-
Notifications
You must be signed in to change notification settings - Fork 836
/
pymatgen.io.lammps.inputs.html
680 lines (633 loc) · 63.4 KB
/
pymatgen.io.lammps.inputs.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.io.lammps.inputs module — pymatgen 2023.5.10 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="canonical" href="https://pymatgen.orgpymatgen.io.lammps.inputs.html"/>
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="pymatgen.io.lammps.outputs module" href="pymatgen.io.lammps.outputs.html" />
<link rel="prev" title="pymatgen.io.lammps.generators module" href="pymatgen.io.lammps.generators.html" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.1/jquery.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33990148-1']);
_gaq.push(['_trackPageview']);
</script>
</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 class="version">
2023.5.10
</div>
<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">
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="change_log.html">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="compatibility.html">Compatibility</a></li>
<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="team.html">Development Team</a></li>
<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">API Docs</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="pymatgen.html">pymatgen namespace</a><ul class="current">
<li class="toctree-l3 current"><a class="reference internal" href="pymatgen.html#subpackages">Subpackages</a><ul class="current">
<li class="toctree-l4"><a class="reference internal" href="pymatgen.alchemy.html">pymatgen.alchemy package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.html">pymatgen.analysis namespace</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.apps.html">pymatgen.apps package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.cli.html">pymatgen.cli package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.command_line.html">pymatgen.command_line package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.core.html">pymatgen.core package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.electronic_structure.html">pymatgen.electronic_structure package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.entries.html">pymatgen.entries package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.ext.html">pymatgen.ext namespace</a></li>
<li class="toctree-l4 current"><a class="reference internal" href="pymatgen.io.html">pymatgen.io namespace</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.optimization.html">pymatgen.optimization package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.phonon.html">pymatgen.phonon package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.symmetry.html">pymatgen.symmetry package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.transformations.html">pymatgen.transformations package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.util.html">pymatgen.util package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.vis.html">pymatgen.vis package</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.html#submodules">Submodules</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</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"><a href="modules.html">pymatgen</a></li>
<li class="breadcrumb-item"><a href="pymatgen.html">pymatgen namespace</a></li>
<li class="breadcrumb-item"><a href="pymatgen.io.html">pymatgen.io namespace</a></li>
<li class="breadcrumb-item"><a href="pymatgen.io.lammps.html">pymatgen.io.lammps package</a></li>
<li class="breadcrumb-item active">pymatgen.io.lammps.inputs module</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.io.lammps.inputs.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.io.lammps.inputs">
<span id="pymatgen-io-lammps-inputs-module"></span><h1>pymatgen.io.lammps.inputs module<a class="headerlink" href="#module-pymatgen.io.lammps.inputs" title="Permalink to this heading"></a></h1>
<p>This module implements methods for reading/manupilating/writing LAMMPS input files.
It does not implement methods for automatically creating inputs based on a structure
and computation type. For this, see the InputSet and InputGenerator in sets.py, or
<a class="reference external" href="https://github.com/Matgenix/atomate2-lammps">https://github.com/Matgenix/atomate2-lammps</a></p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LammpsInputFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L35-L840"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.io.core.html#pymatgen.io.core.InputFile" title="pymatgen.io.core.InputFile"><code class="xref py py-class docutils literal notranslate"><span class="pre">InputFile</span></code></a></p>
<p>Class representing a LAMMPS input settings file, e.g. in.lammps.
Allows for LAMMPS input generation in line/stage wise manner. A stage
here is defined as a block of LAMMPS input commands usually performing a
specific task during the simulation such as energy minimization or
NPT/NVT runs. But more broadly, a stage can also be a block of LAMMPS
input where the simulation box is set up, a set of variables are declared or
quantities are computed.</p>
<p>The LammpsInputFile is defined by the attribute <cite>stages</cite>,
i.e. a list of dicts each with keys <cite>stage_name</cite> and <cite>commands</cite>,
defining the stage names and the corresponding LAMMPS input settings (list of tuples of two strings each).
The structure is the following:
<a href="#id1"><span class="problematic" id="id2">``</span></a>`
stages = [</p>
<blockquote>
<div><p>{“stage_name”: “Stage 1”, “commands”: [(cmd1, args1), (cmd2, args2)]},
{“stage_name”: “Stage 2”, “commands”: [(cmd3, args3)]}</p>
</div></blockquote>
<section id="id3">
<h2>]<a class="headerlink" href="#id3" title="Permalink to this heading"></a></h2>
<p>where cmd’s are the LAMMPS command names (e.g., “units”, or “pair_coeff”)
and the args are the corresponding arguments.
“Stage 1” and “Stage 2” are examples of stage names.</p>
<dl class="field-list simple">
<dt class="field-odd">param stages<span class="colon">:</span></dt>
<dd class="field-odd"><p>list of LAMMPS input settings.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.add_commands">
<span class="sig-name descname"><span class="pre">add_commands</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">commands</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L350-L403"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.add_commands" title="Permalink to this definition"></a></dt>
<dd><p>Method to add a LAMMPS commands and their arguments to a stage of
the LammpsInputFile. The stage name should be provided: a default behavior
is avoided here to avoid mistakes (e.g., the commands are added to the wrong stage).</p>
<p class="rubric">Example</p>
<p>In order to add the command <code class="docutils literal notranslate"><span class="pre">pair_coeff</span> <span class="pre">1</span> <span class="pre">1</span> <span class="pre">morse</span> <span class="pre">0.0580</span> <span class="pre">3.987</span> <span class="pre">3.404</span></code>
to the stage “Definition of the potential”, simply use
<a href="#id4"><span class="problematic" id="id5">``</span></a>`
your_input_file.add_commands(</p>
<blockquote>
<div><p>stage_name=”Definition of the potential”,
commands=”pair_coeff 1 1 morse 0.0580 3.987 3.404”</p>
</div></blockquote>
<section id="id6">
<h3>)<a class="headerlink" href="#id6" title="Permalink to this heading"></a></h3>
<p>To add multiple commands, use a dict or a list, e.g.,
<a href="#id7"><span class="problematic" id="id8">``</span></a>`
your_input_file.add_commands(</p>
<blockquote>
<div><p>stage_name=”Definition of the potential”,
commands=[“pair_coeff 1 1 morse 0.0580 3.987 3.404”, “units atomic”]</p>
</div></blockquote>
<p>)
your_input_file.add_commands(</p>
<blockquote>
<div><p>stage_name=”Definition of the potential”,
commands={“pair_coeff”: “1 1 morse 0.0580 3.987 3.404”, “units”: “atomic”}</p>
</div></blockquote>
</section>
<section id="id9">
<h3>)<a class="headerlink" href="#id9" title="Permalink to this heading"></a></h3>
<dl class="field-list simple">
<dt class="field-odd">param stage_name<span class="colon">:</span></dt>
<dd class="field-odd"><p>name of the stage to which the command should be added.</p>
</dd>
<dt class="field-even">type stage_name<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
<dt class="field-odd">param commands<span class="colon">:</span></dt>
<dd class="field-odd"><p>LAMMPS command, with or without the arguments.</p>
</dd>
<dt class="field-even">type commands<span class="colon">:</span></dt>
<dd class="field-even"><p>str or list or dict</p>
</dd>
</dl>
</section>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.add_stage">
<span class="sig-name descname"><span class="pre">add_stage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">commands</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">after_stage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L184-L281"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.add_stage" title="Permalink to this definition"></a></dt>
<dd><p>Adds a new stage to the LammpsInputFile, either from a whole stage (dict) or
from a stage_name and commands. Both ways are mutually exclusive.</p>
<p class="rubric">Examples</p>
<p>1) In order to add a stage defining the force field to be used, you can use:
<a href="#id10"><span class="problematic" id="id11">``</span></a>`
your_input_file.add_stage(</p>
<blockquote>
<div><p>commands=[“pair_coeff 1 1 morse 0.0580 3.987 3.404”, “pair_coeff 1 4 morse 0.0408 1.399 3.204”],
stage_name=”Definition of the force field”</p>
</div></blockquote>
<section id="id12">
<h3>)<a class="headerlink" href="#id12" title="Permalink to this heading"></a></h3>
</section>
<section id="or">
<h3>or<a class="headerlink" href="#or" title="Permalink to this heading"></a></h3>
<dl>
<dt>your_input_file.add_stage(</dt><dd><dl>
<dt>{</dt><dd><p>“stage_name”: “Definition of the force field”,
“commands”: [</p>
<blockquote>
<div><p>(“pair_coeff”, “1 1 morse 0.0580 3.987 3.404”),
(“pair_coeff”, “1 4 morse 0.0408 1.399 3.204”)</p>
</div></blockquote>
<p>],</p>
</dd>
</dl>
<p>}</p>
</dd>
</dl>
</section>
<section id="id13">
<h3>)<a class="headerlink" href="#id13" title="Permalink to this heading"></a></h3>
<p>2) Another stage could consist in an energy minimization. In that case, the commands could look like
<a href="#id14"><span class="problematic" id="id15">``</span></a>`
commands = [</p>
<blockquote>
<div><p>“thermo 1”,
“thermo_style custom step lx ly lz press pxx pyy pzz pe”,
“dump dmp all atom 5 run.dump”,
“min_style cg”,
“fix 1 all box/relax iso 0.0 vmax 0.001”,
“minimize 1.0e-16 1.0e-16 5000 10000”,
“write_data run.data”</p>
</div></blockquote>
</section>
<section id="id16">
<h3>]<a class="headerlink" href="#id16" title="Permalink to this heading"></a></h3>
<p>or a dictionary such as <cite>{“thermo”: 1, …}</cite>, or a string with a single command (e.g., “units atomic”).</p>
<dl class="field-list simple">
<dt class="field-odd">param stage<span class="colon">:</span></dt>
<dd class="field-odd"><p>if provided, this is the stage that will be added to the LammpsInputFile.stages</p>
</dd>
<dt class="field-even">type stage<span class="colon">:</span></dt>
<dd class="field-even"><p>dict</p>
</dd>
<dt class="field-odd">param commands<span class="colon">:</span></dt>
<dd class="field-odd"><p>if provided, these are the LAMMPS command(s)
that will be included in the stage to add.
Can pass a list of LAMMPS commands with their arguments.
Also accepts a dictionary of LAMMPS commands and
corresponding arguments as key, value pairs.
A single string can also be passed (single command together with its arguments).
Not used in case a whole stage is given.</p>
</dd>
<dt class="field-even">type commands<span class="colon">:</span></dt>
<dd class="field-even"><p>str or list or dict</p>
</dd>
<dt class="field-odd">param stage_name<span class="colon">:</span></dt>
<dd class="field-odd"><p>If a stage name is mentioned, the commands are added
under that stage block, else the new stage is named from numbering.
If given, stage_name cannot be one of the already present stage names.
Not used in case a whole stage is given.</p>
</dd>
<dt class="field-even">type stage_name<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
<dt class="field-odd">param after_stage<span class="colon">:</span></dt>
<dd class="field-odd"><p>Name of the stage after which this stage should be added.
If None, the stage is added at the end of the LammpsInputFile.</p>
</dd>
<dt class="field-even">type after_stage<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
</dl>
</section>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.append">
<span class="sig-name descname"><span class="pre">append</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lmp_input_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.io.lammps.inputs.LammpsInputFile" title="pymatgen.io.lammps.inputs.LammpsInputFile"><span class="pre">LammpsInputFile</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L445-L471"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.append" title="Permalink to this definition"></a></dt>
<dd><p>Appends a LammpsInputFile to another. The <cite>stages</cite> are merged,
and the numbering of stages/comments is either kept the same or updated.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>lmp_input_file</strong> (<a class="reference internal" href="#pymatgen.io.lammps.inputs.LammpsInputFile" title="pymatgen.io.lammps.inputs.LammpsInputFile"><em>LammpsInputFile</em></a>) – LammpsInputFile to append.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.contains_command">
<span class="sig-name descname"><span class="pre">contains_command</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">command</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</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">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L128-L140"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.contains_command" title="Permalink to this definition"></a></dt>
<dd><p>Returns whether a given command is present in the LammpsInputFile.
A stage name can be given; in this case the search will happen only for this stage.</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>command</strong> (<em>str</em>) – String with the command to find in the input file (e.g., “units”).</p></li>
<li><p><strong>stage_name</strong> (<em>str</em>) – String giving the stage name where the change should take place.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if the command is present, False if not.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.from_file">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.io.lammps.inputs.LammpsInputFile" title="pymatgen.io.lammps.inputs.LammpsInputFile"><span class="pre">LammpsInputFile</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L604-L620"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.from_file" title="Permalink to this definition"></a></dt>
<dd><p>Creates an InputFile object from a file.</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>path</strong> (<em>str</em><em> or </em><em>path</em>) – Filename to read, including path.</p></li>
<li><p><strong>ignore_comments</strong> (<em>bool</em>) – True if only the commands should be kept from the input file.</p></li>
<li><p><strong>keep_stages</strong> (<em>bool</em>) – True if the block structure from the input file should be kept.
If False, a single block is assumed.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>LammpsInputFile</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.from_string">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contents</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.io.lammps.inputs.LammpsInputFile" title="pymatgen.io.lammps.inputs.LammpsInputFile"><span class="pre">LammpsInputFile</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L524-L602"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.from_string" title="Permalink to this definition"></a></dt>
<dd><p>Helper method to parse string representation of LammpsInputFile.
If you created the input file by hand, there is no guarantee that the representation
will be perfect as it is difficult to account for all the cosmetic changes you
could have done on your input script. Always check that you have what you want !
By default, a single stage containing all the input settings is created.
If the block structure of your input file should be kept and stored as
different stages, set keep_stages to True.</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>contents</strong> (<em>str</em>) – String representation of LammpsInputFile.</p></li>
<li><p><strong>ignore_comments</strong> (<em>bool</em>) – True if only the commands should be kept from the input file.</p></li>
<li><p><strong>keep_stages</strong> (<em>bool</em>) – True if the block structure from the input file should be kept.
If False, a single block is assumed.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>LammpsInputFile</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.get_args">
<span class="sig-name descname"><span class="pre">get_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">command</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</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="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L102-L126"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.get_args" title="Permalink to this definition"></a></dt>
<dd><p>Given a command, returns the corresponding arguments (or list of arguments) in the LammpsInputFile.
A stage name can be given; in this case the search will happen only for this stage.
If a stage name is not given, the command will be searched for through all of them.
If the command is not found, an empty list is returned.</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>command</strong> (<em>str</em>) – String with the command to find in the input file (e.g., “units”).</p></li>
<li><p><strong>stage_name</strong> (<em>str</em>) – String giving the stage name where the change should take place.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Value of the argument corresponding to the command.
List if the same command is used multiple times.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.get_string">
<span class="sig-name descname"><span class="pre">get_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ignore_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</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">str</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L473-L508"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.get_string" title="Permalink to this definition"></a></dt>
<dd><p>Generates and ² the string representation of the LammpsInputFile.
Stages are separated by empty lines.
The headers of the stages will be put in comments preceding each stage.
Other comments will be put inline within stages, where they have been added.</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>ignore_comments</strong> (<em>bool</em>) – True if only the commands should be kept from the InputFile.</p></li>
<li><p><strong>keep_stages</strong> (<em>bool</em>) – If True, the string is formatted in a block structure with stage names
and newlines that differentiate commands in the respective stages of the InputFile.
If False, stage names are not printed and all commands appear in a single block.</p></li>
</ul>
</dd>
</dl>
<p>Returns: String representation of the LammpsInputFile.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.merge_stages">
<span class="sig-name descname"><span class="pre">merge_stages</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stage_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L314-L348"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.merge_stages" title="Permalink to this definition"></a></dt>
<dd><p>Merges multiple stages of a LammpsInputFile together.
The merged stage will be at the same index as the first of the stages to be merged.
The others will appear in the same order as provided in the list. Other non-merged stages will follow.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>stage_names</strong> (<em>list</em>) – list of strings giving the names of the stages to be merged.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.ncomments">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ncomments</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">int</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/lammps/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.ncomments" title="Permalink to this definition"></a></dt>
<dd><p>Returns the number of comments in the current LammpsInputFile. Includes the blocks of comments as well
as inline comments (comment lines within blocks of LAMMPS commands).</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.nstages">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">nstages</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">int</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/lammps/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.nstages" title="Permalink to this definition"></a></dt>
<dd><p>Returns the number of stages in the current LammpsInputFile.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.remove_command">
<span class="sig-name descname"><span class="pre">remove_command</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">command</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_empty_stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L405-L443"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.remove_command" title="Permalink to this definition"></a></dt>
<dd><p>Removes a given command from a given stage. If no stage is given, removes all occurrences of the command.
In case removing a command completely empties a stage, the choice whether to keep this stage in the
LammpsInputFile is given by remove_empty_stages.</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>command</strong> (<em>str</em>) – command to be removed.</p></li>
<li><p><strong>stage_name</strong> (<em>str</em><em> or </em><em>list</em>) – names of the stages where the command should be removed.</p></li>
<li><p><strong>remove_empty_stages</strong> (<em>bool</em>) – whether to remove the stages emptied by removing the command or not.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.remove_stage">
<span class="sig-name descname"><span class="pre">remove_stage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L283-L294"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.remove_stage" title="Permalink to this definition"></a></dt>
<dd><p>Removes a whole stage from the LammpsInputFile.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>stage_name</strong> (<em>str</em>) – name of the stage to remove.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.rename_stage">
<span class="sig-name descname"><span class="pre">rename_stage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L296-L312"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.rename_stage" title="Permalink to this definition"></a></dt>
<dd><p>Renames a stage <cite>stage_name</cite> from LammpsInputFile into <cite>new_name</cite>.
First checks that the stage to rename is present, and that
the new name is not already a stage name.</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>stage_name</strong> (<em>str</em>) – name of the stage to rename.</p></li>
<li><p><strong>new_name</strong> (<em>str</em>) – new name of the stage.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.set_args">
<span class="sig-name descname"><span class="pre">set_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">command</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">argument</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">how</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></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">'all'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L142-L182"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.set_args" title="Permalink to this definition"></a></dt>
<dd><p>Sets the arguments for the given command to the given string.
If the command is not found, nothing is done. Use LammpsInputFile.add_commands instead.
If a stage name is specified, it will be replaced or set only for this stage.
If no stage name is given, it will apply the change in all of them that contain the given command.
If the command is set multiple times in the file/stage, it will be replaced based on “how”:
either the first occurrence, all of them, or the index of the occurrence.</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>command</strong> (<em>str</em>) – String representing the command to change, e.g., “units”.</p></li>
<li><p><strong>argument</strong> (<em>str</em>) – String with the new value for the command, e.g., “atomic”.</p></li>
<li><p><strong>stage_name</strong> (<em>str</em>) – String giving the stage name where the change should take place.</p></li>
<li><p><strong>how</strong> (<em>str</em><em> or </em><em>int</em><em> or </em><em>list</em>) – “all” for changing all occurrences of the command within the stage_name
or the whole InputFile, “first” for the first occurrence, int i for the i-th time the command
is present in the stage_name or the whole InputFile, starting at 0. Can be a list of indexes as well.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.stages_names">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">stages_names</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/lammps/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.stages_names" title="Permalink to this definition"></a></dt>
<dd><p>List of names for all the stages present in <cite>stages</cite>.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsInputFile.write_file">
<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_comments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_stages</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L510-L522"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsInputFile.write_file" title="Permalink to this definition"></a></dt>
<dd><p>Writes the input file.</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>filename</strong> (<em>str</em><em> or </em><em>path</em>) – The filename to output to, including path.</p></li>
<li><p><strong>ignore_comments</strong> (<em>bool</em>) – True if only the commands should be kept from the InputFile.</p></li>
<li><p><strong>keep_stages</strong> (<em>bool</em>) – True if the block structure from the InputFile should be kept.
If False, a single block is assumed.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsRun">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LammpsRun</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">script_template</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">settings</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">script_filename</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L843-L918"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsRun" title="Permalink 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>Examples for various simple LAMMPS runs with given simulation box,
force field and a few more settings. Experienced LAMMPS users should
consider using write_lammps_inputs method with more sophisticated
templates.</p>
<p>Base constructor.</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>script_template</strong> (<em>str</em>) – String template for input script
with placeholders. The format for placeholders has to
be ‘$variable_name’, e.g., ‘$temperature’</p></li>
<li><p><strong>settings</strong> (<em>dict</em>) – Contains values to be written to the
placeholders, e.g., {‘temperature’: 1}.</p></li>
<li><p><strong>data</strong> (<a class="reference internal" href="pymatgen.io.lammps.data.html#pymatgen.io.lammps.data.LammpsData" title="pymatgen.io.lammps.data.LammpsData"><em>LammpsData</em></a><em> or </em><em>str</em>) – Data file as a LammpsData
instance or path to an existing data file. Default to
None, i.e., no data file supplied. Useful only when
read_data cmd is in the script.</p></li>
<li><p><strong>script_filename</strong> (<em>str</em>) – Filename for the input script.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsRun.md">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">md</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_field</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nsteps</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">other_settings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L892-L918"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsRun.md" title="Permalink to this definition"></a></dt>
<dd><p>Example for a simple MD run based on template md.template.</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>data</strong> (<a class="reference internal" href="pymatgen.io.lammps.data.html#pymatgen.io.lammps.data.LammpsData" title="pymatgen.io.lammps.data.LammpsData"><em>LammpsData</em></a><em> or </em><em>str</em>) – Data file as a LammpsData
instance or path to an existing data file.</p></li>
<li><p><strong>force_field</strong> (<em>str</em>) – Combined force field related cmds. For
example, ‘pair_style eamnpair_coeff * * Cu_u3.eam’.</p></li>
<li><p><strong>temperature</strong> (<em>float</em>) – Simulation temperature.</p></li>
<li><p><strong>nsteps</strong> (<em>int</em>) – No. of steps to run.</p></li>
<li><p><strong>other_settings</strong> (<em>dict</em>) – other settings to be filled into
placeholders.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsRun.template_dir">
<span class="sig-name descname"><span class="pre">template_dir</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'/Users/janosh/dev/pmg/pymatgen/io/lammps/templates'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/lammps/inputs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsRun.template_dir" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsRun.write_inputs">
<span class="sig-name descname"><span class="pre">write_inputs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_dir</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/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L874-L890"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsRun.write_inputs" title="Permalink to this definition"></a></dt>
<dd><p>Writes all input files (input script, and data if needed).
Other supporting files are not handled at this moment.</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>output_dir</strong> (<em>str</em>) – Directory to output the input files.</p></li>
<li><p><strong>**kwargs</strong> – kwargs supported by LammpsData.write_file.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsTemplateGen">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LammpsTemplateGen</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L921-L961"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsTemplateGen" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.io.template.html#pymatgen.io.template.TemplateInputGen" title="pymatgen.io.template.TemplateInputGen"><code class="xref py py-class docutils literal notranslate"><span class="pre">TemplateInputGen</span></code></a></p>
<p>Creates an InputSet object for a LAMMPS run based on a template file.
The input script is constructed by substituting variables into placeholders
in the template file using python’s Template.safe_substitute() function.
The data file containing coordinates and topology information can be provided
as a LammpsData instance. Alternatively, you can include a read_data command
in the template file that points to an existing data file.
Other supporting files are not handled at the moment.</p>
<p>To write the input files to a directory, call LammpsTemplateSet.write_input()
See pymatgen.io.template.py for additional documentation of this method.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.lammps.inputs.LammpsTemplateGen.get_input_set">
<span class="sig-name descname"><span class="pre">get_input_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">script_template</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">settings</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">script_filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'in.lammps'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.lammps.data.html#pymatgen.io.lammps.data.LammpsData" title="pymatgen.io.lammps.data.LammpsData"><span class="pre">LammpsData</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.io.lammps.data.html#pymatgen.io.lammps.data.CombinedData" title="pymatgen.io.lammps.data.CombinedData"><span class="pre">CombinedData</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'system.data'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/lammps/inputs.py#L935-L961"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.lammps.inputs.LammpsTemplateGen.get_input_set" title="Permalink 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>script_template</strong> – String template for input script with
placeholders. The format for placeholders has to be
‘$variable_name’, e.g., ‘$temperature’</p></li>
<li><p><strong>settings</strong> – Contains values to be written to the
placeholders, e.g., {‘temperature’: 1}. Default to None.</p></li>
<li><p><strong>data</strong> – Data file as a LammpsData instance. Default to None, i.e., no
data file supplied. Note that a matching ‘read_data’ command
must be provided in the script template in order for the data
file to actually be read.</p></li>
<li><p><strong>script_filename</strong> – Filename for the input file.</p></li>
<li><p><strong>data_filename</strong> – Filename for the data file, if provided.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
</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>
<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>