-
Notifications
You must be signed in to change notification settings - Fork 855
/
cif.py
1472 lines (1278 loc) · 58.8 KB
/
cif.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Wrapper classes for Cif input and output from Structures.
"""
import math
import os
import re
import textwrap
import warnings
from collections import deque
from functools import partial
from inspect import getfullargspec as getargspec
from io import StringIO
from itertools import groupby
from pathlib import Path
import numpy as np
from monty.io import zopen
from monty.string import remove_non_ascii
from pymatgen.core.composition import Composition
from pymatgen.core.lattice import Lattice
from pymatgen.core.operations import MagSymmOp, SymmOp
from pymatgen.core.periodic_table import DummySpecies, Element, Species, get_el_sp
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.core import Magmom
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer, SpacegroupOperations
from pymatgen.symmetry.groups import SYMM_DATA, SpaceGroup
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
from pymatgen.symmetry.structure import SymmetrizedStructure
from pymatgen.util.coord import find_in_coord_list_pbc, in_coord_list_pbc
__author__ = "Shyue Ping Ong, Will Richards, Matthew Horton"
sub_spgrp = partial(re.sub, r"[\s_]", "")
space_groups = {sub_spgrp(k): k for k in SYMM_DATA["space_group_encoding"].keys()} # type: ignore
space_groups.update({sub_spgrp(k): k for k in SYMM_DATA["space_group_encoding"].keys()}) # type: ignore
_COD_DATA = None
def _get_cod_data():
global _COD_DATA
if _COD_DATA is None:
import pymatgen
with open(os.path.join(pymatgen.symmetry.__path__[0], "symm_ops.json")) as f:
import json
_COD_DATA = json.load(f)
return _COD_DATA
class CifBlock:
"""
Object for storing cif data. All data is stored in a single dictionary.
Data inside loops are stored in lists in the data dictionary, and
information on which keys are grouped together are stored in the loops
attribute.
"""
maxlen = 70 # not quite 80 so we can deal with semicolons and things
def __init__(self, data, loops, header):
"""
Args:
data: dict of data to go into the cif. Values should be convertible to string,
or lists of these if the key is in a loop
loops: list of lists of keys, grouped by which loop they should appear in
header: name of the block (appears after the data_ on the first line)
"""
self.loops = loops
self.data = data
# AJ says: CIF Block names cannot be more than 75 characters or you
# get an Exception
self.header = header[:74]
def __eq__(self, other):
return self.loops == other.loops and self.data == other.data and self.header == other.header
def __getitem__(self, key):
return self.data[key]
def __str__(self):
"""
Returns the cif string for the data block
"""
s = [f"data_{self.header}"]
keys = self.data.keys()
written = []
for k in keys:
if k in written:
continue
for l in self.loops:
# search for a corresponding loop
if k in l:
s.append(self._loop_to_string(l))
written.extend(l)
break
if k not in written:
# k didn't belong to a loop
v = self._format_field(self.data[k])
if len(k) + len(v) + 3 < self.maxlen:
s.append(f"{k} {v}")
else:
s.extend([k, v])
return "\n".join(s)
def _loop_to_string(self, loop):
s = "loop_"
for l in loop:
s += "\n " + l
for fields in zip(*(self.data[k] for k in loop)):
line = "\n"
for val in map(self._format_field, fields):
if val[0] == ";":
s += line + "\n" + val
line = "\n"
elif len(line) + len(val) + 2 < self.maxlen:
line += " " + val
else:
s += line
line = "\n " + val
s += line
return s
def _format_field(self, v):
v = str(v).strip()
if len(v) > self.maxlen:
return ";\n" + textwrap.fill(v, self.maxlen) + "\n;"
# add quotes if necessary
if v == "":
return '""'
if (" " in v or v[0] == "_") and not (v[0] == "'" and v[-1] == "'") and not (v[0] == '"' and v[-1] == '"'):
if "'" in v:
q = '"'
else:
q = "'"
v = q + v + q
return v
@classmethod
def _process_string(cls, string):
# remove comments
string = re.sub(r"(\s|^)#.*$", "", string, flags=re.MULTILINE)
# remove empty lines
string = re.sub(r"^\s*\n", "", string, flags=re.MULTILINE)
# remove non_ascii
string = remove_non_ascii(string)
# since line breaks in .cif files are mostly meaningless,
# break up into a stream of tokens to parse, rejoining multiline
# strings (between semicolons)
q = deque()
multiline = False
ml = []
# this regex splits on spaces, except when in quotes.
# starting quotes must not be preceded by non-whitespace
# (these get eaten by the first expression)
# ending quotes must not be followed by non-whitespace
p = re.compile(r"""([^'"\s][\S]*)|'(.*?)'(?!\S)|"(.*?)"(?!\S)""")
for l in string.splitlines():
if multiline:
if l.startswith(";"):
multiline = False
q.append(("", "", "", " ".join(ml)))
ml = []
l = l[1:].strip()
else:
ml.append(l)
continue
if l.startswith(";"):
multiline = True
ml.append(l[1:].strip())
else:
for s in p.findall(l):
# s is tuple. location of the data in the tuple
# depends on whether it was quoted in the input
q.append(s)
return q
@classmethod
def from_string(cls, string):
"""
Reads CifBlock from string.
:param string: String representation.
:return: CifBlock
"""
q = cls._process_string(string)
header = q.popleft()[0][5:]
data = {}
loops = []
while q:
s = q.popleft()
# cif keys aren't in quotes, so show up in s[0]
if s[0] == "_eof":
break
if s[0].startswith("_"):
try:
data[s[0]] = "".join(q.popleft())
except IndexError:
data[s[0]] = ""
elif s[0].startswith("loop_"):
columns = []
items = []
while q:
s = q[0]
if s[0].startswith("loop_") or not s[0].startswith("_"):
break
columns.append("".join(q.popleft()))
data[columns[-1]] = []
while q:
s = q[0]
if s[0].startswith("loop_") or s[0].startswith("_"):
break
items.append("".join(q.popleft()))
n = len(items) // len(columns)
assert len(items) % n == 0
loops.append(columns)
for k, v in zip(columns * n, items):
data[k].append(v.strip())
elif "".join(s).strip() != "":
warnings.warn(f"Possible issue in cif file at line: {''.join(s).strip()}")
return cls(data, loops, header)
class CifFile:
"""
Reads and parses CifBlocks from a .cif file or string
"""
def __init__(self, data, orig_string=None, comment=None):
"""
Args:
data (dict): Of CifBlock objects.
orig_string (str): The original cif string.
comment (str): Comment string.
"""
self.data = data
self.orig_string = orig_string
self.comment = comment or "# generated using pymatgen"
def __str__(self):
s = [f"{v}" for v in self.data.values()]
return self.comment + "\n" + "\n".join(s) + "\n"
@classmethod
def from_string(cls, string):
"""
Reads CifFile from a string.
:param string: String representation.
:return: CifFile
"""
d = {}
for x in re.split(r"^\s*data_", "x\n" + string, flags=re.MULTILINE | re.DOTALL)[1:]:
# Skip over Cif block that contains powder diffraction data.
# Some elements in this block were missing from CIF files in
# Springer materials/Pauling file DBs.
# This block anyway does not contain any structure information, and
# CifParser was also not parsing it.
if "powder_pattern" in re.split(r"\n", x, 1)[0]:
continue
c = CifBlock.from_string("data_" + x)
d[c.header] = c
return cls(d, string)
@classmethod
def from_file(cls, filename):
"""
Reads CifFile from a filename.
:param filename: Filename
:return: CifFile
"""
with zopen(str(filename), "rt", errors="replace") as f:
return cls.from_string(f.read())
class CifParser:
"""
Parses a CIF file. Attempts to fix CIFs that are out-of-spec, but will
issue warnings if corrections applied. These are also stored in the
CifParser's errors attribute.
"""
def __init__(self, filename, occupancy_tolerance=1.0, site_tolerance=1e-4):
"""
Args:
filename (str): CIF filename, bzipped or gzipped CIF files are fine too.
occupancy_tolerance (float): If total occupancy of a site is between 1
and occupancy_tolerance, the occupancies will be scaled down to 1.
site_tolerance (float): This tolerance is used to determine if two
sites are sitting in the same position, in which case they will be
combined to a single disordered site. Defaults to 1e-4.
"""
self._occupancy_tolerance = occupancy_tolerance
self._site_tolerance = site_tolerance
if isinstance(filename, (str, Path)):
self._cif = CifFile.from_file(filename)
else:
self._cif = CifFile.from_string(filename.read())
# store if CIF contains features from non-core CIF dictionaries
# e.g. magCIF
self.feature_flags = {}
self.warnings = []
def is_magcif():
"""
Checks to see if file appears to be a magCIF file (heuristic).
"""
# Doesn't seem to be a canonical way to test if file is magCIF or
# not, so instead check for magnetic symmetry datanames
prefixes = [
"_space_group_magn",
"_atom_site_moment",
"_space_group_symop_magn",
]
for d in self._cif.data.values():
for k in d.data.keys():
for prefix in prefixes:
if prefix in k:
return True
return False
self.feature_flags["magcif"] = is_magcif()
def is_magcif_incommensurate():
"""
Checks to see if file contains an incommensurate magnetic
structure (heuristic).
"""
# Doesn't seem to be a canonical way to test if magCIF file
# describes incommensurate structure or not, so instead check
# for common datanames
if not self.feature_flags["magcif"]:
return False
prefixes = ["_cell_modulation_dimension", "_cell_wave_vector"]
for d in self._cif.data.values():
for k in d.data.keys():
for prefix in prefixes:
if prefix in k:
return True
return False
self.feature_flags["magcif_incommensurate"] = is_magcif_incommensurate()
for k in self._cif.data.keys():
# pass individual CifBlocks to _sanitize_data
self._cif.data[k] = self._sanitize_data(self._cif.data[k])
@staticmethod
def from_string(cif_string, occupancy_tolerance=1.0):
"""
Creates a CifParser from a string.
Args:
cif_string (str): String representation of a CIF.
occupancy_tolerance (float): If total occupancy of a site is
between 1 and occupancy_tolerance, the occupancies will be
scaled down to 1.
Returns:
CifParser
"""
stream = StringIO(cif_string)
return CifParser(stream, occupancy_tolerance)
def _sanitize_data(self, data):
"""
Some CIF files do not conform to spec. This function corrects
known issues, particular in regards to Springer materials/
Pauling files.
This function is here so that CifParser can assume its
input conforms to spec, simplifying its implementation.
:param data: CifBlock
:return: data CifBlock
"""
"""
This part of the code deals with handling formats of data as found in
CIF files extracted from the Springer Materials/Pauling File
databases, and that are different from standard ICSD formats.
"""
# check for implicit hydrogens, warn if any present
if "_atom_site_attached_hydrogens" in data.data.keys():
attached_hydrogens = [str2float(x) for x in data.data["_atom_site_attached_hydrogens"] if str2float(x) != 0]
if len(attached_hydrogens) > 0:
self.warnings.append(
"Structure has implicit hydrogens defined, "
"parsed structure unlikely to be suitable for use "
"in calculations unless hydrogens added."
)
# Check to see if "_atom_site_type_symbol" exists, as some test CIFs do
# not contain this key.
if "_atom_site_type_symbol" in data.data.keys():
# Keep a track of which data row needs to be removed.
# Example of a row: Nb,Zr '0.8Nb + 0.2Zr' .2a .m-3m 0 0 0 1 14
# 'rhombic dodecahedron, Nb<sub>14</sub>'
# Without this code, the above row in a structure would be parsed
# as an ordered site with only Nb (since
# CifParser would try to parse the first two characters of the
# label "Nb,Zr") and occupancy=1.
# However, this site is meant to be a disordered site with 0.8 of
# Nb and 0.2 of Zr.
idxs_to_remove = []
new_atom_site_label = []
new_atom_site_type_symbol = []
new_atom_site_occupancy = []
new_fract_x = []
new_fract_y = []
new_fract_z = []
for idx, el_row in enumerate(data["_atom_site_label"]):
# CIF files from the Springer Materials/Pauling File have
# switched the label and symbol. Thus, in the
# above shown example row, '0.8Nb + 0.2Zr' is the symbol.
# Below, we split the strings on ' + ' to
# check if the length (or number of elements) in the label and
# symbol are equal.
if len(data["_atom_site_type_symbol"][idx].split(" + ")) > len(
data["_atom_site_label"][idx].split(" + ")
):
# Dictionary to hold extracted elements and occupancies
els_occu = {}
# parse symbol to get element names and occupancy and store
# in "els_occu"
symbol_str = data["_atom_site_type_symbol"][idx]
symbol_str_lst = symbol_str.split(" + ")
for elocc_idx, sym in enumerate(symbol_str_lst):
# Remove any bracketed items in the string
symbol_str_lst[elocc_idx] = re.sub(r"\([0-9]*\)", "", sym.strip())
# Extract element name and its occupancy from the
# string, and store it as a
# key-value pair in "els_occ".
els_occu[
str(re.findall(r"\D+", symbol_str_lst[elocc_idx].strip())[1]).replace("<sup>", "")
] = float("0" + re.findall(r"\.?\d+", symbol_str_lst[elocc_idx].strip())[1])
x = str2float(data["_atom_site_fract_x"][idx])
y = str2float(data["_atom_site_fract_y"][idx])
z = str2float(data["_atom_site_fract_z"][idx])
for et, occu in els_occu.items():
# new atom site labels have 'fix' appended
new_atom_site_label.append(et + "_fix" + str(len(new_atom_site_label)))
new_atom_site_type_symbol.append(et)
new_atom_site_occupancy.append(str(occu))
new_fract_x.append(str(x))
new_fract_y.append(str(y))
new_fract_z.append(str(z))
idxs_to_remove.append(idx)
# Remove the original row by iterating over all keys in the CIF
# data looking for lists, which indicates
# multiple data items, one for each row, and remove items from the
# list that corresponds to the removed row,
# so that it's not processed by the rest of this function (which
# would result in an error).
for original_key in data.data:
if isinstance(data.data[original_key], list):
for id in sorted(idxs_to_remove, reverse=True):
del data.data[original_key][id]
if len(idxs_to_remove) > 0:
self.warnings.append("Pauling file corrections applied.")
data.data["_atom_site_label"] += new_atom_site_label
data.data["_atom_site_type_symbol"] += new_atom_site_type_symbol
data.data["_atom_site_occupancy"] += new_atom_site_occupancy
data.data["_atom_site_fract_x"] += new_fract_x
data.data["_atom_site_fract_y"] += new_fract_y
data.data["_atom_site_fract_z"] += new_fract_z
"""
This fixes inconsistencies in naming of several magCIF tags
as a result of magCIF being in widespread use prior to
specification being finalized (on advice of Branton Campbell).
"""
if self.feature_flags["magcif"]:
# CIF-1 style has all underscores, interim standard
# had period before magn instead of before the final
# component (e.g. xyz)
# we want to standardize on a specific key, to simplify
# parsing code
correct_keys = [
"_space_group_symop_magn_operation.xyz",
"_space_group_symop_magn_centering.xyz",
"_space_group_magn.name_BNS",
"_space_group_magn.number_BNS",
"_atom_site_moment_crystalaxis_x",
"_atom_site_moment_crystalaxis_y",
"_atom_site_moment_crystalaxis_z",
"_atom_site_moment_label",
]
# cannot mutate dict during enumeration, so store changes we want to make
changes_to_make = {}
for original_key in data.data:
for correct_key in correct_keys:
# convert to all underscore
trial_key = "_".join(correct_key.split("."))
test_key = "_".join(original_key.split("."))
if trial_key == test_key:
changes_to_make[correct_key] = original_key
# make changes
for correct_key, original_key in changes_to_make.items():
data.data[correct_key] = data.data[original_key]
# renamed_keys maps interim_keys to final_keys
renamed_keys = {
"_magnetic_space_group.transform_to_standard_Pp_abc": "_space_group_magn.transform_BNS_Pp_abc"
}
changes_to_make = {}
for interim_key, final_key in renamed_keys.items():
if data.data.get(interim_key):
changes_to_make[final_key] = interim_key
if len(changes_to_make) > 0:
self.warnings.append("Keys changed to match new magCIF specification.")
for final_key, interim_key in changes_to_make.items():
data.data[final_key] = data.data[interim_key]
# check for finite precision frac coordinates (e.g. 0.6667 instead of 0.6666666...7)
# this can sometimes cause serious issues when applying symmetry operations
important_fracs = (1 / 3.0, 2 / 3.0)
fracs_to_change = {}
for label in ("_atom_site_fract_x", "_atom_site_fract_y", "_atom_site_fract_z"):
if label in data.data.keys():
for idx, frac in enumerate(data.data[label]):
try:
frac = str2float(frac)
except Exception:
# coordinate might not be defined e.g. '?'
continue
for comparison_frac in important_fracs:
if abs(1 - frac / comparison_frac) < 1e-4:
fracs_to_change[(label, idx)] = str(comparison_frac)
if fracs_to_change:
self.warnings.append(
"Some fractional coordinates rounded to ideal values to avoid issues with finite precision."
)
for (label, idx), val in fracs_to_change.items():
data.data[label][idx] = val
return data
def _unique_coords(self, coords_in, magmoms_in=None, lattice=None):
"""
Generate unique coordinates using coord and symmetry positions
and also their corresponding magnetic moments, if supplied.
"""
coords = []
if magmoms_in:
magmoms = []
if len(magmoms_in) != len(coords_in):
raise ValueError
for tmp_coord, tmp_magmom in zip(coords_in, magmoms_in):
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if isinstance(op, MagSymmOp):
# Up to this point, magmoms have been defined relative
# to crystal axis. Now convert to Cartesian and into
# a Magmom object.
magmom = Magmom.from_moment_relative_to_crystal_axes(
op.operate_magmom(tmp_magmom), lattice=lattice
)
else:
magmom = Magmom(tmp_magmom)
if not in_coord_list_pbc(coords, coord, atol=self._site_tolerance):
coords.append(coord)
magmoms.append(magmom)
return coords, magmoms
for tmp_coord in coords_in:
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if not in_coord_list_pbc(coords, coord, atol=self._site_tolerance):
coords.append(coord)
return coords, [Magmom(0)] * len(coords) # return dummy magmoms
def get_lattice(
self,
data,
length_strings=("a", "b", "c"),
angle_strings=("alpha", "beta", "gamma"),
lattice_type=None,
):
"""
Generate the lattice from the provided lattice parameters. In
the absence of all six lattice parameters, the crystal system
and necessary parameters are parsed
"""
try:
lengths = [str2float(data["_cell_length_" + i]) for i in length_strings]
angles = [str2float(data["_cell_angle_" + i]) for i in angle_strings]
if not lattice_type:
return Lattice.from_parameters(*lengths, *angles)
return getattr(Lattice, lattice_type)(*(lengths + angles))
except KeyError:
# Missing Key search for cell setting
for lattice_lable in [
"_symmetry_cell_setting",
"_space_group_crystal_system",
]:
if data.data.get(lattice_lable):
lattice_type = data.data.get(lattice_lable).lower()
try:
required_args = getargspec(getattr(Lattice, lattice_type)).args
lengths = (l for l in length_strings if l in required_args)
angles = (a for a in angle_strings if a in required_args)
return self.get_lattice(data, lengths, angles, lattice_type=lattice_type)
except AttributeError as exc:
self.warnings.append(str(exc))
warnings.warn(exc)
else:
return None
return None
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in [
"_symmetry_equiv_pos_as_xyz",
"_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_",
]:
if data.data.get(symmetry_label):
xyz = data.data.get(symmetry_label)
if isinstance(xyz, str):
msg = "A 1-line symmetry op P1 CIF is detected!"
warnings.warn(msg)
self.warnings.append(msg)
xyz = [xyz]
try:
symops = [SymmOp.from_xyz_string(s) for s in xyz]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in [
"_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall",
"_space_group_name_Hall_",
"_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_",
]:
sg = data.data.get(symmetry_label)
msg_template = "No _symmetry_equiv_pos_as_xyz type key found. Spacegroup from {} used."
if sg:
sg = sub_spgrp(sg)
try:
spg = space_groups.get(sg)
if spg:
symops = SpaceGroup(spg).symmetry_ops
msg = msg_template.format(symmetry_label)
warnings.warn(msg)
self.warnings.append(msg)
break
except ValueError:
# Ignore any errors
pass
try:
for d in _get_cod_data():
if sg == re.sub(r"\s+", "", d["hermann_mauguin"]):
xyz = d["symops"]
symops = [SymmOp.from_xyz_string(s) for s in xyz]
msg = msg_template.format(symmetry_label)
warnings.warn(msg)
self.warnings.append(msg)
break
except Exception:
continue
if symops:
break
if not symops:
# Try to parse International number
for symmetry_label in [
"_space_group_IT_number",
"_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_",
]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
msg = "No _symmetry_equiv_pos_as_xyz type key found. Defaulting to P1."
warnings.warn(msg)
self.warnings.append(msg)
symops = [SymmOp.from_xyz_string(s) for s in ["x", "y", "z"]]
return symops
def get_magsymops(self, data):
"""
Equivalent to get_symops except for magnetic symmetry groups.
Separate function since additional operation for time reversal symmetry
(which changes magnetic moments on sites) needs to be returned.
"""
magsymmops = []
# check to see if magCIF file explicitly contains magnetic symmetry operations
if data.data.get("_space_group_symop_magn_operation.xyz"):
xyzt = data.data.get("_space_group_symop_magn_operation.xyz")
if isinstance(xyzt, str):
xyzt = [xyzt]
magsymmops = [MagSymmOp.from_xyzt_string(s) for s in xyzt]
if data.data.get("_space_group_symop_magn_centering.xyz"):
xyzt = data.data.get("_space_group_symop_magn_centering.xyz")
if isinstance(xyzt, str):
xyzt = [xyzt]
centering_symops = [MagSymmOp.from_xyzt_string(s) for s in xyzt]
all_ops = []
for op in magsymmops:
for centering_op in centering_symops:
new_translation = [
i - np.floor(i) for i in op.translation_vector + centering_op.translation_vector
]
new_time_reversal = op.time_reversal * centering_op.time_reversal
all_ops.append(
MagSymmOp.from_rotation_and_translation_and_time_reversal(
rotation_matrix=op.rotation_matrix,
translation_vec=new_translation,
time_reversal=new_time_reversal,
)
)
magsymmops = all_ops
# else check to see if it specifies a magnetic space group
elif data.data.get("_space_group_magn.name_BNS") or data.data.get("_space_group_magn.number_BNS"):
if data.data.get("_space_group_magn.name_BNS"):
# get BNS label for MagneticSpaceGroup()
id = data.data.get("_space_group_magn.name_BNS")
else:
# get BNS number for MagneticSpaceGroup()
# by converting string to list of ints
id = list(map(int, (data.data.get("_space_group_magn.number_BNS").split("."))))
if data.data.get("_space_group_magn.transform_BNS_Pp_abc"):
if data.data.get("_space_group_magn.transform_BNS_Pp_abc") != "a,b,c;0,0,0":
jf = data.data.get("_space_group_magn.transform_BNS_Pp_abc")
msg = MagneticSpaceGroup(id, jf)
elif data.data.get("_space_group_magn.transform_BNS_Pp"):
return NotImplementedError("Incomplete specification to implement.")
else:
msg = MagneticSpaceGroup(id)
magsymmops = msg.symmetry_ops
if not magsymmops:
msg = "No magnetic symmetry detected, using primitive symmetry."
warnings.warn(msg)
self.warnings.append(msg)
magsymmops = [MagSymmOp.from_xyzt_string("x, y, z, 1")]
return magsymmops
@staticmethod
def parse_oxi_states(data):
"""
Parse oxidation states from data dictionary
"""
try:
oxi_states = {
data["_atom_type_symbol"][i]: str2float(data["_atom_type_oxidation_number"][i])
for i in range(len(data["_atom_type_symbol"]))
}
# attempt to strip oxidation state from _atom_type_symbol
# in case the label does not contain an oxidation state
for i, symbol in enumerate(data["_atom_type_symbol"]):
oxi_states[re.sub(r"\d?[\+,\-]?$", "", symbol)] = str2float(data["_atom_type_oxidation_number"][i])
except (ValueError, KeyError):
oxi_states = None
return oxi_states
@staticmethod
def parse_magmoms(data, lattice=None):
"""
Parse atomic magnetic moments from data dictionary
"""
if lattice is None:
raise Exception("Magmoms given in terms of crystal axes in magCIF spec.")
try:
magmoms = {
data["_atom_site_moment_label"][i]: np.array(
[
str2float(data["_atom_site_moment_crystalaxis_x"][i]),
str2float(data["_atom_site_moment_crystalaxis_y"][i]),
str2float(data["_atom_site_moment_crystalaxis_z"][i]),
]
)
for i in range(len(data["_atom_site_moment_label"]))
}
except (ValueError, KeyError):
return None
return magmoms
def _parse_symbol(self, sym):
"""
Parse a string with a symbol to extract a string representing an element.
Args:
sym (str): A symbol to be parsed.
Returns:
A string with the parsed symbol. None if no parsing was possible.
"""
# Common representations for elements/water in cif files
# TODO: fix inconsistent handling of water
special = {
"Hw": "H",
"Ow": "O",
"Wat": "O",
"wat": "O",
"OH": "",
"OH2": "",
"NO3": "N",
}
parsed_sym = None
# try with special symbols, otherwise check the first two letters,
# then the first letter alone. If everything fails try extracting the
# first letters.
m_sp = re.match("|".join(special.keys()), sym)
if m_sp:
parsed_sym = special[m_sp.group()]
elif Element.is_valid_symbol(sym[:2].title()):
parsed_sym = sym[:2].title()
elif Element.is_valid_symbol(sym[0].upper()):
parsed_sym = sym[0].upper()
else:
m = re.match(r"w?[A-Z][a-z]*", sym)
if m:
parsed_sym = m.group()
if parsed_sym is not None and (m_sp or not re.match(rf"{parsed_sym}\d*", sym)):
msg = f"{sym} parsed as {parsed_sym}"
warnings.warn(msg)
self.warnings.append(msg)
return parsed_sym
def _get_structure(self, data, primitive, symmetrized):
"""
Generate structure from part of the cif.
"""
def get_num_implicit_hydrogens(sym):
num_h = {"Wat": 2, "wat": 2, "O-H": 1}
return num_h.get(sym[:3], 0)
lattice = self.get_lattice(data)
# if magCIF, get magnetic symmetry moments and magmoms
# else standard CIF, and use empty magmom dict
if self.feature_flags["magcif_incommensurate"]:
raise NotImplementedError("Incommensurate structures not currently supported.")
if self.feature_flags["magcif"]:
self.symmetry_operations = self.get_magsymops(data)
magmoms = self.parse_magmoms(data, lattice=lattice)
else:
self.symmetry_operations = self.get_symops(data)
magmoms = {}
oxi_states = self.parse_oxi_states(data)
coord_to_species = {}
coord_to_magmoms = {}
def get_matching_coord(coord):
keys = list(coord_to_species.keys())
coords = np.array(keys)
for op in self.symmetry_operations:
c = op.operate(coord)
inds = find_in_coord_list_pbc(coords, c, atol=self._site_tolerance)
# can't use if inds, because python is dumb and np.array([0]) evaluates
# to False
if len(inds) > 0:
return keys[inds[0]]
return False
for i in range(len(data["_atom_site_label"])):
try:
# If site type symbol exists, use it. Otherwise, we use the
# label.
symbol = self._parse_symbol(data["_atom_site_type_symbol"][i])
num_h = get_num_implicit_hydrogens(data["_atom_site_type_symbol"][i])
except KeyError:
symbol = self._parse_symbol(data["_atom_site_label"][i])
num_h = get_num_implicit_hydrogens(data["_atom_site_label"][i])
if not symbol:
continue
if oxi_states is not None:
o_s = oxi_states.get(symbol, 0)
# use _atom_site_type_symbol if possible for oxidation state
if "_atom_site_type_symbol" in data.data.keys():
oxi_symbol = data["_atom_site_type_symbol"][i]
o_s = oxi_states.get(oxi_symbol, o_s)
try:
el = Species(symbol, o_s)
except Exception:
el = DummySpecies(symbol, o_s)
else:
el = get_el_sp(symbol)
x = str2float(data["_atom_site_fract_x"][i])
y = str2float(data["_atom_site_fract_y"][i])
z = str2float(data["_atom_site_fract_z"][i])
magmom = magmoms.get(data["_atom_site_label"][i], np.array([0, 0, 0]))
try:
occu = str2float(data["_atom_site_occupancy"][i])
except (KeyError, ValueError):
occu = 1
if occu > 0:
coord = (x, y, z)
match = get_matching_coord(coord)
comp_d = {el: occu}
if num_h > 0:
comp_d["H"] = num_h
self.warnings.append(
"Structure has implicit hydrogens defined, "
"parsed structure unlikely to be suitable for use "
"in calculations unless hydrogens added."
)
comp = Composition(comp_d)
if not match:
coord_to_species[coord] = comp
coord_to_magmoms[coord] = magmom
else:
coord_to_species[match] += comp
# disordered magnetic not currently supported
coord_to_magmoms[match] = None
sum_occu = [