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
|
<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="./">
<head>
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.analysis.structure_prediction package — pymatgen 2025.6.14 documentation</title>
<link rel="stylesheet" type="text/css" href="assets/pygments.css?v=03e43079" />
<link rel="stylesheet" type="text/css" href="assets/css/theme.css?v=e59714d7" />
<link rel="stylesheet" type="text/css" href="assets/css/custom.css" />
<link rel="canonical" href="https://pymatgen.orgpymatgen.analysis.structure_prediction.html"/>
<script src="assets/jquery.js?v=5d32c60e"></script>
<script src="assets/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="assets/documentation_options.js?v=03bec786"></script>
<script src="assets/doctools.js?v=9bcbadda"></script>
<script src="assets/sphinx_highlight.js?v=dc90522c"></script>
<script src="assets/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" style="background: linear-gradient(0deg, rgba(23,63,162,1) 0%, rgba(0,70,192,1) 100%)" >
<a href="index.html">
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">pymatgen.analysis.structure_prediction package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_prediction.dopant_predictor">pymatgen.analysis.structure_prediction.dopant_predictor module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_shannon_radii"><code class="docutils literal notranslate"><span class="pre">get_dopants_from_shannon_radii()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_substitution_probabilities"><code class="docutils literal notranslate"><span class="pre">get_dopants_from_substitution_probabilities()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_prediction.substitution_probability">pymatgen.analysis.structure_prediction.substitution_probability module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor.composition_prediction()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor.list_prediction()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.as_dict"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.cond_prob()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob_list"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.cond_prob_list()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.from_dict"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_lambda"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.get_lambda()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_px"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.get_px()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.pair_corr"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.pair_corr()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.prob"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.prob()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_prediction.substitutor">pymatgen.analysis.structure_prediction.substitutor module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor"><code class="docutils literal notranslate"><span class="pre">Substitutor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.as_dict"><code class="docutils literal notranslate"><span class="pre">Substitutor.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.charge_balanced_tol"><code class="docutils literal notranslate"><span class="pre">Substitutor.charge_balanced_tol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.from_dict"><code class="docutils literal notranslate"><span class="pre">Substitutor.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.get_allowed_species"><code class="docutils literal notranslate"><span class="pre">Substitutor.get_allowed_species()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_comp"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_comp()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_list"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_list()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_structures"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_structures()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_prediction.volume_predictor">pymatgen.analysis.structure_prediction.volume_predictor module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.get_predicted_structure"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor.get_predicted_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.predict"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor.predict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.get_predicted_structure"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor.get_predicted_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.predict"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor.predict()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" style="background: linear-gradient(0deg, rgba(23,63,162,1) 0%, rgba(0,70,192,1) 100%)" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">pymatgen</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content style-external-links">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">pymatgen.analysis.structure_prediction package</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.analysis.structure_prediction.rst" class="fa fa-github"> Edit on GitHub</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="module-pymatgen.analysis.structure_prediction">
<span id="pymatgen-analysis-structure-prediction-package"></span><h1>pymatgen.analysis.structure_prediction package<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction" title="Link to this heading"></a></h1>
<p>Utilities to predict new structures.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.analysis.structure_prediction.dopant_predictor">
<span id="pymatgen-analysis-structure-prediction-dopant-predictor-module"></span><h2>pymatgen.analysis.structure_prediction.dopant_predictor module<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction.dopant_predictor" title="Link to this heading"></a></h2>
<p>Predicting potential dopants.</p>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_shannon_radii">
<span class="sig-name descname"><span class="pre">get_dopants_from_shannon_radii</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonded_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_dopants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">match_oxi_sign</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/dopant_predictor.py#L60-L125"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_shannon_radii" title="Link to this definition"></a></dt>
<dd><p>Get dopant suggestions based on Shannon radii differences.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonded_structure</strong> (<a class="reference internal" href="pymatgen.analysis.html#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – A pymatgen structure graph
decorated with oxidation states. For example, generated using the
CrystalNN.get_bonded_structure() method.</p></li>
<li><p><strong>num_dopants</strong> (<em>int</em>) – The number of suggestions to return for
n- and p-type dopants.</p></li>
<li><p><strong>match_oxi_sign</strong> (<em>bool</em>) – Whether to force the dopant and original species
to have the same sign of oxidation state. E.g. If the original site
is in a negative charge state, then only negative dopants will be
returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Dopant suggestions, given as a dictionary with keys “n_type” and</dt><dd><p>”p_type”. The suggestions for each doping type are given as a list of
dictionaries, each with they keys:</p>
<ul class="simple">
<li><p>”radii_diff”: The difference between the Shannon radii of the species.</p></li>
<li><p>”dopant_species”: The dopant species.</p></li>
<li><p>”original_species”: The substituted species.</p></li>
</ul>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_substitution_probabilities">
<span class="sig-name descname"><span class="pre">get_dopants_from_substitution_probabilities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_dopants</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">match_oxi_sign</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/dopant_predictor.py#L13-L57"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_substitution_probabilities" title="Link to this definition"></a></dt>
<dd><p>Get dopant suggestions based on substitution probabilities.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – A pymatgen structure decorated with
oxidation states.</p></li>
<li><p><strong>num_dopants</strong> (<em>int</em>) – The number of suggestions to return for
n- and p-type dopants.</p></li>
<li><p><strong>threshold</strong> (<em>float</em>) – Probability threshold for substitutions.</p></li>
<li><p><strong>match_oxi_sign</strong> (<em>bool</em>) – Whether to force the dopant and original species
to have the same sign of oxidation state. E.g. If the original site
is in a negative charge state, then only negative dopants will be
returned.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Dopant suggestions, given as a dictionary with keys “n_type” and</dt><dd><p>”p_type”. The suggestions for each doping type are given as a list of
dictionaries, each with they keys:</p>
<ul class="simple">
<li><p>”probability”: The probability of substitution.</p></li>
<li><p>”dopant_species”: The dopant species.</p></li>
<li><p>”original_species”: The substituted species.</p></li>
</ul>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.structure_prediction.substitution_probability">
<span id="pymatgen-analysis-structure-prediction-substitution-probability-module"></span><h2>pymatgen.analysis.structure_prediction.substitution_probability module<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction.substitution_probability" title="Link to this heading"></a></h2>
<p>This module provides classes for representing species substitution probabilities.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SubstitutionPredictor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lambda_table</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L184-L281"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Predicts likely substitutions either to or from a given composition
or species list using the SubstitutionProbability.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lambda_table</strong> (<em>dict</em>) – Input lambda table.</p></li>
<li><p><strong>alpha</strong> (<em>float</em>) – weight function for never observed substitutions</p></li>
<li><p><strong>threshold</strong> (<em>float</em>) – Threshold to use to identify high probability structures.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction">
<span class="sig-name descname"><span class="pre">composition_prediction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_this_composition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L252-L281"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction" title="Link to this definition"></a></dt>
<dd><p>Get charged balanced substitutions from a starting or ending
composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>composition</strong> – starting or ending composition</p></li>
<li><p><strong>to_this_composition</strong> – If true, substitutions with this as a final composition
will be found. If false, substitutions with this as a
starting composition will be found (these are slightly
different)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of predictions in the form of dictionaries.
If to_this_composition is true, the values of the dictionary
will be from the list species. If false, the keys will be
from that list.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction">
<span class="sig-name descname"><span class="pre">list_prediction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">species</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_this_composition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L200-L250"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – list of species</p></li>
<li><p><strong>to_this_composition</strong> – If true, substitutions with this as a final composition
will be found. If false, substitutions with this as a
starting composition will be found (these are slightly
different).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of predictions in the form of dictionaries.
If to_this_composition is true, the values of the dictionary
will be from the list species. If false, the keys will be
from that list.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SubstitutionProbability</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L35-L181"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class finds substitution probabilities given lists of atoms
to substitute. The inputs make more sense if you look through the
from_defaults static method.</p>
<p>The substitution prediction algorithm is presented in:
Hautier, G., Fischer, C., Ehrlacher, V., Jain, A., and Ceder, G. (2011)
Data Mined Ionic Substitutions for the Discovery of New Compounds.
Inorganic Chemistry, 50(2), 656-663. doi:10.1021/ic102031h</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lambda_table</strong> – JSON table of the weight functions lambda if None,
will use the default lambda.json table</p></li>
<li><p><strong>alpha</strong> (<em>float</em>) – weight function for never observed substitutions.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L162-L170"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob">
<span class="sig-name descname"><span class="pre">cond_prob</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">s2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L119-L132"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob" title="Link to this definition"></a></dt>
<dd><p>Conditional probability of substituting s1 for s2.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>s1</strong> – The <em>variable</em> specie</p></li>
<li><p><strong>s2</strong> – The <em>fixed</em> specie</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Conditional probability used by structure predictor.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob_list">
<span class="sig-name descname"><span class="pre">cond_prob_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">l1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L143-L160"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob_list" title="Link to this definition"></a></dt>
<dd><p>Find the probabilities of 2 lists. These should include ALL species.
This is the probability conditional on l2.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>l1</strong> – lists of species</p></li>
<li><p><strong>l2</strong> – lists of species</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The conditional probability (assuming these species are in
l2)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.from_dict">
<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L172-L181"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Class</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_lambda">
<span class="sig-name descname"><span class="pre">get_lambda</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">s2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L88-L98"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_lambda" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>s1</strong> (<em>SpeciesLike</em>) – Ion in 1st structure.</p></li>
<li><p><strong>s2</strong> (<em>SpeciesLike</em>) – Ion in 2nd structure.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Lambda values</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_px">
<span class="sig-name descname"><span class="pre">get_px</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SpeciesLike</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L100-L108"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_px" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>sp</strong> (<em>SpeciesLike</em>) – Species.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Probability</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.pair_corr">
<span class="sig-name descname"><span class="pre">pair_corr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">s2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L134-L141"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.pair_corr" title="Link to this definition"></a></dt>
<dd><p>Pair correlation of two species.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>The pair correlation of 2 species</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.prob">
<span class="sig-name descname"><span class="pre">prob</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">s2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitution_probability.py#L110-L117"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.prob" title="Link to this definition"></a></dt>
<dd><p>Get the probability of 2 species substitution. Not used by the
structure predictor.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Probability of s1 and s2 substitution.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.structure_prediction.substitutor">
<span id="pymatgen-analysis-structure-prediction-substitutor-module"></span><h2>pymatgen.analysis.structure_prediction.substitutor module<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction.substitutor" title="Link to this heading"></a></h2>
<p>This module provides classes for predicting new structures from existing ones.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Substitutor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L34-L265"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>This object uses a data mined ionic substitution approach to propose
compounds likely to be stable. It relies on an algorithm presented in
Hautier, G., Fischer, C., Ehrlacher, V., Jain, A., and Ceder, G. (2011).
Data Mined Ionic Substitutions for the Discovery of New Compounds.
Inorganic Chemistry, 50(2), 656-663. doi:10.1021/ic102031h.</p>
<p>Use the substitution probability class to find good substitutions for a given chemistry or structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>threshold</strong> – probability threshold for predictions</p></li>
<li><p><strong>symprec</strong> – symmetry precision to determine if two structures
are duplicates</p></li>
<li><p><strong>kwargs</strong> – kwargs for the SubstitutionProbability object
lambda_table, alpha</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L243-L252"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.charge_balanced_tol">
<span class="sig-name descname"><span class="pre">charge_balanced_tol</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-09</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/analysis/structure_prediction/substitutor.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.charge_balanced_tol" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.from_dict">
<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L254-L265"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Class</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.get_allowed_species">
<span class="sig-name descname"><span class="pre">get_allowed_species</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L67-L71"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.get_allowed_species" title="Link to this definition"></a></dt>
<dd><p>Get the species in the domain of the probability function
any other specie will not work.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_comp">
<span class="sig-name descname"><span class="pre">pred_from_comp</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L226-L241"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_comp" title="Link to this definition"></a></dt>
<dd><p>Similar to pred_from_list except this method returns a list after
checking that compositions are charge balanced.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_list">
<span class="sig-name descname"><span class="pre">pred_from_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">species_list</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L173-L224"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_list" title="Link to this definition"></a></dt>
<dd><p>There are an exceptionally large number of substitutions to
look at (260^n), where n is the number of species in the
list. We need a more efficient than brute force way of going
through these possibilities. The brute force method would be:</p>
<blockquote>
<div><p>output = []
for p in itertools.product(self._sp.species_list, repeat=len(species_list)):</p>
<blockquote>
<div><dl class="simple">
<dt>if self._sp.conditional_probability_list(p, species_list) > self._threshold:</dt><dd><p>output.append(dict(zip(species_list, p)))</p>
</dd>
</dl>
</div></blockquote>
<p>return output</p>
</div></blockquote>
<p>Instead of that we do a branch and bound.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>species_list</strong> – list of species in the starting structure</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of dictionaries, each including a substitutions
dictionary, and a probability value</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_structures">
<span class="sig-name descname"><span class="pre">pred_from_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_species</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structures</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_duplicates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_existing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.alchemy.html#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">TransformedStructure</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/substitutor.py#L73-L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_structures" title="Link to this definition"></a></dt>
<dd><p>Performs a structure prediction targeting compounds containing all of
the target_species, based on a list of structure (those structures
can for instance come from a database like the ICSD). It will return
all the structures formed by ionic substitutions with a probability
higher than the threshold.</p>
<p class="rubric">Notes</p>
<p>If the default probability model is used, input structures must
be oxidation state decorated. See AutoOxiStateDecorationTransformation</p>
<p>This method does not change the number of species in a structure. i.e
if the number of target species is 3, only input structures containing
3 species will be considered.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target_species</strong> – a list of species with oxidation states
e.g. [Species(‘Li+’), Species(‘Ni2+’), Species(‘O-2’)]</p></li>
<li><p><strong>structures_list</strong> – list of dictionary of the form {‘structure’: Structure object, ‘id’: some id where it comes from}
The id can for instance refer to an ICSD id.</p></li>
<li><p><strong>remove_duplicates</strong> – if True, the duplicates in the predicted structures will
be removed</p></li>
<li><p><strong>remove_existing</strong> – if True, the predicted structures that already exist in the
structures_list will be removed</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a list of TransformedStructure objects.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.structure_prediction.volume_predictor">
<span id="pymatgen-analysis-structure-prediction-volume-predictor-module"></span><h2>pymatgen.analysis.structure_prediction.volume_predictor module<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction.volume_predictor" title="Link to this heading"></a></h2>
<p>Predict volumes of crystal structures.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DLSVolumePredictor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_scaling</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_scaling</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L132-L241"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Data-mined lattice scaling (DLS) scheme that relies on data-mined bond
lengths to predict the crystal volume of a given structure.</p>
<p>As of 2/12/19, we suggest this method be used in conjunction with
min_scaling and max_scaling to prevent instances of very large, unphysical
predicted volumes found in a small subset of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius added to site radius for finding
site pairs. Necessary to increase only if your initial
structure guess is extremely bad (atoms way too far apart). In
all other instances, increasing cutoff gives same answer
but takes more time.</p></li>
<li><p><strong>min_scaling</strong> (<em>float</em>) – if not None, this will ensure that the new
volume is at least this fraction of the original (preventing
too-small volumes)</p></li>
<li><p><strong>max_scaling</strong> (<em>float</em>) – if not None, this will ensure that the new
volume is at most this fraction of the original (preventing
too-large volumes).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.get_predicted_structure">
<span class="sig-name descname"><span class="pre">get_predicted_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">icsd_vol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L228-L241"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.get_predicted_structure" title="Link to this definition"></a></dt>
<dd><p>Given a structure, returns back the structure scaled to predicted
volume.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure w/unknown volume</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a Structure object with predicted volume</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">icsd_vol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L161-L226"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.predict" title="Link to this definition"></a></dt>
<dd><p>Given a structure, returns the predicted volume.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – a crystal structure with an unknown volume.</p></li>
<li><p><strong>icsd_vol</strong> (<em>bool</em>) – True if the input structure’s volume comes from ICSD.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a float value of the predicted volume.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">RLSVolumePredictor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">check_isostructural</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radii_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ionic-atomic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_bv</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L23-L129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Reference lattice scaling (RLS) scheme that predicts the volume of a
structure based on a known crystal structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>check_isostructural</strong> – Whether to test that the two structures are
isostructural. This algo works best for isostructural compounds.
Defaults to True.</p></li>
<li><p><strong>radii_type</strong> (<em>str</em>) – Types of radii to use. You can specify “ionic”
(only uses ionic radii), “atomic” (only uses atomic radii) or
“ionic-atomic” (uses either ionic or atomic radii, with a
preference for ionic where possible).</p></li>
<li><p><strong>use_bv</strong> (<em>bool</em>) – Whether to use BVAnalyzer to determine oxidation
states if not present.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.get_predicted_structure">
<span class="sig-name descname"><span class="pre">get_predicted_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L113-L129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.get_predicted_structure" title="Link to this definition"></a></dt>
<dd><p>Given a structure, returns back the structure scaled to predicted
volume.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure w/unknown volume</p></li>
<li><p><strong>ref_structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – A reference structure with a similar
structure but different species.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a Structure object with predicted volume</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../analysis/structure_prediction/volume_predictor.py#L46-L111"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.predict" title="Link to this definition"></a></dt>
<dd><p>Given a structure, returns the predicted volume.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure w/unknown volume</p></li>
<li><p><strong>ref_structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – A reference structure with a similar
structure but different species.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a float value of the predicted volume</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
</section>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>© Copyright 2011, Pymatgen Development Team.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
|
