pyiron.base.pyio.parser module

class pyiron.base.pyio.parser.LogTag(tag_dict, h5_dict=None, key_dict=None)[source]

Bases: object

LogTag object to parse for a specific pattern in the output file

Parameters

  • tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

  • h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

  • key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

apply_func(val)[source]

Apply the function on a given value

Parameters

val (dict, list, float, int) – value to apply the function on

Returns

result of applying the function

Return type

dict, list, float, int

arg()[source]

Get tag argument

Returns

tag arguments

Return type

str

property current

Get the current tag

Returns

current tag

Return type

dict

property dyn_tags

Get dynamic tags

Returns

dynamic tags

Return type

dict

get_item(item, default)[source]

If item is part of the current dictionary keys the corresponding value is returned otherwise the default is returned.

Parameters

  • item (str) – dictionary key

  • default (list, dict, int, float) – Default value

Returns

The values connected to the key item in the current dictionary and if item is not a

key in the current dictionary return the default value.

Return type

list, dict, int, float

h5()[source]

Translate current tag to HDF5 tag using the tag dictionary

Returns

hdf5 key name

Return type

str

property h5_dict

Get translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

Returns

h5 dictionary

Return type

dict

is_func()[source]

Check if a function is defined to convert the data - if “func” is included in the tag_dict dictionary

Returns

[True/ False]

Return type

bool

is_item(item_line, start=0)[source]

Check if the current line - item_line - matches one of the provided tags, if that is the case set the tag to be the current tag and update the val_list with the corresponding values.

Parameters

  • item_line (str) – Line of the output file

  • start (int) – Character to start with when parsing the item_line - default=0

Returns

[True/False]

Return type

bool

property key_dict

Get translation dictionary of python internal tags as keys to the output tags as values.

Returns

key dictionary

Return type

dict

line_skip()[source]

Check how many lines should be skipped.

Returns

[True/ False]

Return type

bool

resolve_dynamic_variable(val)[source]

Resolve dynamic variable using the key_dict dictionary

Parameters

val – values to resolve

rows()[source]

Number of rows to parse

Returns

number of rows

Return type

int, str

set_item(tag_vals, log_file)[source]

Set LogTag item

Parameters

  • tag_vals (dict) – tag value dictionary

  • log_file (Logstatus) – Logstatus object

Returns

tag name, tag values, rows, line skip [True/False]

Return type

list

property tag_dict

Get tag dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

Returns

tag dictionary

Return type

dict

property tag_first_word

Get first word of the tag

Returns

first word

Return type

str

property tag_name

Get tag name

Returns

tag name

Return type

str

test_split()[source]

Check if the argument or the tag should be split - if “splitArg” or “splitTag” is included in the tag_dict dictionary.

Returns

[True/ False]

Return type

bool

translate(item)[source]

Translate current tag to HDF5 tag using the h5_dict dictionary

Parameters

item (str) – Python tag

Returns

HDF5 tag

Return type

str

class pyiron.base.pyio.parser.Logstatus(h5=None, iter_levels=1)[source]

Bases: object

Generic Parser for parsing output files by searching for a specific pattern structure and extracting the data that follows the pattern into the status_dict dictionary.

Parameters

iter_levels (int) – Levels of iteration - default = 1

append(title, data_to_append, vec=False)[source]

Append data to the LogStatus object status_dict dictionary

Parameters

  • title (str) – Title of the data to append

  • data_to_append (list,dict) – the data can be of various types

  • vec (bool) – [True/False] if the data is a single vector instead of a matrix or a tensor

combine_mat(x_key, xy_key, xz_key, y_key, yz_key, z_key, combined_key)[source]

Combine three lists representing the x,y,z coordinates, by accessing them from the status_dict dictionary, combining them, store them under the combined_key and remove the other three keys.

Parameters

  • x_key (str) – key of the x coordinates

  • y_key (str) – key of the y coordinates

  • z_key (str) – key of the z coordinates

  • combined_key (str) – name of the combined coordinates

combine_xyz(x_key, y_key, z_key, combined_key, as_vector=False)[source]

Combine three lists representing the x,y,z coordinates, by accessing them from the status_dict dictionary, combining them, store them under the combined_key and remove the other three keys.

Parameters

  • x_key (str) – key of the x coordinates

  • y_key (str) – key of the y coordinates

  • z_key (str) – key of the z coordinates

  • combined_key (str) – name of the combined coordinates

convert_unit(key, factor)[source]
extract_file(file_name, tag_dict, h5_dict=None, key_dict=None)[source]

Main function of the LogStatus class to extract data from an output file by searching for the tag dictionary

Parameters

  • file_name (str) – absolute path to the output file

  • tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

  • h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

  • key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

extract_from_list(list_of_lines, tag_dict, h5_dict=None, key_dict=None)[source]

Main function of the LogStatus class to extract data from an output file by searching for the tag dictionary

Parameters

  • file_name (str) – absolute path to the output file

  • tag_dict (dict) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure. The data structure dictionary can contain the following keys: - “arg”: position of the argument - or dimension (“:”, “:,:”) - “type”: Python data type - “h5”: HDF5 key to store the information - “rows”: number of rows from the line where the tag was found - “splitTag”: split the tag - [True/False] - “splitArg”: split the argument - [True/False] - “lineSkip”: skip a line - “func”: function to convert the data

  • h5_dict (dict) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values.

  • key_dict (dict) – Translation dictionary of python internal tags as keys to the output tags as values.

static extract_item(l_item)[source]

Method to extract information from a single line - currently very specific for the Lammps output

Parameters

l_item (str) – line to extract information from

Returns

the tag_string as string and the arguments as list

Return type

str, list

raise_iter(dim=0)[source]

Increase the iteration level

Parameters

dim (int) – position - default = 0

reset_iter(dim=0)[source]

Reset iteration level

Parameters

dim (int) – reset value - default = 0

to_hdf(hdf)[source]

Store the LogStatus object status_dict dictionary in an HDF5 file

Parameters

hdf (ProjectHDFio) – HDF5 object to store the dictionary in.

pyiron.base.pyio.parser.extract_data_from_file(file_name, tag, num_args=1)[source]

General purpose routine to extract any static from a log (text) file

Parameters

  • file_name (str) – file name or path to the file, can either be absolute or relative

  • tag (str) – string at the beginning of the line

  • num_args (int) – number of arguments separated by ‘ ‘ or ‘,’ to extract after the tag

Returns

List of arguments extracted as strings

Return type

list

pyiron.base.pyio.parser.extract_data_from_str_lst(str_lst, tag, num_args=1)[source]

General purpose routine to extract any static from a log (text) file

Parameters

  • file_name (str) – file name or path to the file, can either be absolute or relative

  • tag (str) – string at the beginning of the line

  • num_args (int) – number of arguments separated by ‘ ‘ or ‘,’ to extract after the tag

Returns

List of arguments extracted as strings

Return type

list