sdynpy.fem.sdynpy_exodus.Exodus

class Exodus(filename, mode='r', title=None, num_dims=None, num_nodes=None, num_elem=None, num_blocks=None, num_node_sets=None, num_side_sets=None, clobber=False)[source]

Bases: object

Read or write exodus files.

This class creates functionality to read or write exodus files using the netCDF4 python module.

Parameters

filename (str) – The path string to the file that will be opened
mode (str) – Mode with which the file is opened, ‘r’ - Read, ‘w’ - Write, ‘a’ - Append. Default is ‘r’.
title (str) – Title of the exodus file, only required if mode=’w’.
num_dims (int) – Number of dimensions in the exodus file, only required if mode=’w’.
num_nodes (int) – Number of nodes in the exodus file, only required if mode=’w’.
num_elem (int) – Number of elements in the exodus file, only required if mode=’w’.
num_blocks (int) – Number of blocks in the exodus file, only required if mode=’w’.
num_node_sets (int) – Number of node sets in the exodus file, only required if mode = ‘w’.
num_side_sets (int) – Number of side sets in the exodus file, only required if mode=’w’.

__init__(filename, mode='r', title=None, num_dims=None, num_nodes=None, num_elem=None, num_blocks=None, num_node_sets=None, num_side_sets=None, clobber=False)[source]

Methods

`__init__`(filename[, mode, title, num_dims, ...])
`close`()
`extract_sharp_edges`(args, *kwargs)
`get_block_surface`(block_id[, ...])	Gets the node indices and element connectivity of surface elements
`get_coord`(index)	Retrieve the coordinates of the specified node in the exodus file.
`get_coord_names`()	Retrieve the coordinate names in the exodus file.
`get_coords`()	Retrieve the coordinates of the nodes in the exodus file.
`get_displacements`([displacement_name, ...])
`get_elem_attr`(id)	Gets the element attributes for a given block
`get_elem_blk_ids`()	Gets a list of the element block ID numbers in the exodus file
`get_elem_blk_info`(id)	Gets the element block information for the specified element block ID
`get_elem_connectivity`(id)	Gets the element connectivity matrix for a given block
`get_elem_num_map`()	Retrieve the list of local element IDs from the exodus file.
`get_elem_type`(id)	Gets the element type for a given block
`get_elem_variable_names`()	Gets a tuple of element variable names from the exodus file
`get_elem_variable_table`()	Gets the element variable table
`get_elem_variable_value`(block_id, ...[, step])	Gets an element's variable value for the specified timestep
`get_elem_variable_values`(block_id, name_or_index)	Gets a block's element variable values for the specified timestep
`get_element_property_names`()
`get_element_property_value`()
`get_global_variable_names`()	Gets a tuple of global variable names from the exodus file
`get_global_variable_values`(name_or_index[, step])	Gets the global variable value for the specified timesteps
`get_info_records`()	Get the information records in the exodus file
`get_node_num_map`()	Retrieve the list of local node IDs from the exodus file.
`get_node_set_dist_factors`(id)	Get the distribution factors of the specified node set
`get_node_set_ids`()	Gets a list of the node set ID numbers in the exodus file
`get_node_set_names`()	Retrieve the node set names in the exodus file.
`get_node_set_nodes`(id)	Get the nodes in the specified node set
`get_node_set_num_nodes`(id)	Get the number of nodes in the specified node set
`get_node_variable_names`()	Gets a tuple of nodal variable names from the exodus file
`get_node_variable_value`(name_or_index, ...)	Gets a node variable value for the specified timestep
`get_node_variable_values`(name_or_index[, step])	Gets the node variable values for the specified timestep
`get_qa_records`()	Get the quality assurance records in the exodus file
`get_side_set_dist_factors`(id)	Get the distribution factors of the specified side set
`get_side_set_faces`(id)	Get the faces in the specified side set
`get_side_set_ids`()	Gets a list of the side set ID numbers in the exodus file
`get_side_set_names`()	Retrieve the side set names in the exouds file.
`get_side_set_node_list`(id)
`get_side_set_num_faces`(id)	Get the number of faces in the specified side set
`get_times`([indices])	Gets the time values from the exodus file
`load_into_memory`([close, variables, ...])	Loads the exodus file into an ExodusInMemory object
`num_attr`(id)	Gets the number of attributes per element for an element block
`num_elems_in_blk`(id)	Gets the number of elements in an element block
`num_nodes_per_elem`(id)	Gets the number of nodes per element in an element block
`put_coord_names`(coord_names)	Puts the coordinate names into the exodus file
`put_coords`(coords)	Puts the coordinate values into the exodus file
`put_elem_blk_ids`(block_ids)	Puts a list of the element block ID numbers in the exodus file
`put_elem_blk_info`(id, elem_type, ...[, ...])	Puts the element block information for an element block ID into the exodus file
`put_elem_num_map`(elem_num_map)	Puts a list of local element IDs into the exodus file.
`put_elem_variable_names`(elem_var_names[, ...])	Puts the specified variable names in the exodus file
`put_element_property_names`()
`put_element_property_value`()
`put_global_variable_names`(global_var_names)	Puts the specified global variable names in the exodus file
`put_info_records`(records)	Puts the information records in the exodus file
`put_node_num_map`(node_num_map)	Puts a list of local node IDs into the exodus file.
`put_node_set_ids`(ns_ids)	Puts a list of the node set ID numbers in the exodus file
`put_node_set_info`(id, nodes[, dist_fact])	Puts the node set information for a node set ID into the exodus file
`put_node_set_names`(ns_names)	Puts the node set names into the exodus file
`put_node_variable_names`(node_var_names)	Puts the specified variable names in the exodus file
`put_qa_records`(records)	Puts the quality assurance records in the exodus file
`put_side_set_ids`(ss_ids)	Puts a list of the side set ID numbers in the exodus file
`put_side_set_info`(id, elements, sides[, ...])	Puts the side set information for a side set ID into the exodus file
`put_side_set_names`(ss_names)	Puts the side set names into the exodus file
`reduce_to_surfaces`(args, *kwargs)
`set_elem_attr`(id, attributes)	Sets the element attributes for a given block
`set_elem_connectivity`(id, connectivity)	Sets the element connectivity matrix for a given block
`set_elem_variable_value`(block_id, ...)	Sets an element variable value for the specified timestep
`set_elem_variable_values`(block_id, ...)	Sets a block's element variable values for the specified timestep
`set_global_variable_values`(name_or_index, ...)	Sets the global variable values for the specified timestep
`set_node_variable_value`(name_or_index, ...)	Sets the node variable values for the specified timestep
`set_node_variable_values`(name_or_index, ...)	Sets the node variable values for the specified timestep
`set_time`(step, value)	Sets the time value of a given step in the exodus file
`set_times`(values)	Sets the time vector for the exodus file
`triangulate_surface_mesh`()	Triangulate a surface mesh for plotting patches

Attributes

`num_blks`
`num_dimensions`
`num_elem_variables`
`num_elems`
`num_global_variables`
`num_node_sets`
`num_node_variables`
`num_nodes`
`num_side_sets`
`num_times`
`title`	Get the title of the exodus file

close()[source]

extract_sharp_edges(*args, **kwargs)[source]

get_block_surface(block_id, keep_midside_nodes=False, warn=True)[source]

Gets the node indices and element connectivity of surface elements

This function “skins” the element block, returning a list of node indices and a surface connectivity matrix.

Parameters

block_id (int) – The ID number of the block that will be skinned.
keep_midside_nodes (bool) – Specifies whether or not to keep midside nodes in the surface mesh. Default is False.
warn (bool) – Specifies whether or not to warn the user if the block ID doesn’t have a skinning method defined for its element type. Default is True.

Returns

element_block_information – A list of tuples of element information. These data are element_type, node_indices, block_surface_connectivity, and block_surface_original_elements. The element_type is a string representing the new block element type (‘quad4’,’tri3’,etc.). The node_indices can be used as an index into the coordinate or nodal variable arrays to select nodes corresponding to this block. The block_surface_connectivity represents the connectivity array of the surface faces of the block. Values in this array correspond to indices into the node_indices array. To recover the connectivity array in the original node indices of the exodus file, it can be passed through the node_indices as node_indices[block_surface_connectivity]. The block_surface_original_elements array shows the original element indices of the block that each surface came from. This can be used to map element variables to the new surface mesh. This list will normally be length 1 unless an element type is processed that has two different surface elements in it (e.g. wedges have tris and quads)

Return type

list

get_coord(index)[source]

Retrieve the coordinates of the specified node in the exodus file.

Parameters: index (int) – The global node index (not node number) of the node of which the coordinates are desired
Returns: coords – Returns an array with size num_dims
Return type: np.array

get_coord_names()[source]

Retrieve the coordinate names in the exodus file.

Returns: coord_names – Returns a tuple of strings containing the coordinate names in the exodus file.
Return type: tuple

get_coords()[source]

Retrieve the coordinates of the nodes in the exodus file.

Returns: coords – Returns a 2D array with size num_dims x num_nodes
Return type: np.array

get_displacements(displacement_name='Disp', capital_coordinates=True)[source]

get_elem_attr(id)[source]

Gets the element attributes for a given block

Parameters: id (int) – The block id for which the element connectivity matrix is desired.
Returns: attributes – The 2d attribute matrix for the block with dimensions num_elem x num_attributes
Return type: np.masked_array

get_elem_blk_ids()[source]

Gets a list of the element block ID numbers in the exodus file

Returns: block_ids – A tuple containing the block ID numbers
Return type: tuple

get_elem_blk_info(id)[source]

Gets the element block information for the specified element block ID

Parameters

id (int) – Element Block ID number

Returns

element_type (str) – Name of the Element Type
elements_in_block (int) – Number of elements in the block
nodes_per_element (int) – Number of nodes per element in the block
attributes_per_element (int) – Number of attributes per element

get_elem_connectivity(id)[source]

Gets the element connectivity matrix for a given block

Parameters: id (int) – The block id for which the element connectivity matrix is desired.
Returns: connectivity – The 2d connectivity matrix for the block with dimensions num_elem x num_nodes_per_element. The returned value is converted from the 1-based Exodus indexing to 0-based Python/NumPy indexing.
Return type: np.masked_array

get_elem_num_map()[source]

Retrieve the list of local element IDs from the exodus file.

Returns: elem_num_map – Returns a 1D array with size num_elems, denoting the element number for the element in each index
Return type: np.array

Notes

If there is no elem_num_map in the exodus file, this function simply returns an array from 1 to self.num_elems

get_elem_type(id)[source]

Gets the element type for a given block

Parameters: id (int) – The block id for which the element connectivity matrix is desired.
Returns: type – The element type of the block
Return type: str

get_elem_variable_names()[source]

Gets a tuple of element variable names from the exodus file

Returns: elem_var_names – Returns a tuple containing the names of the element variables in the exodus file.
Return type: tuple of strings

get_elem_variable_table()[source]

Gets the element variable table

Gets the element variable table showing which elements are defined for which blocks.

Returns: elem_var_table – A 2D array with dimension num_blocks x num_element_variables. If the jth element variable is defined for the ith block, elem_var_table[i,j] == True
Return type: np.masked_array

get_elem_variable_value(block_id, name_or_index, element_index, step=None)[source]

Gets an element’s variable value for the specified timestep

Parameters

block_id (int) – Block id number for the block from which element variable value is desired.
name_or_index (str or int) – Name or Index of the element variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
element_index (int) – element index at which to recover the nodal variable
step (int) – Time step at which to recover the nodal variable

Returns

elem_variable_value – The variable values for the specified element at the specified time step.

Return type

float

get_elem_variable_values(block_id, name_or_index, step=None)[source]

Gets a block’s element variable values for the specified timestep

Parameters

block_id (int) – Block id number for the block from which element variable values are desired.
name_or_index (str or int) – Name or Index of the element variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
step (int) – Time step at which to recover the element variable

Returns

elem_variable_values – A 1d array consisting of the variable values for each element in the specified block at the specified time step.

Return type

maskedarray

get_element_property_names()[source]

get_element_property_value()[source]

get_global_variable_names()[source]

Gets a tuple of global variable names from the exodus file

Returns: global_var_names – Returns a tuple containing the names of the global variables in the exodus file.
Return type: tuple of strings

get_global_variable_values(name_or_index, step=None)[source]

Gets the global variable value for the specified timesteps

Parameters

name_or_index (str or int) – Name or Index of the global variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
step (int) – Time step at which to recover the nodal variable

Returns

global_variable_values – A 1d array or floating point number consisting of the variable values at the specified time steps.

Return type

maskedarray or float

get_info_records()[source]

Get the information records in the exodus file

Returns: info_records – Returns a tuple of strings where the index is the record number.
Return type: tuple

get_node_num_map()[source]

Retrieve the list of local node IDs from the exodus file.

Returns: node_num_map – Returns a 1D array with size num_nodes, denoting the node number for the node in each index
Return type: np.array

Notes

If there is no node_num_map in the exodus file, this function simply returns an array from 1 to self.num_nodes

get_node_set_dist_factors(id)[source]

Get the distribution factors of the specified node set

Parameters: id (int) – Node set ID (not index)
Returns: dist_factor – The distribution factors in the node set
Return type: np.array

get_node_set_ids()[source]

Gets a list of the node set ID numbers in the exodus file

Returns: ns_ids – A tuple containing the node set ID numbers
Return type: tuple

get_node_set_names()[source]

Retrieve the node set names in the exodus file.

Returns: ns_names – Returns a tuple of strings containing the node set names in the exodus file.
Return type: tuple

get_node_set_nodes(id)[source]

Get the nodes in the specified node set

Parameters: id (int) – Node set ID (not index)
Returns: nodes – The node indices of nodes in the node set. Note that while the Exodus file format uses 1-based indexing, the returned nodes array is converted so it is 0-based.
Return type: np.array

get_node_set_num_nodes(id)[source]

Get the number of nodes in the specified node set

Parameters: id (int) – Node set ID (not index)
Returns: num_nodes – The number of nodes in the node set.
Return type: int

get_node_variable_names()[source]

Gets a tuple of nodal variable names from the exodus file

Returns: node_var_names – Returns a tuple containing the names of the nodal variables in the exodus file.
Return type: tuple of strings

get_node_variable_value(name_or_index, node_index, step=None)[source]

Gets a node variable value for the specified timestep

Parameters

name_or_index (str or int) – Name or Index of the nodal variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
node_index (int) – Node index at which to recover the nodal variable
step (int) – Time step at which to recover the nodal variable

Returns

node_variable_value – The variable values for the specified node at the specified time step.

Return type

float

get_node_variable_values(name_or_index, step=None)[source]

Gets the node variable values for the specified timestep

Parameters

name_or_index (str or int) – Name or Index of the nodal variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
step (int) – Time step at which to recover the nodal variable

Returns

node_variable_values – A 1d array consisting of the variable values for each node at the specified time step.

Return type

maskedarray

get_qa_records()[source]

Get the quality assurance records in the exodus file

Returns: qa_records – Returns a nested tuple of strings where the first index is the record number, and the second is the line in the record.
Return type: tuple

get_side_set_dist_factors(id)[source]

Get the distribution factors of the specified side set

Parameters: id (int) – Side set ID (not index)
Returns: dist_factor – The distribution factors in the node set
Return type: np.array

get_side_set_faces(id)[source]

Get the faces in the specified side set

Parameters

id (int) – Side set ID (not index)

Returns

elements (np.array) – The element of each face in the sideset (converted from 1-based exodus indexing to 0-based python indexing)
sides (np.array) – The element side of each face in the sideset (converted from 1-based exodus indexing to 0-based python indexing)

get_side_set_ids()[source]

Gets a list of the side set ID numbers in the exodus file

Returns: ss_ids – A tuple containing the side set ID numbers
Return type: tuple

get_side_set_names()[source]

Retrieve the side set names in the exouds file.

Returns: ss_names – Returns a tuple of strings containing the side set names in the exodus file
Return type: tuple

get_side_set_node_list(id)[source]

get_side_set_num_faces(id)[source]

Get the number of faces in the specified side set

Parameters: id (int) – Side set ID (not index)
Returns: num_faces – The number of faces in the side set.
Return type: int

get_times(indices=None)[source]

Gets the time values from the exodus file

Returns: time_array – A masked_array containing the time values.
Return type: np.masked_array

load_into_memory(close=True, variables=None, timesteps=None, blocks=None)[source]

Loads the exodus file into an ExodusInMemory object

This function loads the exodus file into memory in an ExodusInMemory format. Not for use with large files.

Parameters

close (bool) – Close the netcdf file upon loading into memory. Optional argument, default is true.
variables (iterable) – A list of variable names that are loaded into memory. Default is to load all variables
timesteps (iterable) – A list of timestep indices that are loaded into memory. Default is to load all timesteps.
blocks (iterable) – A list of block ids that are loaded into memory. Default is to load all blocks.

Returns

fexo – The exodus file in an ExodusInMemory format

Return type

ExodusInMemory

num_attr(id)[source]

Gets the number of attributes per element for an element block

Parameters: d (int) – The block id for which the number of attributes is desired
Returns: attr_per_element – The number of attributes per element in a block
Return type: int

property num_blks

property num_dimensions

property num_elem_variables

property num_elems

num_elems_in_blk(id)[source]

Gets the number of elements in an element block

Parameters: d (int) – The block id for which the number of attributes is desired
Returns: elem_per_element – The number of elements in the block
Return type: int

property num_global_variables

property num_node_sets

property num_node_variables

property num_nodes

num_nodes_per_elem(id)[source]

Gets the number of nodes per element in an element block

Parameters: d (int) – The block id for which the number of attributes is desired
Returns: nodes_per_elem – The number of nodes per element in the block
Return type: int

property num_side_sets

property num_times

put_coord_names(coord_names)[source]

Puts the coordinate names into the exodus file

Parameters: coord_names (sequence of strings) – A sequence (list/tuple/etc.) containing the coordinate names.

put_coords(coords)[source]

Puts the coordinate values into the exodus file

Parameters: coords (np.ndarray) – A 2d array containing coordinate values.

put_elem_blk_ids(block_ids)[source]

Puts a list of the element block ID numbers in the exodus file

Parameters: block_ids (array-like) – A sequency of integers specifying the block id numbers

put_elem_blk_info(id, elem_type, num_elements, num_nodes_per_element, num_attrs_per_elem=0)[source]

Puts the element block information for an element block ID into the exodus file

Parameters

id (int) – The block ID (not index) that the information is being specified for
elem_type (str) – The element type (‘SHELL4’,’HEX8’, etc.) in the block
num_elements (int) – The number of elements in the block
num_nodes_per_element (int) – The number of nodes per element in the block
num_attrs_per_element (int) – The number of attributes per element in the block

put_elem_num_map(elem_num_map)[source]

Puts a list of local element IDs into the exodus file.

Parameters: elem_num_map (np.array) – A 1D array with size num_elems, denoting the element number for the element in each index

put_elem_variable_names(elem_var_names, elem_var_table=None)[source]

Puts the specified variable names in the exodus file

Parameters

elem_var_names (tuple of strings) – A tuple containing the names of the element variables in the exodus file
elem_var_table (2d array-like) – A 2d array of shape num_el_blk x num_elem_var defining which element variables are defined for which element blocks elem_var_table[i,j] should be True if the j-th element variable is defined for the i-th block (index, not id number) in the model. If not specified, it is assumed that all variables are defined for all blocks.

put_element_property_names()[source]

put_element_property_value()[source]

put_global_variable_names(global_var_names)[source]

Puts the specified global variable names in the exodus file

Parameters: global_var_names (tuple of strings) – A tuple containing the names of the global variables in the model

put_info_records(records)[source]

Puts the information records in the exodus file

Parameters: info_records (sequence of strings) – A sequence (list/tuple/etc.) containing the information records.

put_node_num_map(node_num_map)[source]

Puts a list of local node IDs into the exodus file.

Parameters: node_num_map (np.array) – A 1D array with size num_nodes, denoting the node number for the node in each index

put_node_set_ids(ns_ids)[source]

Puts a list of the node set ID numbers in the exodus file

Parameters: ns_ids (array-like) – A sequency of integers specifying the node set id numbers

put_node_set_info(id, nodes, dist_fact=None)[source]

Puts the node set information for a node set ID into the exodus file

Parameters

id (int) – The node set ID (not index)
nodes (array-like) – A 1d array containing the node indices. Note the array should be zero-based, it will be converted to one based when written to the exodus file.
dist_fact (array-like) – A 1d array containing the node set distribution factors. If not specified, the distribution factors will be assumed to be 1.

put_node_set_names(ns_names)[source]

Puts the node set names into the exodus file

Parameters: ns_names (sequence of strings) – A sequence (list/tuple/etc.) containing the node set names.

put_node_variable_names(node_var_names)[source]

Puts the specified variable names in the exodus file

Parameters: node_var_names (tuple of strings) – A tuple containing the names of the nodal variables in the model

put_qa_records(records)[source]

Puts the quality assurance records in the exodus file

Parameters: qa_records (sequence of sequence of strings) – A nested sequence (list/tuple/etc.) containing the quality assurance records.

Notes

Each index in qa_records should consist of a length-4 tuple of strings:

Analysis Code Name
Analysis Code Version
Analysis Date
Analysis Time

put_side_set_ids(ss_ids)[source]

Puts a list of the side set ID numbers in the exodus file

Parameters: ss_ids (array-like) – A sequency of integers specifying the side set id numbers

put_side_set_info(id, elements, sides, dist_fact=None)[source]

Puts the side set information for a side set ID into the exodus file

Parameters

id (int) – The side set ID (not index)
elements (np.array) – The element of each face in the sideset (converted from 1-based exodus indexing to 0-based python indexing)
sides (np.array) – The element side of each face in the sideset (converted from 1-based exodus indexing to 0-based python indexing)
dist_fact (array-like) – A 1d array containing the node set distribution factors. If not specified, the distribution factors will be assumed to be 1.

put_side_set_names(ss_names)[source]

Puts the side set names into the exodus file

Parameters: ss_names (sequence of strings) – A sequence (list/tuple/etc.) containing the side set names.

reduce_to_surfaces(*args, **kwargs)[source]

set_elem_attr(id, attributes)[source]

Sets the element attributes for a given block

Parameters

id (int) – The block id for which the element connectivity matrix is desired.
attributes (2D array-like) – The 2d attribute matrix for the block with dimensions num_elem x num_attributes

set_elem_connectivity(id, connectivity)[source]

Sets the element connectivity matrix for a given block

Parameters

id (int) – The block id for which the element connectivity is being assigned
connectivity (2D array-like) – A 2D array of dimension num_elements x num_nodes_per_element defining the element connectivity. Note that the connectivity matrix should be 0-based (first node index is zero) per Python conventions. It will be converted to one-based when it is written to the Exodus file.

set_elem_variable_value(block_id, name_or_index, element_index, step, value)[source]

Sets an element variable value for the specified timestep

Parameters

block_id (int) – Block id number for the block from which element variable values are desired.
name_or_index (str or int) – Name or Index of the element variable that is desired. If type(name_or_index) == str, then it is assumed to be the name. If type(name_or_index) == int, then it is assumed to be the index.
step (int) – Time step at which to recover the element variable
value (float) – The variable values for the specified element in the specified block at the specified time step.

Notes