-
Notifications
You must be signed in to change notification settings - Fork 836
/
pymatgen.io.fiesta.html
482 lines (431 loc) · 41.5 KB
/
pymatgen.io.fiesta.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
<!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.fiesta 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.fiesta.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.gaussian module" href="pymatgen.io.gaussian.html" />
<link rel="prev" title="pymatgen.io.cssr module" href="pymatgen.io.cssr.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 active">pymatgen.io.fiesta module</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.io.fiesta.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.fiesta">
<span id="pymatgen-io-fiesta-module"></span><h1>pymatgen.io.fiesta module<a class="headerlink" href="#module-pymatgen.io.fiesta" title="Permalink to this heading"></a></h1>
<p>This module implements input and output for Fiesta (<a class="reference external" href="http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html">http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html</a>).</p>
<p>and</p>
<p>-Nwchem2Fiesta class: to create the input files needed for a Fiesta run
-Fiesta_run: run gw_fiesta and bse_fiesta
-Localised Basis set reader</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.BSEOutput">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BSEOutput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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/fiesta.py#L833-L893"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.BSEOutput" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A bse output file parser. The start…</p>
<p>All energies are in eV.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to read.</p>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.BasisSetReader">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BasisSetReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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/fiesta.py#L201-L302"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.BasisSetReader" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A basis set reader.
Basis set are stored in data as a dict:
:key l_zeta_ng for each nl orbitals which contain list of tuple (alpha, coef) for each of the ng gaussians
in l_zeta orbital</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to read.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.BasisSetReader.infos_on_basis_set">
<span class="sig-name descname"><span class="pre">infos_on_basis_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L288-L302"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.BasisSetReader.infos_on_basis_set" title="Permalink to this definition"></a></dt>
<dd><p>infos on the basis set as in Fiesta log</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.BasisSetReader.set_n_nlmo">
<span class="sig-name descname"><span class="pre">set_n_nlmo</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L271-L286"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.BasisSetReader.set_n_nlmo" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>the number of nlm orbitals for the basis set</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FiestaInput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">correlation_grid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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="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">Exc_DFT_option</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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="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">COHSEX_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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="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">GW_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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="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">BSE_TDDFT_options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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="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><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L305-L734"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput" 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>Input File for Fiesta called “cell.in” by default (mandatory in Fiesta for now)</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>mol</strong> – pymatgen mol</p></li>
<li><p><strong>correlation_grid</strong> – dict</p></li>
<li><p><strong>Exc_DFT_option</strong> – dict</p></li>
<li><p><strong>COHSEX_options</strong> – dict</p></li>
<li><p><strong>GW_options</strong> – dict</p></li>
<li><p><strong>BSE_TDDFT_options</strong> – dict</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L558-L569"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.as_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.dump_BSE_data_in_GW_run">
<span class="sig-name descname"><span class="pre">dump_BSE_data_in_GW_run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">BSE_dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L395-L403"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.dump_BSE_data_in_GW_run" 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"><p><strong>BSE_dump</strong> – boolean</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>set the “do_bse” variable to one in cell.in</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.dump_TDDFT_data_in_GW_run">
<span class="sig-name descname"><span class="pre">dump_TDDFT_data_in_GW_run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">TDDFT_dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L405-L413"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.dump_TDDFT_data_in_GW_run" 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"><p><strong>TDDFT_dump</strong> – boolean</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>set the do_tddft variable to one in cell.in</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</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/fiesta.py#L571-L584"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.from_dict" 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"><p><strong>d</strong> – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>FiestaInput</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.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">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/fiesta.py#L721-L734"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.from_file" title="Permalink to this definition"></a></dt>
<dd><p>Read an Fiesta input from a file. Currently tested to work with
files generated from this class itself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to parse.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>FiestaInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.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">string_input</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/fiesta.py#L586-L719"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.from_string" title="Permalink to this definition"></a></dt>
<dd><p>Read an FiestaInput from a string. Currently tested to work with
files generated from this class itself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>string_input</strong> – string_input to parse.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>FiestaInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.infos_on_system">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">infos_on_system</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/fiesta.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.infos_on_system" title="Permalink to this definition"></a></dt>
<dd><p>Returns infos on initial parameters as in the log file of Fiesta</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.make_FULL_BSE_Densities_folder">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">make_FULL_BSE_Densities_folder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">folder</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/fiesta.py#L374-L383"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.make_FULL_BSE_Densities_folder" title="Permalink to this definition"></a></dt>
<dd><p>mkdir “FULL_BSE_Densities” folder (needed for bse run) in the desired folder</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.molecule">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecule</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/io/fiesta.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.molecule" title="Permalink to this definition"></a></dt>
<dd><p>Returns molecule associated with this FiestaInput.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.set_BSE_options">
<span class="sig-name descname"><span class="pre">set_BSE_options</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n_excitations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nit_bse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">200</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/fiesta.py#L385-L393"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.set_BSE_options" title="Permalink to this definition"></a></dt>
<dd><p>Set parameters in cell.in for a BSE computation
:param nv_bse: number of valence bands
:param nc_bse: number of conduction bands
:param n_excitations: number of excitations
:param nit_bse: number of iterations</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.set_GW_options">
<span class="sig-name descname"><span class="pre">set_GW_options</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nv_band</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nc_band</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_iteration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_grid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dE_grid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.5</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/fiesta.py#L363-L372"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.set_GW_options" title="Permalink to this definition"></a></dt>
<dd><p>Set parameters in cell.in for a GW computation
:param nv__band: number of valence bands to correct with GW
:param nc_band: number of conduction bands to correct with GW
:param n_iteration: number of iteration
:param n_grid and dE_grid:: number of points and spacing in eV for correlation grid</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.set_auxiliary_basis_set">
<span class="sig-name descname"><span class="pre">set_auxiliary_basis_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">folder</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auxiliary_folder</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auxiliary_basis_set_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'aug_cc_pvtz'</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/fiesta.py#L349-L361"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.set_auxiliary_basis_set" title="Permalink to this definition"></a></dt>
<dd><p>copy in the desired folder the needed auxiliary basis set “X2.ion” where X is a specie.
:param auxiliary_folder: folder where the auxiliary basis sets are stored
:param auxiliary_basis_set_type: type of basis set (string to be found in the extension of the file name; must</p>
<blockquote>
<div><p>be in lower case). ex: C2.ion_aug_cc_pvtz_RI_Weigend find “aug_cc_pvtz”</p>
</div></blockquote>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaInput.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></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L550-L556"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaInput.write_file" title="Permalink to this definition"></a></dt>
<dd><p>Write FiestaInput to a file
:param filename: Filename</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaOutput">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FiestaOutput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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/fiesta.py#L737-L830"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaOutput" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A Fiesta output file parser.</p>
<p>All energies are in eV.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to read.</p>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaRun">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FiestaRun</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">folder</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">grid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </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">(2,</span> <span class="pre">2,</span> <span class="pre">2)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_file</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">'log'</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/fiesta.py#L97-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaRun" 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>
<dl class="simple">
<dt>To run FIESTA inside python:</dt><dd><p>if grid is [x,x] then bse runs
if grid is [x,x,y] the fiesta(gw) runs
otherwise it breaks</p>
</dd>
</dl>
<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>folder</strong> – Folder to look for runs.</p></li>
<li><p><strong>grid</strong> – </p></li>
<li><p><strong>log_file</strong> – logfile of Fiesta</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaRun.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L180-L190"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaRun.as_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaRun.bse_run">
<span class="sig-name descname"><span class="pre">bse_run</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L156-L178"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaRun.bse_run" title="Permalink to this definition"></a></dt>
<dd><p>Performs BSE run</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaRun.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</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/fiesta.py#L192-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaRun.from_dict" 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"><p><strong>d</strong> – Dict representation</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>FiestaRun</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.FiestaRun.run">
<span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L118-L129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.FiestaRun.run" title="Permalink to this definition"></a></dt>
<dd><p>Performs FIESTA (gw) run.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.Nwchem2Fiesta">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Nwchem2Fiesta</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">folder</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nwchem'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'log_n2f'</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/fiesta.py#L31-L94"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.Nwchem2Fiesta" 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>To run NWCHEM2FIESTA inside python:</p>
<p>If nwchem.nw is the input, nwchem.out the output, and structure.movecs the
“movecs” file, the syntax to run NWCHEM2FIESTA is: NWCHEM2FIESTA
nwchem.nw nwchem.nwout structure.movecs > log_n2f</p>
<p>folder: where are stored the nwchem
filename: name of nwchem files read by NWCHEM2FIESTA (filename.nw, filename.nwout and filename.movecs)
logfile: logfile of NWCHEM2FIESTA</p>
<p>the run method launches NWCHEM2FIESTA</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.Nwchem2Fiesta.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L77-L86"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.Nwchem2Fiesta.as_dict" title="Permalink to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.Nwchem2Fiesta.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</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/fiesta.py#L88-L94"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.Nwchem2Fiesta.from_dict" 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"><p><strong>d</strong> – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Nwchem2Fiesta</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.fiesta.Nwchem2Fiesta.run">
<span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/fiesta.py#L57-L75"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.fiesta.Nwchem2Fiesta.run" title="Permalink to this definition"></a></dt>
<dd><p>Performs actual NWCHEM2FIESTA run</p>
</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>