
Definition at line 4159 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::node_sets_node_list, libMesh::ExodusII_IO_Helper::NODESET, libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::nodeset_var_names, libMesh::ExodusII_IO_Helper::num_node_sets, libMesh::ExodusII_IO_Helper::num_nodes_per_set, libMesh::ExodusII_IO_Helper::num_nodeset_vars, and libMesh::ExodusII_IO_Helper::read_var_names().
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inherited |
Reads information about all of the nodesets in the ExodusII
mesh file.
Definition at line 1521 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_to_ns_names, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::num_node_df_per_set, libMesh::ExodusII_IO_Helper::num_node_sets, and libMesh::ExodusII_IO_Helper::num_nodes_per_set.
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inherited |
Reads the number of timesteps currently stored in the Exodus file and stores it in the num_time_steps variable.
Definition at line 1808 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::num_time_steps.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info(), and libMesh::ExodusII_IO_Helper::read_time_steps().
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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.
Definition at line 761 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::out, and libMesh::ExodusII_IO_Helper::verbose.
Reads information about sideset id
and inserts it into the global sideset array at the position offset
.
Definition at line 1590 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elem_list, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_list, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_df_per_set, libMesh::ExodusII_IO_Helper::num_sides_per_set, libMesh::ExodusII_IO_Helper::side_list, and libMesh::ExodusII_IO_Helper::ss_ids.
Referenced by libMesh::ExodusII_IO_Helper::write_sideset_data().
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inherited |
Read sideset variables, if any, into the provided data structures.
Definition at line 3627 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::elem_list, libMesh::MeshBase::elem_ptr(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::ExodusII_IO_Helper::Conversion::get_side_map(), mesh, libMesh::ExodusII_IO_Helper::num_side_sets, libMesh::ExodusII_IO_Helper::num_sides_per_set, libMesh::ExodusII_IO_Helper::num_sideset_vars, libMesh::ExodusII_IO_Helper::read_var_names(), libMesh::ExodusII_IO_Helper::side_list, libMesh::ExodusII_IO_Helper::SIDESET, libMesh::ExodusII_IO_Helper::sideset_var_names, libMesh::ExodusII_IO_Helper::ss_ids, and libMesh::Elem::type().
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inherited |
Reads information about all of the sidesets in the ExodusII
mesh file.
Definition at line 1486 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elem_list, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::id_list, libMesh::ExodusII_IO_Helper::id_to_ss_names, libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::num_df_per_set, libMesh::ExodusII_IO_Helper::num_elem_all_sidesets, libMesh::ExodusII_IO_Helper::num_side_sets, libMesh::ExodusII_IO_Helper::num_sides_per_set, libMesh::ExodusII_IO_Helper::side_list, and libMesh::ExodusII_IO_Helper::ss_ids.
Referenced by libMesh::ExodusII_IO_Helper::write_sideset_data().
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inherited |
Reads and stores the timesteps in the 'time_steps' array.
Definition at line 1791 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_time_steps, libMesh::ExodusII_IO_Helper::read_num_time_steps(), and libMesh::ExodusII_IO_Helper::time_steps.
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inherited |
Definition at line 1877 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::elem_var_names, libMesh::ExodusII_IO_Helper::ELEMENTAL, libMesh::ExodusII_IO_Helper::ELEMSET, libMesh::ExodusII_IO_Helper::elemset_var_names, libMesh::ExodusII_IO_Helper::GLOBAL, libMesh::ExodusII_IO_Helper::global_var_names, libMesh::ExodusII_IO_Helper::NODAL, libMesh::ExodusII_IO_Helper::nodal_var_names, libMesh::ExodusII_IO_Helper::NODESET, libMesh::ExodusII_IO_Helper::nodeset_var_names, libMesh::ExodusII_IO_Helper::num_elem_vars, libMesh::ExodusII_IO_Helper::num_elemset_vars, libMesh::ExodusII_IO_Helper::num_global_vars, libMesh::ExodusII_IO_Helper::num_nodal_vars, libMesh::ExodusII_IO_Helper::num_nodeset_vars, libMesh::ExodusII_IO_Helper::num_sideset_vars, libMesh::ExodusII_IO_Helper::read_var_names_impl(), libMesh::ExodusII_IO_Helper::SIDESET, and libMesh::ExodusII_IO_Helper::sideset_var_names.
Referenced by libMesh::ExodusII_IO_Helper::check_existing_vars(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), and libMesh::ExodusII_IO_Helper::read_sideset_data().
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overrideprotectedvirtual |
read_var_names() dispatches to this function.
We need to override it slightly for Nemesis.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 2763 of file nemesis_io_helper.C.
References TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::DofObject::invalid_processor_id, libMesh::libmesh_assert(), TIMPI::Communicator::min(), libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::read_var_names_impl().
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inlineinherited |
Sets whether or not to write extra "side" elements.
This is useful for plotting SIDE_DISCONTINUOUS data.
Definition at line 1289 of file exodusII_io_helper.h.
References libMesh::ExodusII_IO_Helper::_add_sides.
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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
Definition at line 4665 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_coordinate_offset.
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inherited |
Set to true (the default) to write files in an HDF5-based file format (when HDF5 is available), or to false to write files in the old NetCDF3-based format.
If HDF5 is unavailable, this setting does nothing.
Definition at line 4650 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_write_hdf5.
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inherited |
Uses ex_update() to flush buffers to file.
Definition at line 4615 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, and libMesh::ExodusII_IO_Helper::ex_id.
Referenced by write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_values(), and libMesh::ExodusII_IO_Helper::write_timestep().
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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.
Definition at line 4644 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_use_mesh_dimension_instead_of_spatial_dimension.
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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.
Definition at line 4658 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_write_as_dimension, and dim.
void libMesh::Nemesis_IO_Helper::write_complex_magnitude | ( | bool | val | ) |
Set the flag indicating whether the complex modulus should be written when complex numbers are enabled.
By default this flag is set to true.
void libMesh::Nemesis_IO_Helper::write_element_values | ( | const MeshBase & | mesh, |
const EquationSystems & | es, | ||
const std::vector< std::pair< unsigned int, unsigned int >> & | var_nums, | ||
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.
Definition at line 2632 of file nemesis_io_helper.C.
References std::abs(), libMesh::CONSTANT, libMesh::System::current_local_solution, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::EquationSystems::get_system(), global_elem_blk_ids, libMesh::if(), libMesh::index_range(), mesh, libMesh::MONOMIAL_VEC, subdomain_map, libMesh::ExodusII_IO_Helper::update(), libMesh::System::variable_type(), and write_complex_abs.
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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.
Definition at line 4303 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_block_id(), mesh, libMesh::MeshTools::n_elem(), libMesh::MeshBase::n_elem(), libMesh::ExodusII_IO_Helper::num_elem_vars, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
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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.
Definition at line 4388 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::MappedOutputVector::data(), distance(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_block_id(), mesh, libMesh::ExodusII_IO_Helper::num_elem_vars, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
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overridevirtual |
This function is specialized to write the connectivity.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 2269 of file nemesis_io_helper.C.
References block_id_to_elem_connectivity, libMesh::MeshBase::elem_ref(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::exodus_elem_num_to_libmesh, libMesh::ExodusII_IO_Helper::NamesData::get_char_star_star(), libMesh::ExodusII_IO_Helper::get_conversion(), global_elem_blk_ids, libMesh::make_range(), mesh, libMesh::Elem::n_nodes(), num_elem_blks_global, libMesh::ExodusII_IO_Helper::num_nodes_per_elem, libMesh::ExodusII_IO_Helper::NamesData::push_back_entry(), and subdomain_map.
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inherited |
Write elemset data for the requested timestep.
Definition at line 3884 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ELEMSET, libMesh::ExodusII_IO_Helper::elemset_ids, libMesh::ExodusII_IO_Helper::elemset_list, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), libMesh::ExodusII_IO_Helper::num_elem_sets, libMesh::ExodusII_IO_Helper::num_elems_per_set, libMesh::ParallelObject::processor_id(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_info(), and libMesh::ExodusII_IO_Helper::write_var_names().
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inherited |
Write elemsets stored on the Mesh to the exo file.
Definition at line 3390 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::MeshBase::get_elem_integer_index(), libMesh::MeshBase::get_elemsets(), libMesh::MeshBase::has_elem_integer(), libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus, mesh, libMesh::MeshBase::n_elemsets(), libMesh::ExodusII_IO_Helper::num_elem_sets, and libMesh::ParallelObject::processor_id().
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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.
Definition at line 900 of file nemesis_io_helper.C.
References distance(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, global_nodeset_ids, global_sideset_ids, libMesh::ExodusII_IO_Helper::num_dim, libMesh::ExodusII_IO_Helper::num_elem, libMesh::ExodusII_IO_Helper::num_elem_blk, num_elem_blks_global, libMesh::ExodusII_IO_Helper::num_node_sets, libMesh::ExodusII_IO_Helper::num_nodes, and libMesh::ExodusII_IO_Helper::num_side_sets.
Referenced by initialize().
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inherited |
Writes the vector of global variables.
Definition at line 4591 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_global_vars, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
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inherited |
Writes the vector of information records.
Definition at line 4553 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::err, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
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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.
Definition at line 2210 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh, libMesh::make_range(), mesh, libMesh::ExodusII_IO_Helper::x, libMesh::ExodusII_IO_Helper::y, and libMesh::ExodusII_IO_Helper::z.
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.
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). |
Definition at line 2392 of file nemesis_io_helper.C.
References std::abs(), distance(), libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh, libMesh::NumericVector< T >::localize(), libMesh::ExodusII_IO_Helper::num_nodes, and libMesh::ExodusII_IO_Helper::write_nodal_values().
void libMesh::Nemesis_IO_Helper::write_nodal_solution | ( | const EquationSystems & | es, |
const std::vector< std::pair< unsigned int, unsigned int >> & | var_nums, | ||
int | timestep, | ||
const std::vector< std::string > & | output_names | ||
) |
Outputs EquationSystems current_local_solution nodal values.
Definition at line 2452 of file nemesis_io_helper.C.
References std::abs(), libMesh::Variable::active_on_subdomain(), libMesh::System::current_local_solution, distance(), libMesh::DofMap::dof_indices(), libMesh::DofObject::dof_number(), libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh, libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), libMesh::index_range(), libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus, mesh, libMesh::DofObject::n_comp(), libMesh::Quality::name(), libMesh::FEInterface::nodal_soln(), libMesh::ExodusII_IO_Helper::num_nodes, libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::System::variable(), libMesh::System::variable_name(), libMesh::System::variable_type(), and libMesh::ExodusII_IO_Helper::write_nodal_values().
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.
Definition at line 2354 of file nemesis_io_helper.C.
References std::abs(), libMesh::ExodusII_IO_Helper::exodus_node_num_to_libmesh, libMesh::ExodusII_IO_Helper::num_nodes, value, and libMesh::ExodusII_IO_Helper::write_nodal_values().
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inherited |
Writes the vector of values to a nodal variable.
Definition at line 4525 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::num_nodes, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
Referenced by write_nodal_solution().
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inherited |
Write nodeset data for the requested timestep.
Definition at line 3779 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::index_range(), libMesh::ExodusII_IO_Helper::node_sets_node_index, libMesh::ExodusII_IO_Helper::node_sets_node_list, libMesh::ExodusII_IO_Helper::NODESET, libMesh::ExodusII_IO_Helper::nodeset_ids, libMesh::ExodusII_IO_Helper::num_node_sets, libMesh::ExodusII_IO_Helper::num_nodes_per_set, libMesh::ParallelObject::processor_id(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), and libMesh::ExodusII_IO_Helper::write_var_names().
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overridevirtual |
Writes the nodesets for this processor.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 1915 of file nemesis_io_helper.C.
References libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, global_nodeset_ids, libMesh::ExodusII_IO_Helper::libmesh_node_num_to_exodus, mesh, libMesh::out, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::verbose.
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inherited |
Write sideset data for the requested timestep.
Definition at line 3487 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::elem_list, libMesh::MeshBase::elem_ptr(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_conversion(), libMesh::ExodusII_IO_Helper::Conversion::get_side_map(), libMesh::index_range(), libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus, mesh, libMesh::ExodusII_IO_Helper::num_side_sets, libMesh::ExodusII_IO_Helper::num_sides_per_set, libMesh::ParallelObject::processor_id(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_info(), side_id, libMesh::ExodusII_IO_Helper::side_list, libMesh::ExodusII_IO_Helper::SIDESET, libMesh::ExodusII_IO_Helper::ss_ids, libMesh::Elem::type(), and libMesh::ExodusII_IO_Helper::write_var_names().
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Writes the sidesets for this processor.
Reimplemented from libMesh::ExodusII_IO_Helper.
Definition at line 2066 of file nemesis_io_helper.C.
References libMesh::Elem::active_family_tree_by_side(), libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ExodusII_IO_Helper::get_conversion(), global_sideset_ids, libMesh::ExodusII_IO_Helper::libmesh_elem_num_to_exodus, mesh, libMesh::out, libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), libMesh::Elem::type(), and libMesh::ExodusII_IO_Helper::verbose.
Writes the time for the timestep.
Definition at line 3367 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::_run_only_on_proc0, libMesh::ExodusII_IO_Helper::_single_precision, libMesh::ExodusII_IO_Helper::ex_err, libMesh::ExodusII_IO_Helper::ex_id, libMesh::ParallelObject::processor_id(), and libMesh::ExodusII_IO_Helper::update().
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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.
Definition at line 1947 of file exodusII_io_helper.C.
References libMesh::ExodusII_IO_Helper::ELEMENTAL, libMesh::ExodusII_IO_Helper::ELEMSET, libMesh::ExodusII_IO_Helper::GLOBAL, libMesh::ExodusII_IO_Helper::NODAL, libMesh::ExodusII_IO_Helper::NODESET, libMesh::ExodusII_IO_Helper::num_elem_vars, libMesh::ExodusII_IO_Helper::num_elemset_vars, libMesh::ExodusII_IO_Helper::num_global_vars, libMesh::ExodusII_IO_Helper::num_nodal_vars, libMesh::ExodusII_IO_Helper::num_nodeset_vars, libMesh::ExodusII_IO_Helper::num_sideset_vars, libMesh::ExodusII_IO_Helper::SIDESET, and libMesh::ExodusII_IO_Helper::write_var_names_impl().
Referenced by libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
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If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS variables, _added_side_node_offsets[p] gives us the total solution vector offset to use on processor p+1 from the nodes on those previous ranks' sides.
Definition at line 982 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::added_node_offset_on(), libMesh::ExodusII_IO_Helper::initialize(), and libMesh::ExodusII_IO_Helper::node_id_to_vec_id().
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Definition at line 120 of file parallel_object.h.
Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), and libMesh::BoundaryInfo::regenerate_id_sets().
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Definition at line 971 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::set_coordinate_offset(), and libMesh::ExodusII_IO_Helper::write_nodal_coordinates().
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Definition at line 946 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_element_variables(), and initialize_element_variables().
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Definition at line 964 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::end_elem_id(), and libMesh::ExodusII_IO_Helper::read_elem_num_map().
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Definition at line 949 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_global_variables().
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Definition at line 952 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_nodal_variables().
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Definition at line 943 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), and libMesh::ExodusII_IO_Helper::create().
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Definition at line 940 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::create(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::ExodusII_IO_Helper::write_sidesets(), and libMesh::ExodusII_IO_Helper::write_timestep().
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Definition at line 974 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::create(), libMesh::ExodusII_IO_Helper::open(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), libMesh::ExodusII_IO_Helper::read_nodes(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_time_steps(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_global_values(), write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::ExodusII_IO_Helper::write_sideset_data(), and libMesh::ExodusII_IO_Helper::write_timestep().
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If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS variables, we also need to know how many real nodes from previous ranks are taking up space in a solution vector.
Definition at line 989 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::added_node_offset_on(), libMesh::ExodusII_IO_Helper::initialize(), and libMesh::ExodusII_IO_Helper::node_id_to_vec_id().
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Definition at line 957 of file exodusII_io_helper.h.
Referenced by initialize(), libMesh::ExodusII_IO_Helper::initialize(), and libMesh::ExodusII_IO_Helper::use_mesh_dimension_instead_of_spatial_dimension().
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Definition at line 968 of file exodusII_io_helper.h.
Referenced by initialize(), libMesh::ExodusII_IO_Helper::initialize(), and libMesh::ExodusII_IO_Helper::write_as_dimension().
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Definition at line 961 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::create(), and libMesh::ExodusII_IO_Helper::set_hdf5_writing().
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Definition at line 786 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elem_in_block().
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Definition at line 790 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_bex_cv_blocks().
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Definition at line 783 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elem_in_block().
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 465 of file nemesis_io_helper.h.
Referenced by build_element_and_node_maps(), and write_elements().
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Definition at line 698 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), libMesh::ExodusII_IO_Helper::get_block_id(), libMesh::ExodusII_IO_Helper::get_block_name(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), and libMesh::ExodusII_IO_Helper::write_elements().
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A set of border elem IDs for this processor.
Definition at line 659 of file nemesis_io_helper.h.
Referenced by compute_element_maps(), and compute_internal_and_border_elems_and_internal_nodes().
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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 622 of file nemesis_io_helper.h.
Referenced by compute_border_node_ids(), compute_internal_and_border_elems_and_internal_nodes(), and compute_node_maps().
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Definition at line 704 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_edge_blocks(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), and libMesh::ExodusII_IO_Helper::write_elements().
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Definition at line 869 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::create(), and libMesh::ExodusII_IO_Helper::open().
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Definition at line 701 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_block_info(), and libMesh::ExodusII_IO_Helper::read_edge_blocks().
std::vector<int> libMesh::Nemesis_IO_Helper::elem_cmap_elem_cnts |
Definition at line 567 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), get_cmap_params(), get_elem_cmap(), and initialize().
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 587 of file nemesis_io_helper.h.
Referenced by compute_elem_communication_maps(), get_elem_cmap(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::elem_cmap_ids |
Definition at line 566 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), compute_elem_communication_maps(), get_cmap_params(), get_elem_cmap(), initialize(), and put_elem_cmap().
std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::elem_cmap_proc_ids |
Definition at line 589 of file nemesis_io_helper.h.
Referenced by compute_elem_communication_maps(), get_elem_cmap(), and initialize().
std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::elem_cmap_side_ids |
Definition at line 588 of file nemesis_io_helper.h.
Referenced by compute_elem_communication_maps(), get_elem_cmap(), and initialize().
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Definition at line 750 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
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 532 of file nemesis_io_helper.h.
Referenced by compute_element_maps(), get_elem_map(), and initialize().
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 525 of file nemesis_io_helper.h.
Referenced by compute_element_maps(), get_elem_map(), and initialize().
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Definition at line 768 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::end_elem_id(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), and libMesh::ExodusII_IO_Helper::write_elements().
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Definition at line 793 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::ExodusII_IO_Helper(), libMesh::ExodusII_IO_Helper::get_elem_type(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), and libMesh::ExodusII_IO_Helper::read_elem_in_block().
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Definition at line 826 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 829 of file exodusII_io_helper.h.
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Definition at line 762 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elemset(), and libMesh::ExodusII_IO_Helper::read_elemset_info().
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Definition at line 713 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_elemset_data_indices(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), and libMesh::ExodusII_IO_Helper::write_elemset_data().
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Definition at line 759 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_elemset_data_indices(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), and libMesh::ExodusII_IO_Helper::write_elemset_data().
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Definition at line 841 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elemset_data(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 630 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_bex_cv_blocks(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::ExodusII_IO_Helper::read_nodes(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), libMesh::ExodusII_IO_Helper::read_qa_records(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), libMesh::ExodusII_IO_Helper::read_time_steps(), libMesh::ExodusII_IO_Helper::read_var_names_impl(), libMesh::ExodusII_IO_Helper::update(), write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), write_elements(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), write_exodus_initialization_info(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::ExodusII_IO_Helper::write_information_records(), write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_sideset_data(), write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_timestep(), libMesh::ExodusII_IO_Helper::write_var_names_impl(), and ~Nemesis_IO_Helper().
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Definition at line 627 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::create(), get_cmap_params(), get_eb_info_global(), get_elem_cmap(), get_elem_map(), get_init_global(), get_init_info(), get_loadbal_param(), get_node_cmap(), get_node_map(), get_ns_param_global(), get_ss_param_global(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::open(), put_cmap_params(), put_eb_info_global(), put_elem_cmap(), put_elem_map(), put_init_global(), put_init_info(), put_loadbal_param(), put_node_cmap(), put_node_map(), put_ns_param_global(), put_ss_param_global(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_bex_cv_blocks(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO_Helper::read_header(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::ExodusII_IO_Helper::read_nodes(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), libMesh::ExodusII_IO_Helper::read_qa_records(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), libMesh::ExodusII_IO_Helper::read_time_steps(), libMesh::ExodusII_IO_Helper::read_var_names_impl(), libMesh::ExodusII_IO_Helper::update(), write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), write_elements(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), write_exodus_initialization_info(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::ExodusII_IO_Helper::write_information_records(), write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_sideset_data(), write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_timestep(), libMesh::ExodusII_IO_Helper::write_var_names_impl(), and ~Nemesis_IO_Helper().
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Definition at line 798 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), and write_elements().
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Definition at line 803 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), write_nodal_coordinates(), and write_nodal_solution().
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 414 of file nemesis_io_helper.h.
Referenced by get_init_info().
std::vector<int> libMesh::Nemesis_IO_Helper::global_elem_blk_cnts |
Definition at line 449 of file nemesis_io_helper.h.
Referenced by compute_num_global_elem_blocks(), get_eb_info_global(), and initialize().
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 448 of file nemesis_io_helper.h.
Referenced by compute_num_global_elem_blocks(), get_eb_info_global(), initialize(), initialize_element_variables(), write_element_values(), and write_elements().
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 438 of file nemesis_io_helper.h.
Referenced by compute_num_global_nodesets(), get_ns_param_global(), initialize(), put_ns_param_global(), write_exodus_initialization_info(), and write_nodesets().
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 426 of file nemesis_io_helper.h.
Referenced by compute_num_global_sidesets(), get_ss_param_global(), initialize(), put_ss_param_global(), write_exodus_initialization_info(), and write_sidesets().
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Definition at line 832 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_global_variables(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 633 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info().
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Definition at line 756 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_sideset(), and libMesh::ExodusII_IO_Helper::read_sideset_info().
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Definition at line 844 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_block_name(), and libMesh::ExodusII_IO_Helper::read_block_info().
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Definition at line 845 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_block_info(), and libMesh::ExodusII_IO_Helper::read_edge_blocks().
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Definition at line 848 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elemset_info().
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Definition at line 847 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_node_set_name(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), and libMesh::ExodusII_IO_Helper::read_nodeset_info().
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Definition at line 846 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_side_set_name(), and libMesh::ExodusII_IO_Helper::read_sideset_info().
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A set of internal elem IDs for this processor.
Definition at line 654 of file nemesis_io_helper.h.
Referenced by compute_element_maps(), and compute_internal_and_border_elems_and_internal_nodes().
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A set of internal node IDs for this processor.
Definition at line 649 of file nemesis_io_helper.h.
Referenced by compute_internal_and_border_elems_and_internal_nodes(), and compute_node_maps().
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Definition at line 797 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), compute_elem_communication_maps(), compute_element_maps(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO_Helper::write_sideset_data(), write_sidesets(), and libMesh::ExodusII_IO_Helper::write_sidesets().
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Definition at line 802 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), compute_node_communication_maps(), compute_node_maps(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), write_nodal_solution(), and write_nodesets().
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This map keeps track of the number of elements in each subdomain (block) for this processor.
Definition at line 616 of file nemesis_io_helper.h.
Referenced by build_element_and_node_maps(), and compute_num_global_elem_blocks().
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 384 of file nemesis_io_helper.h.
Referenced by get_cmap_params(), get_eb_info_global(), get_elem_cmap(), get_elem_map(), get_init_global(), get_init_info(), get_loadbal_param(), get_node_cmap(), get_node_map(), get_ns_param_global(), get_ss_param_global(), put_cmap_params(), put_eb_info_global(), put_elem_cmap(), put_elem_map(), put_init_global(), put_init_info(), put_loadbal_param(), put_node_cmap(), put_node_map(), put_ns_param_global(), and put_ss_param_global().
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Definition at line 815 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 820 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_nodal_var_values().
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 564 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), compute_node_communication_maps(), get_cmap_params(), get_node_cmap(), initialize(), and put_node_cmap().
std::vector<int> libMesh::Nemesis_IO_Helper::node_cmap_node_cnts |
Definition at line 565 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), get_cmap_params(), get_node_cmap(), and initialize().
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 578 of file nemesis_io_helper.h.
Referenced by compute_node_communication_maps(), get_node_cmap(), and initialize().
std::vector<std::vector<int> > libMesh::Nemesis_IO_Helper::node_cmap_proc_ids |
Definition at line 579 of file nemesis_io_helper.h.
Referenced by compute_node_communication_maps(), get_node_cmap(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::node_list |
Definition at line 417 of file nemesis_io_helper.h.
Referenced by read_nodeset().
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 548 of file nemesis_io_helper.h.
Referenced by compute_node_maps(), get_node_map(), and initialize().
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 555 of file nemesis_io_helper.h.
Referenced by compute_node_maps(), get_node_map(), and initialize().
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 541 of file nemesis_io_helper.h.
Referenced by compute_node_maps(), get_node_map(), and initialize().
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Definition at line 747 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_all_nodesets().
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Definition at line 739 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_all_nodesets().
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Definition at line 735 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), and libMesh::ExodusII_IO_Helper::write_nodesets().
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Definition at line 743 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_nodeset_data_indices(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), and libMesh::ExodusII_IO_Helper::write_nodesets().
std::set<int> libMesh::Nemesis_IO_Helper::nodes_attached_to_local_elems |
libMesh numbered node ids attached to local elems.
Definition at line 454 of file nemesis_io_helper.h.
Referenced by build_element_and_node_maps(), and compute_internal_and_border_elems_and_internal_nodes().
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Definition at line 710 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_node_set_id(), libMesh::ExodusII_IO_Helper::get_node_set_name(), libMesh::ExodusII_IO_Helper::get_nodeset_data_indices(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), and libMesh::ExodusII_IO_Helper::write_nodesets().
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Definition at line 838 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_nodeset_data(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 689 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elem_in_block().
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 502 of file nemesis_io_helper.h.
Referenced by compute_internal_and_border_elems_and_internal_nodes(), get_elem_map(), get_loadbal_param(), and initialize().
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 482 of file nemesis_io_helper.h.
Referenced by compute_border_node_ids(), compute_internal_and_border_elems_and_internal_nodes(), get_loadbal_param(), get_node_map(), and initialize().
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Definition at line 725 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_sideset(), and libMesh::ExodusII_IO_Helper::read_sideset_info().
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Definition at line 639 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_conversion(), initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), and write_exodus_initialization_info().
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Definition at line 655 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize().
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Definition at line 659 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_edge_blocks(), and libMesh::ExodusII_IO_Helper::write_elements().
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Definition at line 645 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::end_elem_id(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::write_elements(), and write_exodus_initialization_info().
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Definition at line 695 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elemset_info().
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Definition at line 692 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_sideset_info().
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Definition at line 652 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::read_block_info(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), libMesh::ExodusII_IO_Helper::write_elements(), and write_exodus_initialization_info().
int libMesh::Nemesis_IO_Helper::num_elem_blks_global |
Definition at line 392 of file nemesis_io_helper.h.
Referenced by compute_num_global_elem_blocks(), get_eb_info_global(), get_init_global(), initialize(), write_elements(), and write_exodus_initialization_info().
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 516 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), compute_elem_communication_maps(), compute_internal_and_border_elems_and_internal_nodes(), get_cmap_params(), get_elem_cmap(), get_loadbal_param(), and initialize().
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Definition at line 731 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elemset(), and libMesh::ExodusII_IO_Helper::read_elemset_info().
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Definition at line 668 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_elemset_data_indices(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), libMesh::ExodusII_IO_Helper::write_elemset_data(), and libMesh::ExodusII_IO_Helper::write_elemsets().
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Definition at line 683 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elemental_var_values(), and libMesh::ExodusII_IO_Helper::write_elements().
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Definition at line 823 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_element_variables(), initialize_element_variables(), libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_var_names(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), and libMesh::ExodusII_IO_Helper::write_var_names().
int libMesh::Nemesis_IO_Helper::num_elems_global |
Definition at line 391 of file nemesis_io_helper.h.
Referenced by get_init_global().
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Definition at line 722 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_elemset_data_indices(), libMesh::ExodusII_IO_Helper::read_elemset(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_elemset_info(), and libMesh::ExodusII_IO_Helper::write_elemset_data().
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Definition at line 680 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_elemset_data(), libMesh::ExodusII_IO_Helper::read_var_names(), and libMesh::ExodusII_IO_Helper::write_var_names().
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 489 of file nemesis_io_helper.h.
Referenced by get_loadbal_param(), get_node_map(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::num_global_node_counts |
Definition at line 439 of file nemesis_io_helper.h.
Referenced by compute_num_global_nodesets(), get_ns_param_global(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::num_global_node_df_counts |
Definition at line 440 of file nemesis_io_helper.h.
Referenced by get_ns_param_global(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::num_global_side_counts |
Definition at line 427 of file nemesis_io_helper.h.
Referenced by compute_num_global_sidesets(), get_ss_param_global(), and initialize().
std::vector<int> libMesh::Nemesis_IO_Helper::num_global_side_df_counts |
Definition at line 428 of file nemesis_io_helper.h.
Referenced by get_ss_param_global(), and initialize().
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Definition at line 671 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO_Helper::read_var_names(), libMesh::ExodusII_IO_Helper::write_global_values(), and libMesh::ExodusII_IO_Helper::write_var_names().
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 495 of file nemesis_io_helper.h.
Referenced by compute_internal_and_border_elems_and_internal_nodes(), get_elem_map(), get_loadbal_param(), and initialize().
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 475 of file nemesis_io_helper.h.
Referenced by compute_internal_and_border_elems_and_internal_nodes(), get_loadbal_param(), get_node_map(), and initialize().
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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 509 of file nemesis_io_helper.h.
Referenced by compute_border_node_ids(), compute_communication_map_parameters(), compute_node_communication_maps(), get_cmap_params(), get_loadbal_param(), get_node_cmap(), and initialize().
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Definition at line 728 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_all_nodesets(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), and libMesh::ExodusII_IO_Helper::write_nodesets().
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Definition at line 662 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_nodeset_data_indices(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), write_exodus_initialization_info(), and libMesh::ExodusII_IO_Helper::write_nodeset_data().
int libMesh::Nemesis_IO_Helper::num_node_sets_global |
Definition at line 393 of file nemesis_io_helper.h.
Referenced by compute_num_global_nodesets(), get_init_global(), get_ns_param_global(), and initialize().
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Definition at line 642 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::print_nodes(), libMesh::ExodusII_IO_Helper::read_nodal_var_values(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::ExodusII_IO_Helper::read_nodes(), write_exodus_initialization_info(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), write_nodal_solution(), libMesh::ExodusII_IO_Helper::write_nodal_values(), and libMesh::ExodusII_IO_Helper::write_var_names_impl().
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 390 of file nemesis_io_helper.h.
Referenced by get_init_global().
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Definition at line 686 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), write_elements(), and libMesh::ExodusII_IO_Helper::write_elements().
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Definition at line 719 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_nodeset_data_indices(), libMesh::ExodusII_IO_Helper::read_all_nodesets(), read_nodeset(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_nodeset_info(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), and libMesh::ExodusII_IO_Helper::write_nodesets().
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Definition at line 677 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_nodeset_data(), libMesh::ExodusII_IO_Helper::read_var_names(), and libMesh::ExodusII_IO_Helper::write_var_names().
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 400 of file nemesis_io_helper.h.
Referenced by get_init_info().
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 407 of file nemesis_io_helper.h.
Referenced by get_init_info().
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Definition at line 665 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::print_header(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), write_exodus_initialization_info(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
int libMesh::Nemesis_IO_Helper::num_side_sets_global |
Definition at line 394 of file nemesis_io_helper.h.
Referenced by compute_num_global_sidesets(), get_init_global(), get_ss_param_global(), and initialize().
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Definition at line 716 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
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Definition at line 674 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_and_store_header_info(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_var_names(), and libMesh::ExodusII_IO_Helper::write_var_names().
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Definition at line 806 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_num_time_steps(), and libMesh::ExodusII_IO_Helper::read_time_steps().
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Definition at line 859 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), and libMesh::ExodusII_IO_Helper::open().
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Definition at line 855 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::close(), libMesh::ExodusII_IO_Helper::create(), libMesh::ExodusII_IO_Helper::open(), and ~Nemesis_IO_Helper().
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Map between processor ID and (element,side) pairs bordering that processor ID.
Definition at line 639 of file nemesis_io_helper.h.
Referenced by compute_communication_map_parameters(), compute_elem_communication_maps(), and compute_internal_and_border_elems_and_internal_nodes().
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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 629 of file nemesis_io_helper.h.
Referenced by compute_border_node_ids(), compute_communication_map_parameters(), and compute_node_communication_maps().
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Definition at line 753 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
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Definition at line 835 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_sideset_data(), and libMesh::ExodusII_IO_Helper::read_var_names().
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Definition at line 707 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::get_side_set_id(), libMesh::ExodusII_IO_Helper::get_side_set_name(), libMesh::ExodusII_IO_Helper::get_sideset_data_indices(), libMesh::ExodusII_IO_Helper::read_sideset(), libMesh::ExodusII_IO_Helper::read_sideset_data(), libMesh::ExodusII_IO_Helper::read_sideset_info(), and libMesh::ExodusII_IO_Helper::write_sideset_data().
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 459 of file nemesis_io_helper.h.
Referenced by build_element_and_node_maps(), write_element_values(), and write_elements().
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Definition at line 809 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_time_steps().
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Definition at line 636 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::ExodusII_IO_Helper(), and libMesh::ExodusII_IO_Helper::print_header().
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Definition at line 851 of file exodusII_io_helper.h.
Referenced by build_element_and_node_maps(), compute_border_node_ids(), compute_communication_map_parameters(), compute_internal_and_border_elems_and_internal_nodes(), compute_node_communication_maps(), compute_num_global_elem_blocks(), compute_num_global_nodesets(), compute_num_global_sidesets(), construct_nemesis_filename(), libMesh::ExodusII_IO_Helper::create(), get_cmap_params(), get_eb_info_global(), get_elem_cmap(), get_elem_map(), get_init_global(), get_init_info(), get_loadbal_param(), get_node_cmap(), get_node_map(), get_ns_param_global(), get_ss_param_global(), libMesh::ExodusII_IO_Helper::message(), libMesh::ExodusII_IO_Helper::open(), libMesh::ExodusII_IO_Helper::print_header(), put_node_cmap(), libMesh::ExodusII_IO_Helper::read_elem_in_block(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::ExodusII_IO_Helper::read_qa_records(), libMesh::ExodusII_IO_Helper::read_var_names_impl(), write_nodesets(), write_sidesets(), and libMesh::ExodusII_IO_Helper::write_var_names_impl().
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Definition at line 780 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::read_nodes().
bool libMesh::Nemesis_IO_Helper::write_complex_abs |
By default, when complex numbers are enabled, for each variable we write out three values: the real part, "r_u" the imaginary part, "i_u", and the complex modulus, a_u := sqrt(r_u*r_u + i_u*i_u), which is also the value returned by std::abs(std::complex).
Since the modulus is not an independent quantity, we can set this flag to false and save some file space by not writing out.
Definition at line 600 of file nemesis_io_helper.h.
Referenced by write_element_values().
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Definition at line 771 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::print_nodes(), libMesh::ExodusII_IO_Helper::read_nodes(), write_nodal_coordinates(), and libMesh::ExodusII_IO_Helper::write_nodal_coordinates().
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inherited |
Definition at line 774 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::print_nodes(), libMesh::ExodusII_IO_Helper::read_nodes(), write_nodal_coordinates(), and libMesh::ExodusII_IO_Helper::write_nodal_coordinates().
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inherited |
Definition at line 777 of file exodusII_io_helper.h.
Referenced by libMesh::ExodusII_IO_Helper::print_nodes(), libMesh::ExodusII_IO_Helper::read_nodes(), write_nodal_coordinates(), and libMesh::ExodusII_IO_Helper::write_nodal_coordinates().