pyiron_base.storage.parameters module

GenericParameters class defines the typical input file with a key value structure plus an additional column for comments.

class pyiron_base.storage.parameters.GenericParameters(table_name=None, input_file_name=None, val_only=False, comment_char='#', separator_char=' ', end_value_char='')

Bases: HasDict

GenericParameters class defines the typical input file with a key value structure plus an additional column for comments. Convenience class to easily create, read, and modify input files

Parameters:

table_name (str) – name of the input file inside the HDF5 file - optional
input_file_name (str/Nonetype) – name of the input file (if None default parameters are used)
val_only (bool) – input format consists of value (comments) only
comment_char (str) – separator that characterizes comment (e.g. “#” for python)
separator_char (str) – separator that characterizes the split between key and value - default=’ ‘
end_value_char (str) – special character at the end of every line - default=’’

.. attribute:: file_name: file name of the input file

.. attribute:: table_name: name of the input table inside the HDF5 file

.. attribute:: val_only: boolean option to switch from a key value list to an value only input file

.. attribute:: comment_char: separator that characterizes comment

.. attribute:: separator_char: separator that characterizes the split between key and value

.. attribute:: multi_word_separator: multi word separator to have multi word keys

.. attribute:: end_value_char: special character at the end of every line

.. attribute:: replace_char_dict: dictionary to replace certain character combinations

clear_all(): Clears all fields in the object

property comment_char

Get the separator that characterizes comment

Returns:: comment character
Return type:: str

define_blocks(block_dict)

Define a block section within the GenericParameters

Parameters:: block_dict (dict) – dictionary to define the block

property end_value_char

Get the special character at the end of every line

Returns:: end of line character
Return type:: str

property file_name

Get the file name of the input file

Returns:: file name
Return type:: str

from_dict(obj_dict, version: str = None)

Reload GenericParameters from dictionary

Parameters:

obj_dict (dict) – dictionary for reloading GenericParameters object
version (str, optional) – version of the HasDict format that is used

from_hdf(hdf, group_name=None)

Restore the GenericParameters from an HDF5 file

Parameters:

hdf (ProjectHDFio) – HDF5 group object
group_name (str) – HDF5 subgroup name - optional

get(parameter_name, default_value=None)

Get the value of a specific parameter from GenericParameters - if the parameter is not available return default_value if that is set.

Parameters:

parameter_name (str) – parameter key
default_value (str) – default value to return is the parameter is not set

Returns:

value of the parameter

Return type:

str

get_attribute(attribute_name)

Get the value of a specific parameter from GenericParameters

Parameters:: attribute_name (str) – parameter key
Returns:: value of the parameter
Return type:: str

get_pandas()

Output the GenericParameters object as Pandas Dataframe for human readability.

Returns:: Pandas Dataframe of the GenericParameters object
Return type:: pandas.DataFrame

get_string_lst(): Get list of strings from GenericParameters to write to input file

keys(): Return keys of GenericParameters object

load_default(): Load defaults resets the dataset in the background to be empty

load_string(input_str)

Load a multi line string to overwrite the current parameter settings

Parameters:: input_str (str) – multi line string

modify(separator=None, append_if_not_present=False, **modify_dict)

Modify values for existing parameters. The command is called as modify(param1=val1, param2=val2, …)

Parameters:

separator (str) – needed if the parameter name contains special characters such as par: use then as input: modify(separator=”:”, par=val) - optional
append_if_not_present (bool) – do not raise an exception but append the parameter in practice use set(par=val) - default=False
**modify_dict (dict) – dictionary of parameter names and values

property multi_word_separator

Get the multi word separator to have multi word keys

Returns:: multi word separator
Return type:: str

read_input(file_name, ignore_trigger=None)

Read input file and store the data in GenericParameters - this overwrites the current parameter settings

Parameters:

file_name (str) – absolute path to the input file
ignore_trigger (str) – trigger for lines to be ignored

remove_keys(key_list)

Remove a list of keys from the GenericParameters

Parameters:: key_list (list) – list of keys to be removed

property replace_char_dict

Get the dictionary to replace certain character combinations

Returns:: character replace dictionary
Return type:: dict

property separator_char

Get the separator that characterizes the split between key and value

Returns:: separator character
Return type:: str

set(separator=None, **set_dict)

Set the value of multiple parameters or create new parameter key, if they do not exist already.

Parameters:

separator (float/int/str) – separator string - optional
**set_dict (dict) – dictionary containing the parameter keys and their corresponding values to be set

set_dict(dictionary)

Set a dictionary of key value pairs

Parameters:: dictionary (dict) – dictionary of key value pairs

set_value(line, val)

Set the value of a parameter in a specific line

Parameters:

line (float/int/str) – line number - starting with 0
val (str/bytes) – value to be set

property table_name

Get the name of the input table inside the HDF5 file

Returns:: table name
Return type:: str

to_dict()

Convert the GenericParameters object to a dictionary for storage

Returns:: GenericParameters object as a dictionary
Return type:: dict

to_hdf(hdf, group_name=None)

Store the GenericParameters in an HDF5 file

Parameters:

hdf (ProjectHDFio) – HDF5 group object
group_name (str) – HDF5 subgroup name - optional

property val_only

Get the boolean option to switch from a key value list to an value only input file

Returns:: [True/False]
Return type:: bool

write_file(file_name, cwd=None)

Write GenericParameters to input file

Parameters:

file_name (str) – name of the file, either absolute (then cwd must be None) or relative
cwd (str) – path name (default: None)