pyiron_base.utils.parser.Logstatus

pyiron_base.utils.parser.Logstatus#

class pyiron_base.utils.parser.Logstatus(h5: Any | None = None, iter_levels: int = 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

__init__(h5: Any | None = None, iter_levels: int = 1) → None[source]#

Initialize the Logstatus object.

Parameters:

  • h5 (Optional[Any]) – HDF5 object to store the dictionary in. Defaults to None.

  • iter_levels (int) – Levels of iteration. Defaults to 1.

Methods

__init__([h5, iter_levels])

Initialize the Logstatus object.

append(title, data_to_append[, vec])

Append data to the LogStatus object status_dict dictionary

combine_mat(x_key, xy_key, xz_key, y_key, ...)

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.

combine_xyz(x_key, y_key, z_key, combined_key)

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.

convert_unit(key, factor)

Convert the values of a specific key in the status_dict dictionary by multiplying them with a factor.

extract_file(file_name, tag_dict[, h5_dict, ...])

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

extract_from_list(list_of_lines, tag_dict[, ...])

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

extract_item(l_item)

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

raise_iter([dim])

Increase the iteration level

reset_iter([dim])

Reset iteration level

to_hdf(hdf)

Store the LogStatus object status_dict dictionary in an HDF5 file
append(title: str, data_to_append: list | dict, vec: bool = False) → None[source]#

Append data to the LogStatus object status_dict dictionary

Parameters:

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

  • data_to_append (Union[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: str, xy_key: str, xz_key: str, y_key: str, yz_key: str, z_key: str, combined_key: str) → None[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

  • xy_key (str) – key of the xy coordinates

  • xz_key (str) – key of the xz coordinates

  • y_key (str) – key of the y coordinates

  • yz_key (str) – key of the yz coordinates

  • z_key (str) – key of the z coordinates

  • combined_key (str) – name of the combined coordinates

combine_xyz(x_key: str, y_key: str, z_key: str, combined_key: str, as_vector: bool = False) → None[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

  • as_vector (bool) – [True/False] if the combined coordinates should be stored as a single vector instead of a matrix. Defaults to False.

convert_unit(key: str, factor: float) → None[source]#

Convert the values of a specific key in the status_dict dictionary by multiplying them with a factor.

Parameters:

  • key (str) – The key of the values to be converted.

  • factor (float) – The factor to multiply the values with.

extract_file(file_name: str, tag_dict: Dict[str, Any], h5_dict: Dict[str, str] | None = None, key_dict: Dict[str, str] | None = None) → 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: List[str], tag_dict: Dict[str, Any], h5_dict: Dict[str, str] | None = None, key_dict: Dict[str, str] | None = None) → None[source]#

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

Parameters:

  • list_of_lines (List[str]) – List of lines from the output file

  • tag_dict (Dict[str, Any]) – Dictionary with tags/patterns as key and an additional dictionary to describe the data structure.

  • h5_dict (Optional[Dict[str, str]]) – Translation dictionary of output tags as keys to the tags used on the HDF5 file as values. Defaults to None.

  • key_dict (Optional[Dict[str, str]]) – Translation dictionary of python internal tags as keys to the output tags as values. Defaults to None.

static extract_item(l_item: str) → Tuple[str, List[str] | None][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:

Tuple[str, Optional[List[str]]]

raise_iter(dim: int = 0) → None[source]#

Increase the iteration level

Parameters:

dim (int) – position - default = 0

reset_iter(dim: int = 0) → None[source]#

Reset iteration level

Parameters:

dim (int) – reset value - default = 0

to_hdf(hdf: ProjectHDFio) → None[source]#

Store the LogStatus object status_dict dictionary in an HDF5 file

Parameters:

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

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