asaplib.io package¶

Submodules¶

asaplib.io.cscope module¶

Adaptors for generating ChemiScope compatible inputs

asaplib.io.cscope.write_chemiscope_input(filename, frames, meta=None, extra=None, cutoff=None)[source]¶

Write the json file expected by the default chemiscope visualizer at filename. :param str filename: name of the file to use to save the json data. If it

ends with ‘.gz’, a gzip compressed file will be written

Parameters

frames (list) – list of ase.Atoms objects containing all the structures
meta (dict) – optional metadata of the dataset, see below
extra (dict) – optional dictionary of additional properties, see below
cutoff (float) – optional. If present, will be used to generate atom-centered environments

The dataset metadata should be given in the meta dictionary, the possible keys are: .. code-block:: python

meta = {
‘name’: ‘…’, # str, dataset name ‘description’: ‘…’, # str, dataset description ‘authors’: [ # list of str, dataset authors, OPTIONAL

‘…’,

], ‘references’: [ # list of str, references for this dataset,

‘…’, # OPTIONAL

],

}

The written JSON file will contain all the properties defined on the ase.Atoms objects. Values in ase.Atoms.arrays are mapped to target = "atom" properties; while values in ase.Atoms.info are mapped to target = "structure" properties. The only exception is ase.Atoms.arrays["numbers"], which is always ignored. If you want to have the atomic numbers as a property, you should add it to extra manually. Additional properties can be added with the extra parameter. This parameter should be a dictionary containing one entry for each property. Each entry contains a target attribute ('atom' or 'structure') and a set of values. values can be a Python list of float or string; a 1D numpy array of numeric values; or a 2D numpy array of numeric values. In the later case, multiple properties will be generated along the second axis. For example, passing .. code-block:: python

extra = {

‘cheese’: {
‘target’: ‘atom’, ‘values’: np.zeros((300, 4))

}

}

will generate four properties named cheese[1], cheese[2], cheese[3], and cheese[4], each containing 300 values. .. ase.Atoms: https://wiki.fysik.dtu.dk/ase/ase/atoms.html

NOTE: Adapted from: https://github.com/cosmo-epfl/chemiscope/blob/master/utils/chemiscope_input.py

asaplib.io.io_cell module¶

Functions for converting between different simulation cell formats

asaplib.io.io_cell.abc2h(a, b, c, alpha, beta, gamma)[source]¶

Returns a lattice vector matrix given a description in terms of the lattice vector lengths and the angles in between.

Parameters

a – First cell vector length.
b – Second cell vector length.
c – Third cell vector length.
alpha – Angle between sides b and c in radians.
beta – Angle between sides a and c in radians.
gamma – Angle between sides b and a in radians.

Returns

An array giving the lattice vector matrix in upper triangular form.

asaplib.io.io_cell.genh2abc(h)[source]¶

Returns a description of the cell in terms of the length of the: lattice vectors and the angles between them in radians.

Takes the representation of the system box in terms of a full matrix of row vectors, and returns the representation in terms of the lattice vector lengths and the angles between them in radians.

Parameters: h – Cell matrix in upper triangular column vector form.
Returns: A list containing the lattice vector lengths and the angles between them.

asaplib.io.io_cell.h2abc(h)[source]¶

Returns a description of the cell in terms of the length of the: lattice vectors and the angles between them in radians.

Takes the representation of the system box in terms of an upper triangular matrix of column vectors, and returns the representation in terms of the lattice vector lengths and the angles between them in radians.

Parameters: h – Cell matrix in upper triangular column vector form.
Returns: A list containing the lattice vector lengths and the angles between them.

asaplib.io.io_cell.h2abc_deg(h)[source]¶

Returns a description of the cell in terms of the length of the: lattice vectors and the angles between them in degrees.

Takes the representation of the system box in terms of an upper triangular matrix of column vectors, and returns the representation in terms of the lattice vector lengths and the angles between them in degrees.

Parameters: h – Cell matrix in upper triangular column vector form.
Returns: A list containing the lattice vector lengths and the angles between them in degrees.

asaplib.io.io_cell.pbcdist(q1, q2, h, ih)[source]¶

asaplib.io.io_parse module¶

Functions for IO and type conversions

class asaplib.io.io_parse.ConvertStrToList(param_decls=None, show_default=False, prompt=False, confirmation_prompt=False, hide_input=False, is_flag=None, flag_value=None, multiple=False, count=False, allow_from_autoenv=True, type=None, help=None, hidden=False, show_choices=True, show_envvar=False, **attrs)[source]¶

Bases: click.core.Option

type_cast_value(ctx, value)[source]¶: Given a value this runs it properly through the type system. This automatically handles things like nargs and multiple as well as composite types.

class asaplib.io.io_parse.NpDecoder(*, object_hook=None, parse_float=None, parse_int=None, parse_constant=None, strict=True, object_pairs_hook=None)[source]¶

Bases: json.decoder.JSONDecoder

default(obj)[source]¶

class asaplib.io.io_parse.NpEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]¶

Bases: json.encoder.JSONEncoder

default(obj)[source]¶

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

class asaplib.io.io_parse.PythonLiteralOption(param_decls=None, show_default=False, prompt=False, confirmation_prompt=False, hide_input=False, is_flag=None, flag_value=None, multiple=False, count=False, allow_from_autoenv=True, type=None, help=None, hidden=False, show_choices=True, show_envvar=False, **attrs)[source]¶