forked from materialsproject/pymatgen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pymatgen.transformations.standard_transformations.html
1152 lines (1069 loc) · 78.7 KB
/
pymatgen.transformations.standard_transformations.html
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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>pymatgen.transformations.standard_transformations module — pymatgen 2019.5.1 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33990148-1']);
_gaq.push(['_trackPageview']);
</script>
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">pymatgen 2019.5.1 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="module-pymatgen.transformations.standard_transformations">
<span id="pymatgen-transformations-standard-transformations-module"></span><h1>pymatgen.transformations.standard_transformations module<a class="headerlink" href="#module-pymatgen.transformations.standard_transformations" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation">
<em class="property">class </em><code class="descname">AutoOxiStateDecorationTransformation</code><span class="sig-paren">(</span><em>symm_tol=0.1</em>, <em>max_radius=4</em>, <em>max_permutations=100000</em>, <em>distance_scale_factor=1.015</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#AutoOxiStateDecorationTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation automatically decorates a structure with oxidation
states using a bond valence approach.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symm_tol</strong> (<em>float</em>) – Symmetry tolerance used to determine which sites are
symmetrically equivalent. Set to 0 to turn off symmetry.</p></li>
<li><p><strong>max_radius</strong> (<em>float</em>) – Maximum radius in Angstrom used to find nearest
neighbors.</p></li>
<li><p><strong>max_permutations</strong> (<em>int</em>) – Maximum number of permutations of oxidation
states to test.</p></li>
<li><p><strong>distance_scale_factor</strong> (<em>float</em>) – A scale factor to be applied. This is
useful for scaling distances, esp in the case of
calculation-relaxed structures, which may tend to under (GGA) or
over bind (LDA). The default of 1.015 works for GGA. For
experimental structure, set this to 1.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#AutoOxiStateDecorationTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.AutoOxiStateDecorationTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.ChargedCellTransformation">
<em class="property">class </em><code class="descname">ChargedCellTransformation</code><span class="sig-paren">(</span><em>charge=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ChargedCellTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ChargedCellTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>The ChargedCellTransformation applies a charge to a structure (or defect object).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>charge</strong> – A integer charge to apply to the structure.
Defaults to zero. Has to be a single integer. e.g. 2</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.ChargedCellTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ChargedCellTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ChargedCellTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ChargedCellTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ChargedCellTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ChargedCellTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ChargedCellTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.ConventionalCellTransformation">
<em class="property">class </em><code class="descname">ConventionalCellTransformation</code><span class="sig-paren">(</span><em>symprec=0.01</em>, <em>angle_tolerance=5</em>, <em>international_monoclinic=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ConventionalCellTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ConventionalCellTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This class finds the conventional cell of the input structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symprec</strong> (<em>float</em>) – tolerance as in SpacegroupAnalyzer</p></li>
<li><p><strong>angle_tolerance</strong> (<em>float</em>) – angle tolerance as in SpacegroupAnalyzer</p></li>
<li><p><strong>international_monoclinic</strong> (<em>bool</em>) – whether to use beta (True) or alpha (False)</p></li>
<li><p><strong>the non-right-angle in the unit cell</strong> (<em>as</em>) – </p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.ConventionalCellTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ConventionalCellTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ConventionalCellTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns most primitive cell for structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>structure</strong> – A structure</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The same structure in a conventional standard setting</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ConventionalCellTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ConventionalCellTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ConventionalCellTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ConventionalCellTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.DeformStructureTransformation">
<em class="property">class </em><code class="descname">DeformStructureTransformation</code><span class="sig-paren">(</span><em>deformation=((1</em>, <em>0</em>, <em>0)</em>, <em>(0</em>, <em>1</em>, <em>0)</em>, <em>(0</em>, <em>0</em>, <em>1))</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#DeformStructureTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DeformStructureTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation deforms a structure by a deformation gradient matrix</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>deformation</strong> (<em>array</em>) – deformation gradient for the transformation</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.DeformStructureTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#DeformStructureTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DeformStructureTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.DeformStructureTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DeformStructureTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.DeformStructureTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DeformStructureTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation">
<em class="property">class </em><code class="descname">DiscretizeOccupanciesTransformation</code><span class="sig-paren">(</span><em>max_denominator=5</em>, <em>tol=None</em>, <em>fix_denominator=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#DiscretizeOccupanciesTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>Discretizes the site occupancies in a disordered structure; useful for
grouping similar structures or as a pre-processing step for order-disorder
transformations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>max_denominator</strong> – An integer maximum denominator for discretization. A higher
denominator allows for finer resolution in the site occupancies.</p></li>
<li><p><strong>tol</strong> – A float that sets the maximum difference between the original and
discretized occupancies before throwing an error. If None, it is
set to 1 / (4 * max_denominator).</p></li>
<li><p><strong>fix_denominator</strong> (<em>bool</em>) – If True, will enforce a common denominator for all species.
This prevents a mix of denominators (for example, 1/3, 1/4)
that might require large cell sizes to perform an enumeration.
‘tol’ needs to be > 1.0 in some cases.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#DiscretizeOccupanciesTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Discretizes the site occupancies in the structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>structure</strong> – disordered Structure to discretize occupancies</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>A new disordered Structure with occupancies discretized</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.DiscretizeOccupanciesTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation">
<em class="property">class </em><code class="descname">OrderDisorderedStructureTransformation</code><span class="sig-paren">(</span><em>algo=0</em>, <em>symmetrized_structures=False</em>, <em>no_oxi_states=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OrderDisorderedStructureTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>Order a disordered structure. The disordered structure must be oxidation
state decorated for ewald sum to be computed. No attempt is made to perform
symmetry determination to reduce the number of combinations.</p>
<p>Hence, attempting to performing ordering on a large number of disordered
sites may be extremely expensive. The time scales approximately with the
number of possible combinations. The algorithm can currently compute
approximately 5,000,000 permutations per minute.</p>
<p>Also, simple rounding of the occupancies are performed, with no attempt
made to achieve a target composition. This is usually not a problem for
most ordering problems, but there can be times where rounding errors may
result in structures that do not have the desired composition.
This second step will be implemented in the next iteration of the code.</p>
<p>If multiple fractions for a single species are found for different sites,
these will be treated separately if the difference is above a threshold
tolerance. currently this is .1</p>
<p>For example, if a fraction of .25 Li is on sites 0,1,2,3 and .5 on sites
4, 5, 6, 7 then 1 site from [0,1,2,3] will be filled and 2 sites from [4,5,6,7]
will be filled, even though a lower energy combination might be found by
putting all lithium in sites [4,5,6,7].</p>
<p>USE WITH CARE.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>algo</strong> (<em>int</em>) – Algorithm to use.</p></li>
<li><p><strong>symmetrized_structures</strong> (<em>bool</em>) – Whether the input structures are
instances of SymmetrizedStructure, and that their symmetry
should be used for the grouping of sites.</p></li>
<li><p><strong>no_oxi_states</strong> (<em>bool</em>) – Whether to remove oxidation states prior to
ordering.</p></li>
</ul>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_BEST_FIRST">
<code class="descname">ALGO_BEST_FIRST</code><em class="property"> = 2</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_BEST_FIRST" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_COMPLETE">
<code class="descname">ALGO_COMPLETE</code><em class="property"> = 1</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_COMPLETE" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_FAST">
<code class="descname">ALGO_FAST</code><em class="property"> = 0</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.ALGO_FAST" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em>, <em>return_ranked_list=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OrderDisorderedStructureTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>For this transformation, the apply_transformation method will return
only the ordered structure with the lowest Ewald energy, to be
consistent with the method signature of the other transformations.
However, all structures are stored in the all_structures attribute in
the transformation object for easy access.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Oxidation state decorated disordered structure to order</p></li>
<li><p><strong>return_ranked_list</strong> (<em>bool</em>) – Whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Depending on returned_ranked list, either a transformed structure
or a list of dictionaries, where each dictionary is of the form
{“structure” = …. , “other_arguments”}
the key “transformation” is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.lowest_energy_structure">
<code class="descname">lowest_energy_structure</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OrderDisorderedStructureTransformation.lowest_energy_structure" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation">
<em class="property">class </em><code class="descname">OxidationStateDecorationTransformation</code><span class="sig-paren">(</span><em>oxidation_states</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OxidationStateDecorationTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation decorates a structure with oxidation states.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>oxidation_states</strong> (<em>dict</em>) – Oxidation states supplied as a dict,</p></li>
<li><p><strong>{"Li"</strong> (<em>e.g.</em><em>,</em>) – 1, “O”:-2}</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OxidationStateDecorationTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateDecorationTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation">
<em class="property">class </em><code class="descname">OxidationStateRemovalTransformation</code><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OxidationStateRemovalTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation removes oxidation states from a structure.</p>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#OxidationStateRemovalTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.OxidationStateRemovalTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation">
<em class="property">class </em><code class="descname">PartialRemoveSpecieTransformation</code><span class="sig-paren">(</span><em>specie_to_remove</em>, <em>fraction_to_remove</em>, <em>algo=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PartialRemoveSpecieTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>Remove fraction of specie from a structure.</p>
<p>Requires an oxidation state decorated structure for ewald sum to be
computed.</p>
<p>Given that the solution to selecting the right removals is NP-hard, there
are several algorithms provided with varying degrees of accuracy and speed.
Please see
<a class="reference internal" href="pymatgen.transformations.site_transformations.html#pymatgen.transformations.site_transformations.PartialRemoveSitesTransformation" title="pymatgen.transformations.site_transformations.PartialRemoveSitesTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.site_transformations.PartialRemoveSitesTransformation</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>specie_to_remove</strong> – Specie to remove. Must have oxidation state E.g.,
“Li+”</p></li>
<li><p><strong>fraction_to_remove</strong> – Fraction of specie to remove. E.g., 0.5</p></li>
<li><p><strong>algo</strong> – This parameter allows you to choose the algorithm to perform
ordering. Use one of PartialRemoveSpecieTransformation.ALGO_*
variables to set the algo.</p></li>
</ul>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_BEST_FIRST">
<code class="descname">ALGO_BEST_FIRST</code><em class="property"> = 2</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_BEST_FIRST" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_COMPLETE">
<code class="descname">ALGO_COMPLETE</code><em class="property"> = 1</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_COMPLETE" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_ENUMERATE">
<code class="descname">ALGO_ENUMERATE</code><em class="property"> = 3</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_ENUMERATE" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_FAST">
<code class="descname">ALGO_FAST</code><em class="property"> = 0</em><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.ALGO_FAST" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em>, <em>return_ranked_list=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PartialRemoveSpecieTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply the transformation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> (<em>bool/int</em>) – Boolean stating whether or not
multiple structures are returned. If return_ranked_list is
an int, that number of structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Depending on returned_ranked list, either a transformed structure
or a list of dictionaries, where each dictionary is of the form
{“structure” = …. , “other_arguments”}
the key “transformation” is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PartialRemoveSpecieTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.PerturbStructureTransformation">
<em class="property">class </em><code class="descname">PerturbStructureTransformation</code><span class="sig-paren">(</span><em>amplitude=0.01</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PerturbStructureTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PerturbStructureTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation perturbs a structure by a specified distance in random
directions. Used for breaking symmetries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>amplitude</strong> (<em>float</em>) – Amplitude of perturbation in angstroms. All sites
will be perturbed by exactly that amplitude in a random direction.</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.PerturbStructureTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PerturbStructureTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PerturbStructureTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PerturbStructureTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PerturbStructureTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PerturbStructureTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PerturbStructureTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.PrimitiveCellTransformation">
<em class="property">class </em><code class="descname">PrimitiveCellTransformation</code><span class="sig-paren">(</span><em>tolerance=0.5</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PrimitiveCellTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PrimitiveCellTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This class finds the primitive cell of the input structure.
It returns a structure that is not necessarily orthogonalized
Author: Will Richards</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>tolerance</strong> (<em>float</em>) – Tolerance for each coordinate of a particular
site. For example, [0.5, 0, 0.5] in cartesian coordinates will be
considered to be on the same coordinates as [0, 0, 0] for a
tolerance of 0.5. Defaults to 0.5.</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#PrimitiveCellTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns most primitive cell for structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>structure</strong> – A structure</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The most primitive structure found. The returned structure is
guaranteed to have len(new structure) <= len(structure).</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.PrimitiveCellTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation">
<em class="property">class </em><code class="descname">RemoveSpeciesTransformation</code><span class="sig-paren">(</span><em>species_to_remove</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#RemoveSpeciesTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>Remove all occurrences of some species from a structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>species_to_remove</strong> – List of species to remove. E.g., [“Li”, “Mn”]</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#RemoveSpeciesTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RemoveSpeciesTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.RotationTransformation">
<em class="property">class </em><code class="descname">RotationTransformation</code><span class="sig-paren">(</span><em>axis</em>, <em>angle</em>, <em>angle_in_radians=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#RotationTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RotationTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>The RotationTransformation applies a rotation to a structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>axis</strong> (<em>3x1 array</em>) – Axis of rotation, e.g., [1, 0, 0]</p></li>
<li><p><strong>angle</strong> (<em>float</em>) – Angle to rotate</p></li>
<li><p><strong>angle_in_radians</strong> (<em>bool</em>) – Set to True if angle is supplied in radians.
Else degrees are assumed.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.RotationTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#RotationTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RotationTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.RotationTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RotationTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.RotationTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.RotationTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation">
<em class="property">class </em><code class="descname">ScaleToRelaxedTransformation</code><span class="sig-paren">(</span><em>unrelaxed_structure</em>, <em>relaxed_structure</em>, <em>species_map=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ScaleToRelaxedTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>Takes the unrelaxed and relaxed structure and applies its site and volume
relaxation to a structurally similar structures (e.g. bulk: NaCl and PbTe
(rock-salt), slab: Sc(10-10) and Mg(10-10) (hcp), GB: Mo(001) sigma 5 GB,
Fe(001) sigma 5). Useful for finding an initial guess of a set of similar
structures closer to its most relaxed state.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>unrelaxed_structure</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Initial, unrelaxed structure</p></li>
<li><p><strong>relaxed_structure</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Relaxed structure</p></li>
<li><p><strong>species_map</strong> (<em>dict</em>) – A dict or list of tuples containing the species mapping in
string-string pairs. The first species corresponds to the relaxed
structure while the second corresponds to the species in the
structure to be scaled. E.g., {“Li”:”Na”} or [(“Fe2+”,”Mn2+”)].
Multiple substitutions can be done. Overloaded to accept
sp_and_occu dictionary E.g. {“Si: {“Ge”:0.75, “C”:0.25}},
which substitutes a single species with multiple species to
generate a disordered structure.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#ScaleToRelaxedTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a copy of structure with lattice parameters
and sites scaled to the same degree as the relaxed_structure.</p>
<dl class="simple">
<dt>Arg:</dt><dd><dl class="simple">
<dt>structure (Structure): A structurally similar structure in</dt><dd><p>regards to crystal and site positions.</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.ScaleToRelaxedTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg
“return_ranked_list” which allows for the transformed structures to be
returned as a ranked list.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.transformations.standard_transformations.SubstitutionTransformation">
<em class="property">class </em><code class="descname">SubstitutionTransformation</code><span class="sig-paren">(</span><em>species_map</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#SubstitutionTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.SubstitutionTransformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.transformation_abc.AbstractTransformation</span></code></a></p>
<p>This transformation substitutes species for one another.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>species_map</strong> – A dict or list of tuples containing the species mapping in
string-string pairs. E.g., {“Li”:”Na”} or [(“Fe2+”,”Mn2+”)].
Multiple substitutions can be done. Overloaded to accept
sp_and_occu dictionary E.g. {“Si: {“Ge”:0.75, “C”:0.25}},
which substitutes a single species with multiple species to
generate a disordered structure.</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.transformations.standard_transformations.SubstitutionTransformation.apply_transformation">
<code class="descname">apply_transformation</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/transformations/standard_transformations.html#SubstitutionTransformation.apply_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.transformations.standard_transformations.SubstitutionTransformation.apply_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies the transformation to a structure. Depending on whether a
transformation is one-to-many, there may be an option to return a
ranked list of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>return_ranked_list</strong> – Boolean stating whether or not multiple structures are
returned. If return_ranked_list is a number, that number of
structures is returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>depending on returned_ranked list, either a transformed structure
or
a list of dictionaries, where each dictionary is of the form
{‘structure’ = …. , ‘other_arguments’}
the key ‘transformation’ is reserved for the transformation that
was actually applied to the structure.
This transformation is parsed by the alchemy classes for generating
a more specific transformation history. Any other information will
be stored in the transformation_parameters dictionary in the
transmuted structure class.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.SubstitutionTransformation.inverse">
<code class="descname">inverse</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.SubstitutionTransformation.inverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the inverse transformation if available.
Otherwise, should return None.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.transformations.standard_transformations.SubstitutionTransformation.is_one_to_many">
<code class="descname">is_one_to_many</code><a class="headerlink" href="#pymatgen.transformations.standard_transformations.SubstitutionTransformation.is_one_to_many" title="Permalink to this definition">¶</a></dt>
<dd><p>Determines if a Transformation is a one-to-many transformation. If a
Transformation is a one-to-many transformation, the
apply_transformation method should have a keyword arg