aiida.tools documentation¶

Tools¶

pw input parser¶

Tools for parsing QE PW input files and creating AiiDa Node objects based on them.

TODO: Parse CONSTRAINTS, OCCUPATIONS, ATOMIC_FORCES once they are implemented: in AiiDA

class aiida.tools.codespecific.quantumespresso.pwinputparser.PwInputFile(pwinput)[source]¶

Class used for parsing Quantum Espresso pw.x input files and using the info.

Members:

namelists:

A nested dictionary of the namelists and their key-value pairs. The namelists will always be upper-case keys, while the parameter keys will always be lower-case.

For example:

{"CONTROL": {"calculation": "bands",
             "prefix": "al",
             "pseudo_dir": "./pseudo",
             "outdir": "./out"},
 "ELECTRONS": {"diagonalization": "cg"},
 "SYSTEM": {"nbnd": 8,
            "ecutwfc": 15.0,
            "celldm(1)": 7.5,
            "ibrav": 2,
            "nat": 1,
            "ntyp": 1}
}

atomic_positions:
A dictionary with
units: the units of the positions (always lower-case) or None

names: list of the atom names (e.g. 'Si', 'Si0', 'Si_0')

positions: list of the [x, y, z] positions

fixed_coords: list of [x, y, z] (bools) of the force modifications (Note: True <–> Fixed, as defined in the BasePwCpInputGenerator._if_pos method)
For example:
{'units': 'bohr', 'names': ['C', 'O'], 'positions': [[0.0, 0.0, 0.0], [0.0, 0.0, 2.5]] 'fixed_coords': [[False, False, False], [True, True, True]]}
cell_parameters:
A dictionary (if CELL_PARAMETERS is present; else: None) with
units: the units of the lattice vectors (always lower-case) or None

cell: 3x3 list with lattice vectors as rows
For example:
{'units': 'angstrom', 'cell': [[16.9, 0.0, 0.0], [-2.6, 8.0, 0.0], [-2.6, -3.5, 7.2]]}
k_points:
A dictionary containing
type: the type of kpoints (always lower-case)

points: an Nx3 list of the kpoints (will not be present if type = ‘gamma’ or type = ‘automatic’)

weights: a 1xN list of the kpoint weights (will not be present if type = ‘gamma’ or type = ‘automatic’)

mesh: a 1x3 list of the number of equally-spaced points in each direction of the Brillouin zone, as in Monkhorst-Pack grids (only present if type = ‘automatic’)

offset: a 1x3 list of the grid offsets in each direction of the Brillouin zone (only present if type = ‘automatic’) (Note: The offset value for each direction will be one of 0.0 [no offset] or 0.5 [offset by half a grid step]. This differs from the Quantum Espresso convention, where an offset value of 1 corresponds to a half-grid-step offset, but adheres to the current AiiDa convention.
Examples:
{'type': 'crystal', 'points': [[0.125, 0.125, 0.0], [0.125, 0.375, 0.0], [0.375, 0.375, 0.0]], 'weights': [1.0, 2.0, 1.0]} {'type': 'automatic', 'points': [8, 8, 8], 'offset': [0.0, 0.5, 0.0]} {'type': 'gamma'}

atomic_species:

A dictionary with

names: list of the atom names (e.g. ‘Si’, ‘Si0’, ‘Si_0’) (case as-is)

masses: list of the masses of the atoms in ‘names’

pseudo_file_names: list of the pseudopotential file names for the atoms in ‘names’ (case as-is)

Example:

{'names': ['Li', 'O', 'Al', 'Si'],
 'masses': [6.941,  15.9994, 26.98154, 28.0855],
 'pseudo_file_names': ['Li.pbe-sl-rrkjus_psl.1.0.0.UPF',
                       'O.pbe-nl-rrkjus_psl.1.0.0.UPF',
                       'Al.pbe-nl-rrkjus_psl.1.0.0.UPF',
                       'Si3 28.0855 Si.pbe-nl-rrkjus_psl.1.0.0.UPF']

__init__(pwinput)[source]¶

Parse inputs’s namelist and cards to create attributes of the info.

Parameters:

pwinput –

Any one of the following

A string of the (existing) absolute path to the pwinput file.

A single string containing the pwinput file’s text.

A list of strings, with the lines of the file as the elements.

A file object. (It will be opened, if it isn’t already.)

Raises:

IOError – if pwinput is a file and there is a problem reading the file.
TypeError – if pwinput is a list containing any non-string element(s).
aiida.common.exceptions.ParsingError – if there are issues parsing the pwinput.

get_kpointsdata()[source]¶

Return a KpointsData object based on the data in the input file.

This uses all of the data in the input file to do the necessary unit conversion, ect. and then creates an AiiDa KpointsData object.

Note: If the calculation uses only the gamma k-point (if self.k_points[‘type’] == ‘gamma’), it is necessary to also attach a settings node to the calculation with gamma_only = True.

Returns:	KpointsData object of the kpoints in the input file
Return type:	aiida.orm.data.array.kpoints.KpointsData
Raises:	NotImplementedError – if the kpoints are in a format not yet supported.

aiida.tools.codespecific.quantumespresso.pwinputparser.parse_k_points(txt)[source]¶

Return a dictionary containing info from the K_POINTS card block in txt.

Note

If the type of kpoints (where type = x in the card header, “K_POINTS x”) is not present, type will be returned as ‘tpiba’, the QE default.

Parameters: txt – A single string containing the QE input text to be parsed.

Returns:

A dictionary containing

type: the type of kpoints (always lower-case)

points: an Nx3 list of the kpoints (will not be present if type = ‘gamma’ or type = ‘automatic’)

weights: a 1xN list of the kpoint weights (will not be present if type = ‘gamma’ or type = ‘automatic’)

mesh: a 1x3 list of the number of equally-spaced points in each direction of the Brillouin zone, as in Monkhorst-Pack grids (only present if type = ‘automatic’)

offset: a 1x3 list of the grid offsets in each direction of the Brillouin zone (only present if type = ‘automatic’) (Note: The offset value for each direction will be one of 0.0 [no offset] or 0.5 [offset by half a grid step]. This differs from the Quantum Espresso convention, where an offset value of 1 corresponds to a half-grid-step offset, but adheres to the current AiiDa convention.

Examples:

{'type': 'crystal',
 'points': [[0.125,  0.125,  0.0],
            [0.125,  0.375,  0.0],
            [0.375,  0.375,  0.0]],
 'weights': [1.0, 2.0, 1.0]}

{'type': 'automatic',
 'points': [8, 8, 8],
 'offset': [0.0, 0.5, 0.0]}

{'type': 'gamma'}

Raises: aiida.common.exceptions.ParsingError – if there are issues parsing the input.