Calculation parsers

This section describes the different parsers classes for calculations.

Quantum ESPRESSO parsers

exception aiida_quantumespresso.parsers.QEOutputParsingError[source]

Exception raised when there is a parsing error in the QE parser

aiida_quantumespresso.parsers.convert_qe2aiida_structure(output_dict, input_structure=None)[source]

Receives the dictionary cell parsed from quantum espresso Convert it into an AiiDA structure object

aiida_quantumespresso.parsers.convert_qe_time_to_sec(timestr)[source]

Given the walltime string of Quantum Espresso, converts it in a number of seconds (float).

aiida_quantumespresso.parsers.get_parser_info(parser_info_template=None)[source]

Return a template dictionary with details about the parser such as the version

Parameters:parser_info_template – template string with single placeholder to be replaced by current version number
Returns:dictionary with parser name, version and empty list for warnings
aiida_quantumespresso.parsers.ldlparse_QE_errors(lines, count, warnings)[source]

Parse QE errors messages (those appearing between some lines with %%%%%%%%)

Parameters:
  • lines – list of strings, the output text file as read by readlines() or as obtained by data.split('\\n') when data is the text file read by read()
  • count – the line at which we identified some %%%%%%%%
  • warnings – the warnings already parsed in the file
Return messages:
 

a list of QE error messages

aiida_quantumespresso.parsers.parse_QE_errors(lines, count, warnings)[source]

Parse QE errors messages (those appearing between some lines with %%%%%%%%)

Parameters:
  • lines – list of strings, the output text file as read by readlines() or as obtained by data.split('\\n') when data is the text file read by read()
  • count – the line at which we identified some %%%%%%%%
  • warnings – the warnings already parsed in the file
Return messages:
 

a list of QE error messages

aiida_quantumespresso.parsers.parse_raw_out_basic(out_file, calc_name)[source]

A very simple parser for the standard out, usually aiida.out. Currently only parses basic warnings and the walltime. :param out_file: the standard out to be parsed :param calc_name: the name of the calculation, e.g. PROJWFC :return: parsed_data

Pw Parser

Raw Pw Parser

A collection of function that are used to parse the output of Quantum Espresso PW. The function that needs to be called from outside is parse_raw_output(). The functions mostly work without aiida specific functionalities. The parsing will try to convert whatever it can in some dictionary, which by operative decision doesn’t have much structure encoded, [the values are simple ]

aiida_quantumespresso.parsers.raw_parser_pw.cell_volume(a1, a2, a3)[source]

returns the volume of the primitive cell: \(|\vec a_1\cdot(\vec a_2\cross \vec a_3)|\)

aiida_quantumespresso.parsers.raw_parser_pw.convert_list_to_matrix(in_matrix, n_rows, n_columns)[source]

converts a list into a list of lists (a matrix like) with n_rows and n_columns

aiida_quantumespresso.parsers.raw_parser_pw.convert_qe_time_to_sec(timestr)[source]

Given the walltime string of Quantum Espresso, converts it in a number of seconds (float).

aiida_quantumespresso.parsers.raw_parser_pw.parse_QE_errors(lines, count, warnings)[source]
Parse QE errors messages (those appearing between some lines with
%%%%%%%%)
Parameters:
  • lines – list of strings, the output text file as read by readlines() or as obtained by data.split('\\n') when data is the text file read by read()
  • count – the line at which we identified some %%%%%%%%
  • warnings – the warnings already parsed in the file
Return messages:
 

a list of QE error messages

aiida_quantumespresso.parsers.raw_parser_pw.parse_pw_text_output(data, xml_data={}, structure_data={}, input_dict={}, parser_opts={})[source]

Parses the text output of QE-PWscf.

Parameters:
  • data – a string, the file as read by read()
  • xml_data – the dictionary with the keys read from xml.
  • structure_data – dictionary, coming from the xml, with info on the structure
  • input_dict – dictionary with the input parameters
  • parser_opts – the parser options from the settings input parameter node
Return parsed_data:
 

dictionary with key values, referring to quantities at the last scf step

Return trajectory_data:
 

key,values referring to intermediate scf steps, as in the case of vc-relax. Empty dictionary if no value is present.

Return critical_messages:
 

a list with critical messages. If any is found in parsed_data[‘warnings’], the calculation is FAILED!

aiida_quantumespresso.parsers.raw_parser_pw.parse_pw_xml_output(data, dir_with_bands=None)[source]

Parse the xml data of QE v5.0.x Input data must be a single string, as returned by file.read() Returns a dictionary with parsed values

aiida_quantumespresso.parsers.raw_parser_pw.parse_raw_output(out_file, input_dict, parser_opts={}, xml_file=None, dir_with_bands=None)[source]

Parses the output of a calculation Receives in input the paths to the output file and the xml file.

3 different keys to check in output: parser_warnings, xml_warnings and warnings. On an upper level, these flags MUST be checked. The first two are expected to be empty unless QE failures or unfinished jobs.

Parameters:
  • out_file – path to pw std output
  • input_dict – dictionary with the input parameters
  • dir_with_bands – path to directory with all k-points (Kxxxxx) folders
  • xml_file – path to QE data-file.xml
Return parsed_data:
 

dictionary with key values, referring to quantities at the last scf step

Return parameter_data:
 

a dictionary with parsed parameters

Return trajectory_data:
 

a dictionary with arrays (for relax & md calcs.)

Return structure_data:
 

a dictionary with data for the output structure

Return bands_data:
 

a dictionary with data for bands (for bands calcs.)

Return job_successful:
 

a boolean that is False in case of failed calculations

Raises:
  • QEOutputParsingError – for errors in the parsing
  • AssertionError – if two keys in the parsed dicts are found to be equal

Basic Raw Pw Parser

This is just a minimal parser for basic quantities.

A collection of function that are used to parse the output of Quantum Espresso PW. The function that needs to be called from outside is parse_raw_output(). The functions mostly work without aiida specific functionalities. The parsing will try to convert whatever it can in some dictionary, which by operative decision doesn’t have much structure encoded, [the values are simple ]

aiida_quantumespresso.parsers.basic_raw_parser_pw.cell_volume(a1, a2, a3)[source]

returns the volume of the primitive cell: |a1.(a2xa3)|

aiida_quantumespresso.parsers.basic_raw_parser_pw.convert_list_to_matrix(in_matrix, n_rows, n_columns)[source]

converts a list into a list of lists (a matrix like) with n_rows and n_columns

aiida_quantumespresso.parsers.basic_raw_parser_pw.convert_qe_time_to_sec(timestr)[source]

Given the walltime string of Quantum Espresso, converts it in a number of seconds (float).

aiida_quantumespresso.parsers.basic_raw_parser_pw.parse_QE_errors(lines, count, warnings)[source]

Parse QE errors messages (those appearing between some lines with '%%%%%%%%')

Parameters:
  • lines – list of strings, the output text file as read by readlines() or as obtained by data.split(‘n’) when data is the text file read by read()
  • count – the line at which we identified some '%%%%%%%%'
  • warnings – the warnings already parsed in the file
Return messages:
 

a list of QE error messages

aiida_quantumespresso.parsers.basic_raw_parser_pw.parse_pw_text_output(data, xml_data=None, structure_data=None, input_dict=None)[source]

Parses the text output of QE-PWscf.

Parameters:
  • data – a string, the file as read by read()
  • xml_data – the dictionary with the keys read from xml.
  • structure_data – dictionary, coming from the xml, with info on the structure
Return parsed_data:
 

dictionary with key values, referring to quantities at the last scf step.

Return trajectory_data:
 

key,values referring to intermediate scf steps, as in the case of vc-relax. Empty dictionary if no value is present.

Return critical_messages:
 

a list with critical messages. If any is found in parsed_data[‘warnings’], the calculation is FAILED!

aiida_quantumespresso.parsers.basic_raw_parser_pw.parse_pw_xml_output(data, dir_with_bands=None)[source]

Parse the xml data of QE v5.0.x Input data must be a single string, as returned by file.read() Returns a dictionary with parsed values

aiida_quantumespresso.parsers.basic_raw_parser_pw.parse_raw_output(out_file, input_dict, parser_opts=None, xml_file=None, dir_with_bands=None)[source]

Parses the output of a calculation Receives in input the paths to the output file and the xml file.

Parameters:
  • out_file – path to pw std output
  • input_dict – not used
  • parser_opts – not used
  • dir_with_bands – path to directory with all k-points (Kxxxxx) folders
  • xml_file – path to QE data-file.xml
Returns out_dict:
 

a dictionary with parsed data

Return successful:
 

a boolean that is False in case of failed calculations

Raises:
  • QEOutputParsingError – for errors in the parsing,
  • AssertionError – if two keys in the parsed dicts are found to be qual

3 different keys to check in output: parser_warnings, xml_warnings and warnings. On an upper level, these flags MUST be checked. The first two are expected to be empty unless QE failures or unfinished jobs.

Cp Parser

Raw Cp Parser

aiida_quantumespresso.parsers.raw_parser_cp.parse_cp_text_output(data, xml_data)[source]

data must be a list of strings, one for each lines, as returned by readlines(). On output, a dictionary with parsed values

aiida_quantumespresso.parsers.raw_parser_cp.parse_cp_traj_stanzas(num_elements, splitlines, prepend_name, rescale=1.0)[source]

num_elements: Number of lines (with three elements) between lines with two only elements (containing step number and time in ps). num_elements is 3 for cell, and the number of atoms for coordinates and positions.

splitlines: a list of lines of the file, already split in pieces using string.split

prepend_name: a string to be prepended to the name of keys returned in the return dictionary.

rescale: the values in each stanza are multiplied by this factor, for units conversion

aiida_quantumespresso.parsers.raw_parser_cp.parse_cp_xml_counter_output(data)[source]

Parse xml file print_counter.xml data must be a single string, as returned by file.read() (notice the difference with parse_text_output!) On output, a dictionary with parsed values.

aiida_quantumespresso.parsers.raw_parser_cp.parse_cp_xml_output(data)[source]

Parse xml data data must be a single string, as returned by file.read() (notice the difference with parse_text_output!) On output, a dictionary with parsed values. Democratically, we have decided to use picoseconds as units of time, eV for energies, Angstrom for lengths.

Basic Raw Cp Parser

This is just a minimal parser for basic quantities.

aiida_quantumespresso.parsers.basic_raw_parser_cp.parse_cp_text_output(data, xml_data)[source]

data must be a list of strings, one for each lines, as returned by readlines(). On output, a dictionary with parsed values

aiida_quantumespresso.parsers.basic_raw_parser_cp.parse_cp_traj_stanzas(num_elements, splitlines, prepend_name, rescale=1.0)[source]

num_elements: Number of lines (with three elements) between lines with two only elements (containing step number and time in ps). num_elements is 3 for cell, and the number of atoms for coordinates and positions.

splitlines: a list of lines of the file, already split in pieces using string.split

prepend_name: a string to be prepended to the name of keys returned in the return dictionary.

rescale: the values in each stanza are multiplied by this factor, for units conversion

aiida_quantumespresso.parsers.basic_raw_parser_cp.parse_cp_xml_counter_output(data)[source]

Parse xml file print_counter.xml data must be a single string, as returned by file.read() (notice the difference with parse_text_output!) On output, a dictionary with parsed values.

aiida_quantumespresso.parsers.basic_raw_parser_cp.parse_cp_xml_output(data)[source]

Parse xml data data must be a single string, as returned by file.read() (notice the difference with parse_text_output!) On output, a dictionary with parsed values. Democratically, we have decided to use picoseconds as units of time, eV for energies, Angstrom for lengths.

Constants

Physical or mathematical constants. Since every code has its own conversion units, this module defines what QE understands as for an eV or other quantities. Whenever possible, we try to use the constants defined in :py:mod:aiida.common.constants:, but if some constants are slightly different among different codes (e.g., different standard definition), we define the constants in this file.

Dos Parser

Projwfc Parser