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Merge pull request #24 from pyiron/pyxtal

Add pyxtal wrapper

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95.24

/structuretoolkit/build/random.py

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

from typing import Union, List, Tuple
import warnings

try:
    from tqdm.auto import tqdm
except ImportError:
    tqdm = lambda x: x

from ase import Atoms
from structuretoolkit.common.helper import center_coordinates_in_unit_cell


def pyxtal(
    group: Union[int, List[int]],
    species: Tuple[str],
    num_ions: Tuple[int],
    dim=3,
    repeat=1,
    allow_exceptions=True,
    **kwargs,
) -> Union[Atoms, List[dict]]:
    """
    Generate random crystal structures with PyXtal.

    `group` must be between 1 and the largest possible value for the given dimensionality:
        dim=3 => 1 - 230 (space groups)
        dim=2 => 1 -  80 (layer groups)
        dim=1 => 1 -  75 (rod groups)
        dim=0 => 1 -  58 (point groups)

    When `group` is passed as a list of integers or `repeat>1`, generate multiple structures and return them in a list
    of dicts containing the keys `atoms`, `symmetry` and `repeat` for the ASE structure, the symmetry group
    number and which iteration it is, respectively.

    Args:
        group (list of int, or int): the symmetry group to generate or a list of them
        species (tuple of str): which species to include, defines the stoichiometry together with `num_ions`
        num_ions (tuple of int): how many of each species to include, defines the stoichiometry together with `species`
        dim (int): dimensionality of the symmetry group, 0 is point groups, 1 is rod groups, 2 is layer groups and 3 is space groups
        repeat (int): how many random structures to generate
        allow_exceptions (bool): when generating multiple structures, silence errors when the requested stoichiometry and symmetry group are incompatible
        **kwargs: passed to `pyxtal.pyxtal` function verbatim

    Returns:
        :class:`~.Atoms`: the generated structure, if repeat==1 and only one symmetry group is requested
        list of dict of all generated structures, if repeat>1 or multiple symmetry groups are requested

    Raises:
        ValueError: if `species` and `num_ions` are not of the same length
        ValueError: if stoichiometry and symmetry group are incompatible and allow_exceptions==False or only one structure is requested
    """
    from pyxtal import pyxtal as _pyxtal
    from pyxtal.msg import Comp_CompatibilityError

    if len(species) != len(num_ions):
        raise ValueError(
            "species and num_ions must be of same length, "
            f"not {species} and {num_ions}!"
        )
    stoich = "".join(f"{s}{n}" for s, n in zip(species, num_ions))

    def generate(group):
        s = _pyxtal()
        try:
            s.from_random(
                dim=dim, group=group, species=species, numIons=num_ions, **kwargs
            )
        except Comp_CompatibilityError as e:
            if not allow_exceptions:
                raise ValueError(
                    f"Symmetry group {group} incompatible with stoichiometry {stoich}!"
                ) from None
            else:
                return None
        s = s.to_ase()
        s = center_coordinates_in_unit_cell(structure=s)
        return s

    # return a single structure
    if repeat == 1 and isinstance(group, int):
        allow_exceptions = False
        return generate(group)
    else:
        structures = []
        if isinstance(group, int):
            group = [group]
        failed_groups = []
        for g in tqdm(group, desc="Spacegroups"):
            for i in range(repeat):
                s = generate(g)
                if s is None:
                    failed_groups.append(g)
                    continue
                structures.append({
                    "atoms": s,
                    "symmetry": g,
                    "repeat": i
                })
        if len(failed_groups) > 0:
            warnings.warn(
                f'Groups [{", ".join(map(str,failed_groups))}] could not be generated with stoichiometry {stoich}!'
            )
        return structures

1	# coding: utf-8
2	# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
3	# Distributed under the terms of "New BSD License", see the LICENSE file.
4
5	from typing import Union, List, Tuple	1✔
6	import warnings	1✔
7
8	try:	1✔
9	from tqdm.auto import tqdm	1✔
10	except ImportError:	×
11	tqdm = lambda x: x	×
12
13	from ase import Atoms	1✔
14	from structuretoolkit.common.helper import center_coordinates_in_unit_cell	1✔
15
16
17	def pyxtal(	1✔
18	group: Union[int, List[int]],
19	species: Tuple[str],
20	num_ions: Tuple[int],
21	dim=3,
22	repeat=1,
23	allow_exceptions=True,
24	**kwargs,
25	) -> Union[Atoms, List[dict]]:
26	"""
27	Generate random crystal structures with PyXtal.
28
29	`group` must be between 1 and the largest possible value for the given dimensionality:
30	dim=3 => 1 - 230 (space groups)
31	dim=2 => 1 - 80 (layer groups)
32	dim=1 => 1 - 75 (rod groups)
33	dim=0 => 1 - 58 (point groups)
34
35	When `group` is passed as a list of integers or `repeat>1`, generate multiple structures and return them in a list
36	of dicts containing the keys `atoms`, `symmetry` and `repeat` for the ASE structure, the symmetry group
37	number and which iteration it is, respectively.
38
39	Args:
40	group (list of int, or int): the symmetry group to generate or a list of them
41	species (tuple of str): which species to include, defines the stoichiometry together with `num_ions`
42	num_ions (tuple of int): how many of each species to include, defines the stoichiometry together with `species`
43	dim (int): dimensionality of the symmetry group, 0 is point groups, 1 is rod groups, 2 is layer groups and 3 is space groups
44	repeat (int): how many random structures to generate
45	allow_exceptions (bool): when generating multiple structures, silence errors when the requested stoichiometry and symmetry group are incompatible
46	**kwargs: passed to `pyxtal.pyxtal` function verbatim
47
48	Returns:
49	:class:`~.Atoms`: the generated structure, if repeat==1 and only one symmetry group is requested
50	list of dict of all generated structures, if repeat>1 or multiple symmetry groups are requested
51
52	Raises:
53	ValueError: if `species` and `num_ions` are not of the same length
54	ValueError: if stoichiometry and symmetry group are incompatible and allow_exceptions==False or only one structure is requested
55	"""
56	from pyxtal import pyxtal as _pyxtal	1✔
57	from pyxtal.msg import Comp_CompatibilityError	1✔
58
59	if len(species) != len(num_ions):	1✔
60	raise ValueError(	1✔
61	"species and num_ions must be of same length, "
62	f"not {species} and {num_ions}!"
63	)
64	stoich = "".join(f"{s}{n}" for s, n in zip(species, num_ions))	1✔
65
66	def generate(group):	1✔
67	s = _pyxtal()	1✔
68	try:	1✔
69	s.from_random(	1✔
70	dim=dim, group=group, species=species, numIons=num_ions, **kwargs
71	)
72	except Comp_CompatibilityError as e:	1✔
73	if not allow_exceptions:	1✔
74	raise ValueError(	1✔
75	f"Symmetry group {group} incompatible with stoichiometry {stoich}!"
76	) from None
77	else:
78	return None	1✔
79	s = s.to_ase()	1✔
80	s = center_coordinates_in_unit_cell(structure=s)	1✔
81	return s	1✔
82
83	# return a single structure
84	if repeat == 1 and isinstance(group, int):	1✔
85	allow_exceptions = False	1✔
86	return generate(group)	1✔
87	else:
88	structures = []	1✔
89	if isinstance(group, int):	1✔
90	group = [group]	1✔
91	failed_groups = []	1✔
92	for g in tqdm(group, desc="Spacegroups"):	1✔
93	for i in range(repeat):	1✔
94	s = generate(g)	1✔
95	if s is None:	1✔
96	failed_groups.append(g)	1✔
97	continue	1✔
98	structures.append({	1✔
99	"atoms": s,
100	"symmetry": g,
101	"repeat": i
102	})
103	if len(failed_groups) > 0:	1✔
104	warnings.warn(	1✔
105	f'Groups [{", ".join(map(str,failed_groups))}] could not be generated with stoichiometry {stoich}!'
106	)
107	return structures	1✔

pyiron / structuretoolkit / 5628806564

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