forked from materialsproject/pymatgen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pymatgen.io.abinit.abiinspect.html
569 lines (515 loc) · 35.1 KB
/
pymatgen.io.abinit.abiinspect.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>pymatgen.io.abinit.abiinspect 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.io.abinit.abiinspect">
<span id="pymatgen-io-abinit-abiinspect-module"></span><h1>pymatgen.io.abinit.abiinspect module<a class="headerlink" href="#module-pymatgen.io.abinit.abiinspect" title="Permalink to this headline">¶</a></h1>
<p>This module provides objects to inspect the status of the Abinit tasks at run-time.
by extracting information from the main output file (text format).</p>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.CyclesPlotter">
<em class="property">class </em><code class="descname">CyclesPlotter</code><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#CyclesPlotter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.CyclesPlotter" 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>Relies on the plot method of cycle objects to build multiple subfigures.</p>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.CyclesPlotter.add_label_cycle">
<code class="descname">add_label_cycle</code><span class="sig-paren">(</span><em>label</em>, <em>cycle</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#CyclesPlotter.add_label_cycle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.CyclesPlotter.add_label_cycle" title="Permalink to this definition">¶</a></dt>
<dd><p>Add new cycle to the plotter with label <cite>label</cite>.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.CyclesPlotter.combiplot">
<code class="descname">combiplot</code><span class="sig-paren">(</span><em>fontsize=8</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#CyclesPlotter.combiplot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.CyclesPlotter.combiplot" title="Permalink to this definition">¶</a></dt>
<dd><p>Compare multiple cycels on a grid: one subplot per quantity,
all cycles on the same subplot.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>fontsize</strong> – Legend fontsize.</p>
</dd>
</dl>
<p>Keyword arguments controlling the display of the figure:</p>
<table class="docutils align-center">
<colgroup>
<col style="width: 23%" />
<col style="width: 77%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>kwargs</p></th>
<th class="head"><p>Meaning</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>title</p></td>
<td><p>Title of the plot (Default: None).</p></td>
</tr>
<tr class="row-odd"><td><p>show</p></td>
<td><p>True to show the figure (default: True).</p></td>
</tr>
<tr class="row-even"><td><p>savefig</p></td>
<td><p>“abc.png” or “abc.eps” to save the figure to a file.</p></td>
</tr>
<tr class="row-odd"><td><p>size_kwargs</p></td>
<td><p>Dictionary with options passed to fig.set_size_inches
e.g. size_kwargs=dict(w=3, h=4)</p></td>
</tr>
<tr class="row-even"><td><p>tight_layout</p></td>
<td><p>True to call fig.tight_layout (default: False)</p></td>
</tr>
<tr class="row-odd"><td><p>ax_grid</p></td>
<td><p>True (False) to add (remove) grid from all axes in fig.
Default: None i.e. fig is left unchanged.</p></td>
</tr>
<tr class="row-even"><td><p>ax_annotate</p></td>
<td><p>Add labels to subplots e.g. (a), (b).
Default: False</p></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.CyclesPlotter.items">
<code class="descname">items</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#CyclesPlotter.items"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.CyclesPlotter.items" title="Permalink to this definition">¶</a></dt>
<dd><p>To iterate over (label, cycle).</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.CyclesPlotter.slideshow">
<code class="descname">slideshow</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#CyclesPlotter.slideshow"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.CyclesPlotter.slideshow" title="Permalink to this definition">¶</a></dt>
<dd><p>Produce slides show of the different cycles. One plot per cycle.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.D2DEScfCycle">
<em class="property">class </em><code class="descname">D2DEScfCycle</code><span class="sig-paren">(</span><em>fields</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#D2DEScfCycle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.D2DEScfCycle" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.ScfCycle" title="pymatgen.io.abinit.abiinspect.ScfCycle"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.io.abinit.abiinspect.ScfCycle</span></code></a></p>
<p>Result of the Phonon self-consistent cycle.</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.D2DEScfCycle.MAGIC">
<code class="descname">MAGIC</code><em class="property"> = 'iter 2DEtotal(Ha)'</em><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.D2DEScfCycle.MAGIC" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.D2DEScfCycle.last_etotal">
<code class="descname">last_etotal</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.D2DEScfCycle.last_etotal" title="Permalink to this definition">¶</a></dt>
<dd><p>The 2-nd order derivative of the energy at the last iteration.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.GroundStateScfCycle">
<em class="property">class </em><code class="descname">GroundStateScfCycle</code><span class="sig-paren">(</span><em>fields</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#GroundStateScfCycle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.GroundStateScfCycle" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.ScfCycle" title="pymatgen.io.abinit.abiinspect.ScfCycle"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.io.abinit.abiinspect.ScfCycle</span></code></a></p>
<p>Result of the Ground State self-consistent cycle.</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.GroundStateScfCycle.MAGIC">
<code class="descname">MAGIC</code><em class="property"> = 'iter Etot(hartree)'</em><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.GroundStateScfCycle.MAGIC" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.GroundStateScfCycle.last_etotal">
<code class="descname">last_etotal</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.GroundStateScfCycle.last_etotal" title="Permalink to this definition">¶</a></dt>
<dd><p>The total energy at the last iteration.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.PhononScfCycle">
<em class="property">class </em><code class="descname">PhononScfCycle</code><span class="sig-paren">(</span><em>fields</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#PhononScfCycle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.PhononScfCycle" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.D2DEScfCycle" title="pymatgen.io.abinit.abiinspect.D2DEScfCycle"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.io.abinit.abiinspect.D2DEScfCycle</span></code></a></p>
<p>Iterations of the DFPT SCF cycle for phonons.</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation">
<em class="property">class </em><code class="descname">Relaxation</code><span class="sig-paren">(</span><em>cycles</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">collections.abc.Iterable</span></code></p>
<p>A list of <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.GroundStateScfCycle" title="pymatgen.io.abinit.abiinspect.GroundStateScfCycle"><code class="xref py py-class docutils literal notranslate"><span class="pre">GroundStateScfCycle</span></code></a> objects.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Forces, stresses and crystal structures are missing.
This object is mainly used to analyze the behavior of the Scf cycles
during the structural relaxation. A more powerful and detailed analysis
can be obtained by using the HIST.nc file.</p>
</div>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.from_file">
<em class="property">classmethod </em><code class="descname">from_file</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Initialize the object from the Abinit main output file.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.from_stream">
<em class="property">classmethod </em><code class="descname">from_stream</code><span class="sig-paren">(</span><em>stream</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.from_stream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.from_stream" title="Permalink to this definition">¶</a></dt>
<dd><p>Extract data from stream. Returns None if some error occurred.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.history">
<code class="descname">history</code><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.history"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.history" title="Permalink to this definition">¶</a></dt>
<dd><p>Ordered Dictionary of lists with the evolution of
the data as function of the relaxation step.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.plot">
<code class="descname">plot</code><span class="sig-paren">(</span><em>ax_list=None</em>, <em>fontsize=12</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot relaxation history i.e. the results of the last iteration of each SCF cycle.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ax_list</strong> – List of axes. If None a new figure is produced.</p></li>
<li><p><strong>fontsize</strong> – legend fontsize.</p></li>
<li><p><strong>kwargs</strong> – keyword arguments are passed to ax.plot</p></li>
</ul>
</dd>
</dl>
<p>Returns: matplotlib figure</p>
<p>Keyword arguments controlling the display of the figure:</p>
<table class="docutils align-center">
<colgroup>
<col style="width: 23%" />
<col style="width: 77%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>kwargs</p></th>
<th class="head"><p>Meaning</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>title</p></td>
<td><p>Title of the plot (Default: None).</p></td>
</tr>
<tr class="row-odd"><td><p>show</p></td>
<td><p>True to show the figure (default: True).</p></td>
</tr>
<tr class="row-even"><td><p>savefig</p></td>
<td><p>“abc.png” or “abc.eps” to save the figure to a file.</p></td>
</tr>
<tr class="row-odd"><td><p>size_kwargs</p></td>
<td><p>Dictionary with options passed to fig.set_size_inches
e.g. size_kwargs=dict(w=3, h=4)</p></td>
</tr>
<tr class="row-even"><td><p>tight_layout</p></td>
<td><p>True to call fig.tight_layout (default: False)</p></td>
</tr>
<tr class="row-odd"><td><p>ax_grid</p></td>
<td><p>True (False) to add (remove) grid from all axes in fig.
Default: None i.e. fig is left unchanged.</p></td>
</tr>
<tr class="row-even"><td><p>ax_annotate</p></td>
<td><p>Add labels to subplots e.g. (a), (b).
Default: False</p></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.slideshow">
<code class="descname">slideshow</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.slideshow"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.slideshow" title="Permalink to this definition">¶</a></dt>
<dd><p>Uses matplotlib to plot the evolution of the structural relaxation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>ax_list</strong> – List of axes. If None a new figure is produced.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><cite>matplotlib</cite> figure</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.Relaxation.to_string">
<code class="descname">to_string</code><span class="sig-paren">(</span><em>verbose=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#Relaxation.to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.Relaxation.to_string" title="Permalink to this definition">¶</a></dt>
<dd><p>String representation.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle">
<em class="property">class </em><code class="descname">ScfCycle</code><span class="sig-paren">(</span><em>fields</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#ScfCycle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">collections.abc.Mapping</span></code></p>
<p>It essentially consists of a dictionary mapping string
to list of floats containing the data at the different iterations.</p>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle.from_file">
<em class="property">classmethod </em><code class="descname">from_file</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#ScfCycle.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the first occurrence of ScfCycle from file.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle.from_stream">
<em class="property">classmethod </em><code class="descname">from_stream</code><span class="sig-paren">(</span><em>stream</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#ScfCycle.from_stream"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle.from_stream" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the first occurrence of ScfCycle from stream.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>None if no <cite>ScfCycle</cite> entry is found.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle.last_iteration">
<code class="descname">last_iteration</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle.last_iteration" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a dictionary with the values of the last iteration.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle.plot">
<code class="descname">plot</code><span class="sig-paren">(</span><em>ax_list=None</em>, <em>fontsize=12</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#ScfCycle.plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle.plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Uses matplotlib to plot the evolution of the SCF cycle.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ax_list</strong> – List of axes. If None a new figure is produced.</p></li>
<li><p><strong>fontsize</strong> – legend fontsize.</p></li>
<li><p><strong>kwargs</strong> – keyword arguments are passed to ax.plot</p></li>
</ul>
</dd>
</dl>
<p>Returns: matplotlib figure</p>
<p>Keyword arguments controlling the display of the figure:</p>
<table class="docutils align-center">
<colgroup>
<col style="width: 23%" />
<col style="width: 77%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>kwargs</p></th>
<th class="head"><p>Meaning</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>title</p></td>
<td><p>Title of the plot (Default: None).</p></td>
</tr>
<tr class="row-odd"><td><p>show</p></td>
<td><p>True to show the figure (default: True).</p></td>
</tr>
<tr class="row-even"><td><p>savefig</p></td>
<td><p>“abc.png” or “abc.eps” to save the figure to a file.</p></td>
</tr>
<tr class="row-odd"><td><p>size_kwargs</p></td>
<td><p>Dictionary with options passed to fig.set_size_inches
e.g. size_kwargs=dict(w=3, h=4)</p></td>
</tr>
<tr class="row-even"><td><p>tight_layout</p></td>
<td><p>True to call fig.tight_layout (default: False)</p></td>
</tr>
<tr class="row-odd"><td><p>ax_grid</p></td>
<td><p>True (False) to add (remove) grid from all axes in fig.
Default: None i.e. fig is left unchanged.</p></td>
</tr>
<tr class="row-even"><td><p>ax_annotate</p></td>
<td><p>Add labels to subplots e.g. (a), (b).
Default: False</p></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.ScfCycle.to_string">
<code class="descname">to_string</code><span class="sig-paren">(</span><em>verbose=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#ScfCycle.to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.ScfCycle.to_string" title="Permalink to this definition">¶</a></dt>
<dd><p>String representation.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc">
<em class="property">class </em><code class="descname">YamlDoc</code><span class="sig-paren">(</span><em>text</em>, <em>lineno</em>, <em>tag=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlDoc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc" 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>Handy object that stores that YAML document, its main tag and the
position inside the file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>text</strong> – String with the YAML document.</p></li>
<li><p><strong>lineno</strong> – The line number where the document is located.</p></li>
<li><p><strong>tag</strong> – The YAML tag associate to the document.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlDoc.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Use Yaml to parse the text (without the tag) and returns a dictionary.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc.lineno">
<code class="descname">lineno</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc.lineno" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc.tag">
<code class="descname">tag</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc.tag" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc.text">
<code class="descname">text</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc.text" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.YamlDoc.text_notag">
<code class="descname">text_notag</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlDoc.text_notag" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the YAML text without the tag.
Useful if we don’t have any constructor registered for the tag
(we used the tag just to locate the document).</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer">
<em class="property">class </em><code class="descname">YamlTokenizer</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">collections.abc.Iterator</span></code></p>
<p>Provides context-manager support so you can use it in a with statement.</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.Error">
<code class="descname">Error</code><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.Error" title="Permalink to this definition">¶</a></dt>
<dd><p>alias of <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.YamlTokenizerError" title="pymatgen.io.abinit.abiinspect.YamlTokenizerError"><code class="xref py py-class docutils literal notranslate"><span class="pre">YamlTokenizerError</span></code></a></p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.all_docs_with_tag">
<code class="descname">all_docs_with_tag</code><span class="sig-paren">(</span><em>doc_tag</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.all_docs_with_tag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.all_docs_with_tag" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns all the documents with the specified tag.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.all_yaml_docs">
<code class="descname">all_yaml_docs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.all_yaml_docs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.all_yaml_docs" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a list with all the YAML docs found in stream.
Seek the stream before returning.</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Assume that all the YAML docs (with the exception of the last one)
are closed explicitely with the sentinel ‘…’</p>
</div>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.close">
<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.close" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.next">
<code class="descname">next</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.next"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.next" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the first YAML document in stream.</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Assume that the YAML document are closed explicitely with the sentinel ‘…’</p>
</div>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.next_doc_with_tag">
<code class="descname">next_doc_with_tag</code><span class="sig-paren">(</span><em>doc_tag</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.next_doc_with_tag"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.next_doc_with_tag" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the next document with the specified tag. Empty string is no doc is found.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizer.seek">
<code class="descname">seek</code><span class="sig-paren">(</span><em>offset</em><span class="optional">[</span>, <em>whence</em><span class="optional">]</span><span class="sig-paren">)</span> → None. Move to new file position.<a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizer.seek"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer.seek" title="Permalink to this definition">¶</a></dt>
<dd><p>Argument offset is a byte count. Optional argument whence defaults to
0 (offset from start of file, offset should be >= 0); other values are 1
(move relative to current position, positive or negative), and 2 (move
relative to end of file, usually negative, although many platforms allow
seeking beyond the end of a file). If the file is opened in text mode,
only offsets returned by tell() are legal. Use of other offsets causes
undefined behavior.
Note that not all file objects are seekable.</p>
</dd></dl>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.io.abinit.abiinspect.YamlTokenizerError">
<em class="property">exception </em><code class="descname">YamlTokenizerError</code><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#YamlTokenizerError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.YamlTokenizerError" 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>Exceptions raised by <a class="reference internal" href="#pymatgen.io.abinit.abiinspect.YamlTokenizer" title="pymatgen.io.abinit.abiinspect.YamlTokenizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">YamlTokenizer</span></code></a>.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.abiinspect.plottable_from_outfile">
<code class="descname">plottable_from_outfile</code><span class="sig-paren">(</span><em>filepath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#plottable_from_outfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.plottable_from_outfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Factory function that returns a plottable object by inspecting the main output file of abinit
Returns None if it is not able to detect the class to instantiate.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.abiinspect.straceback">
<code class="descname">straceback</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#straceback"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.straceback" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a string with the traceback.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.abiinspect.yaml_read_irred_perts">
<code class="descname">yaml_read_irred_perts</code><span class="sig-paren">(</span><em>filename</em>, <em>doc_tag='!IrredPerts'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#yaml_read_irred_perts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.yaml_read_irred_perts" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the list of irreducible perturbations from file.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.abinit.abiinspect.yaml_read_kpoints">
<code class="descname">yaml_read_kpoints</code><span class="sig-paren">(</span><em>filename</em>, <em>doc_tag='!Kpoints'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/abiinspect.html#yaml_read_kpoints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.abiinspect.yaml_read_kpoints" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the K-points from file.</p>
</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.io.abinit.abiinspect.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>