forked from materialsproject/pymatgen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pymatgen.entries.compatibility.html
487 lines (457 loc) · 30.2 KB
/
pymatgen.entries.compatibility.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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>pymatgen.entries.compatibility 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.entries.compatibility">
<span id="pymatgen-entries-compatibility-module"></span><h1>pymatgen.entries.compatibility module<a class="headerlink" href="#module-pymatgen.entries.compatibility" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.entries.compatibility.AnionCorrection">
<em class="property">class </em><code class="descname">AnionCorrection</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#AnionCorrection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.AnionCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.AnionCorrection" title="pymatgen.entries.compatibility.AnionCorrection"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.AnionCorrection</span></code></a></p>
<p>Correct anion energies to obtain the right formation energies. Note that
this depends on calculations being run within the same input set.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>config_file</strong> – Path to the selected compatibility.yaml config file.</p></li>
<li><p><strong>correct_peroxide</strong> – Specify whether peroxide/superoxide/ozonide
corrections are to be applied or not.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.AqueousCorrection">
<em class="property">class </em><code class="descname">AqueousCorrection</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#AqueousCorrection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.AqueousCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.AqueousCorrection" title="pymatgen.entries.compatibility.AqueousCorrection"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.AqueousCorrection</span></code></a></p>
<p>This class implements aqueous phase compound corrections for elements
and H2O.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>config_file</strong> – Path to the selected compatibility.yaml config file.</p>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.Compatibility">
<em class="property">class </em><code class="descname">Compatibility</code><span class="sig-paren">(</span><em>corrections</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>The Compatibility class combines a list of corrections to be applied to
an entry or a set of entries. Note that some of the Corrections have
interdependencies. For example, PotcarCorrection must always be used
before any other compatibility. Also, GasCorrection(“MP”) must be used
with PotcarCorrection(“MP”) (similarly with “MIT”). Typically,
you should use the specific MaterialsProjectCompatibility and
MITCompatibility subclasses instead.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>corrections</strong> – List of corrections to apply.</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Compatibility.explain">
<code class="descname">explain</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility.explain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility.explain" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints an explanation of the corrections that are being applied for a
given compatibility scheme. Inspired by the “explain” methods in many
database methodologies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Compatibility.get_corrections_dict">
<code class="descname">get_corrections_dict</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility.get_corrections_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility.get_corrections_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the corrections applied to a particular entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>value})</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>({correction_name</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Compatibility.get_explanation_dict">
<code class="descname">get_explanation_dict</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility.get_explanation_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility.get_explanation_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Provides an explanation dict of the corrections that are being applied
for a given compatibility scheme. Inspired by the “explain” methods
in many database methodologies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(dict) of the form
{“Compatibility”: “string”,
“Uncorrected_energy”: float,
“Corrected_energy”: float,
“Corrections”: [{“Name of Correction”: {
“Value”: float, “Explanation”: “string”}]}</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Compatibility.process_entries">
<code class="descname">process_entries</code><span class="sig-paren">(</span><em>entries</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility.process_entries"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility.process_entries" title="Permalink to this definition">¶</a></dt>
<dd><p>Process a sequence of entries with the chosen Compatibility scheme.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entries</strong> – A sequence of entries.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>An list of adjusted entries. Entries in the original list which
are not compatible are excluded.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Compatibility.process_entry">
<code class="descname">process_entry</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Compatibility.process_entry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Compatibility.process_entry" title="Permalink to this definition">¶</a></dt>
<dd><p>Process a single entry with the chosen Corrections.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>An adjusted entry if entry is compatible, otherwise None is
returned.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.entries.compatibility.CompatibilityError">
<em class="property">exception </em><code class="descname">CompatibilityError</code><span class="sig-paren">(</span><em>msg</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#CompatibilityError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.CompatibilityError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Exception class for Compatibility. Raised by attempting correction
on incompatible calculation</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.Correction">
<em class="property">class </em><code class="descname">Correction</code><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Correction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Correction" title="Permalink 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>A Correction class is a pre-defined scheme for correction a computed
entry based on the type and chemistry of the structure and the
calculation parameters. All Correction classes must implement a
correct_entry method.</p>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Correction.correct_entry">
<code class="descname">correct_entry</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Correction.correct_entry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Correction.correct_entry" title="Permalink to this definition">¶</a></dt>
<dd><p>Corrects a single entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>An processed entry.</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>CompatibilityError if entry is not compatible.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.Correction.get_correction">
<code class="descname">get_correction</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#Correction.get_correction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.Correction.get_correction" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns correction for a single entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The energy correction to be applied.</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>CompatibilityError if entry is not compatible.</strong> – </p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.GasCorrection">
<em class="property">class </em><code class="descname">GasCorrection</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#GasCorrection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.GasCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.GasCorrection" title="pymatgen.entries.compatibility.GasCorrection"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.GasCorrection</span></code></a></p>
<p>Correct gas energies to obtain the right formation energies. Note that
this depends on calculations being run within the same input set.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>config_file</strong> – Path to the selected compatibility.yaml config file.</p>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.MITAqueousCompatibility">
<em class="property">class </em><code class="descname">MITAqueousCompatibility</code><span class="sig-paren">(</span><em>compat_type='Advanced'</em>, <em>correct_peroxide=True</em>, <em>check_potcar_hash=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#MITAqueousCompatibility"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.MITAqueousCompatibility" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.Compatibility" title="pymatgen.entries.compatibility.Compatibility"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.Compatibility</span></code></a></p>
<p>This class implements the GGA/GGA+U mixing scheme, which allows mixing of
entries. Note that this should only be used for VASP calculations using the
MIT parameters (see pymatgen.io.vaspio_set MITVaspInputSet). Using
this compatibility scheme on runs with different parameters is not valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>compat_type</strong> – Two options, GGA or Advanced. GGA means all GGA+U
entries are excluded. Advanced means mixing scheme is
implemented to make entries compatible with each other,
but entries which are supposed to be done in GGA+U will have the
equivalent GGA entries excluded. For example, Fe oxides should
have a U value under the Advanced scheme. A GGA Fe oxide run
will therefore be excluded under the scheme.</p></li>
<li><p><strong>correct_peroxide</strong> – Specify whether peroxide/superoxide/ozonide
corrections are to be applied or not.</p></li>
<li><p><strong>check_potcar_hash</strong> (<em>bool</em>) – Use potcar hash to verify potcars are correct.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.MITCompatibility">
<em class="property">class </em><code class="descname">MITCompatibility</code><span class="sig-paren">(</span><em>compat_type='Advanced'</em>, <em>correct_peroxide=True</em>, <em>check_potcar_hash=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#MITCompatibility"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.MITCompatibility" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.Compatibility" title="pymatgen.entries.compatibility.Compatibility"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.Compatibility</span></code></a></p>
<p>This class implements the GGA/GGA+U mixing scheme, which allows mixing of
entries. Note that this should only be used for VASP calculations using the
MIT parameters (see pymatgen.io.vaspio_set MITVaspInputSet). Using
this compatibility scheme on runs with different parameters is not valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>compat_type</strong> – Two options, GGA or Advanced. GGA means all GGA+U
entries are excluded. Advanced means mixing scheme is
implemented to make entries compatible with each other,
but entries which are supposed to be done in GGA+U will have the
equivalent GGA entries excluded. For example, Fe oxides should
have a U value under the Advanced scheme. A GGA Fe oxide run
will therefore be excluded under the scheme.</p></li>
<li><p><strong>correct_peroxide</strong> – Specify whether peroxide/superoxide/ozonide
corrections are to be applied or not.</p></li>
<li><p><strong>check_potcar_hash</strong> (<em>bool</em>) – Use potcar hash to verify potcars are correct.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.MaterialsProjectAqueousCompatibility">
<em class="property">class </em><code class="descname">MaterialsProjectAqueousCompatibility</code><span class="sig-paren">(</span><em>compat_type='Advanced'</em>, <em>correct_peroxide=True</em>, <em>check_potcar_hash=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#MaterialsProjectAqueousCompatibility"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.MaterialsProjectAqueousCompatibility" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.Compatibility" title="pymatgen.entries.compatibility.Compatibility"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.Compatibility</span></code></a></p>
<p>This class implements the GGA/GGA+U mixing scheme, which allows mixing of
entries. Note that this should only be used for VASP calculations using the
MaterialsProject parameters (see pymatgen.io.vaspio_set.MPVaspInputSet).
Using this compatibility scheme on runs with different parameters is not
valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>compat_type</strong> – Two options, GGA or Advanced. GGA means all GGA+U
entries are excluded. Advanced means mixing scheme is
implemented to make entries compatible with each other,
but entries which are supposed to be done in GGA+U will have the
equivalent GGA entries excluded. For example, Fe oxides should
have a U value under the Advanced scheme. A GGA Fe oxide run
will therefore be excluded under the scheme.</p></li>
<li><p><strong>correct_peroxide</strong> – Specify whether peroxide/superoxide/ozonide
corrections are to be applied or not.</p></li>
<li><p><strong>check_potcar_hash</strong> (<em>bool</em>) – Use potcar hash to verify potcars are correct.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.MaterialsProjectCompatibility">
<em class="property">class </em><code class="descname">MaterialsProjectCompatibility</code><span class="sig-paren">(</span><em>compat_type='Advanced'</em>, <em>correct_peroxide=True</em>, <em>check_potcar_hash=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#MaterialsProjectCompatibility"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.MaterialsProjectCompatibility" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.Compatibility" title="pymatgen.entries.compatibility.Compatibility"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.Compatibility</span></code></a></p>
<p>This class implements the GGA/GGA+U mixing scheme, which allows mixing of
entries. Note that this should only be used for VASP calculations using the
MaterialsProject parameters (see pymatgen.io.vaspio_set.MPVaspInputSet).
Using this compatibility scheme on runs with different parameters is not
valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>compat_type</strong> – Two options, GGA or Advanced. GGA means all GGA+U
entries are excluded. Advanced means mixing scheme is
implemented to make entries compatible with each other,
but entries which are supposed to be done in GGA+U will have the
equivalent GGA entries excluded. For example, Fe oxides should
have a U value under the Advanced scheme. A GGA Fe oxide run
will therefore be excluded under the scheme.</p></li>
<li><p><strong>correct_peroxide</strong> – Specify whether peroxide/superoxide/ozonide
corrections are to be applied or not.</p></li>
<li><p><strong>check_potcar_hash</strong> (<em>bool</em>) – Use potcar hash to verify potcars are correct.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.PotcarCorrection">
<em class="property">class </em><code class="descname">PotcarCorrection</code><span class="sig-paren">(</span><em>input_set</em>, <em>check_hash=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#PotcarCorrection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.PotcarCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.Correction" title="pymatgen.entries.compatibility.Correction"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.Correction</span></code></a></p>
<p>Checks that POTCARs are valid within a pre-defined input set. This
ensures that calculations performed using different InputSets are not
compared against each other.</p>
<p>Entry.parameters must contain a “potcar_symbols” key that is a list of
all POTCARs used in the run. Again, using the example of an Fe2O3 run
using Materials Project parameters, this would look like
entry.parameters[“potcar_symbols”] = [‘PAW_PBE Fe_pv 06Sep2000’,
‘PAW_PBE O 08Apr2002’].</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input_set</strong> – InputSet object used to generate the runs (used to check
for correct potcar symbols)</p></li>
<li><p><strong>check_hash</strong> (<em>bool</em>) – If true, uses the potcar hash to check for valid
potcars. If false, uses the potcar symbol (Less reliable).
Defaults to True</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>ValueError if entry do not contain "potcar_symbols" key.</strong> – </p></li>
<li><p><strong>CombatibilityError if wrong potcar symbols</strong> – </p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.entries.compatibility.PotcarCorrection.get_correction">
<code class="descname">get_correction</code><span class="sig-paren">(</span><em>entry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#PotcarCorrection.get_correction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.PotcarCorrection.get_correction" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns correction for a single entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A ComputedEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The energy correction to be applied.</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>CompatibilityError if entry is not compatible.</strong> – </p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.entries.compatibility.UCorrection">
<em class="property">class </em><code class="descname">UCorrection</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/entries/compatibility.html#UCorrection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.compatibility.UCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.entries.compatibility.UCorrection" title="pymatgen.entries.compatibility.UCorrection"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.entries.compatibility.UCorrection</span></code></a></p>
<p>This class implements the GGA/GGA+U mixing scheme, which allows mixing of
entries. Entry.parameters must contain a “hubbards” key which is a dict
of all non-zero Hubbard U values used in the calculation. For example,
if you ran a Fe2O3 calculation with Materials Project parameters,
this would look like entry.parameters[“hubbards”] = {“Fe”: 5.3}
If the “hubbards” key is missing, a GGA run is assumed.</p>
<p>It should be noted that ComputedEntries assimilated using the
pymatgen.apps.borg package and obtained via the MaterialsProject REST
interface using the pymatgen.matproj.rest package will automatically have
these fields populated.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>config_file</strong> – Path to the selected compatibility.yaml config file.</p></li>
<li><p><strong>input_set</strong> – InputSet object (to check for the +U settings)</p></li>
<li><p><strong>compat_type</strong> – Two options, GGA or Advanced. GGA means all GGA+U
entries are excluded. Advanced means mixing scheme is
implemented to make entries compatible with each other,
but entries which are supposed to be done in GGA+U will have the
equivalent GGA entries excluded. For example, Fe oxides should
have a U value under the Advanced scheme. A GGA Fe oxide run
will therefore be excluded under the scheme.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/pymatgen.entries.compatibility.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<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"
>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="footer" role="contentinfo">
© Copyright 2011, Pymatgen Development Team.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.0.1.
</div>
<div class="footer">This page uses <a href="http://analytics.google.com/">
Google Analytics</a> to collect statistics. You can disable it by blocking
the JavaScript coming from www.google-analytics.com.
<script type="text/javascript">
(function() {
var ga = document.createElement('script');
ga.src = ('https:' == document.location.protocol ?
'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
ga.setAttribute('async', 'true');
document.documentElement.firstChild.appendChild(ga);
})();
</script>
</div>
</body>
</html>