-
Notifications
You must be signed in to change notification settings - Fork 836
/
pymatgen.io.cp2k.utils.html
337 lines (215 loc) · 13.9 KB
/
pymatgen.io.cp2k.utils.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
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>pymatgen.io.cp2k.utils module — pymatgen 2021.1.28 documentation</title>
<link rel="canonical" href="https://pymatgen.orgpymatgen.io.cp2k.utils.html"/>
<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="pymatgen.io.exciting package" href="pymatgen.io.exciting.html" />
<link rel="prev" title="pymatgen.io.cp2k.sets module" href="pymatgen.io.cp2k.sets.html" />
<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" class="icon icon-home"> pymatgen
</a>
<div class="version">
2021.1.28
</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" />
<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="main navigation">
<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="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 package</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 package</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 package</a></li>
<li class="toctree-l4 current"><a class="reference internal" href="pymatgen.io.html">pymatgen.io package</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.plugins.html">pymatgen.plugins 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>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.html#module-pymatgen">Module contents</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="top navigation">
<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="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li><a href="modules.html">pymatgen</a> »</li>
<li><a href="pymatgen.html">pymatgen package</a> »</li>
<li><a href="pymatgen.io.html">pymatgen.io package</a> »</li>
<li><a href="pymatgen.io.cp2k.html">pymatgen.io.cp2k package</a> »</li>
<li>pymatgen.io.cp2k.utils module</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.io.cp2k.utils.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">
<div class="section" id="module-pymatgen.io.cp2k.utils">
<span id="pymatgen-io-cp2k-utils-module"></span><h1>pymatgen.io.cp2k.utils module<a class="headerlink" href="#module-pymatgen.io.cp2k.utils" title="Permalink to this headline">¶</a></h1>
<p>Utility functions for assisting with cp2k IO</p>
<dl class="py function">
<dt id="pymatgen.io.cp2k.utils.get_aux_basis">
<code class="sig-name descname">get_aux_basis</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">basis_type</span></em>, <em class="sig-param"><span class="n">default_basis_type</span><span class="o">=</span><span class="default_value">'cFIT'</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/io/cp2k/utils.py#L183-L222"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.cp2k.utils.get_aux_basis" title="Permalink to this definition">¶</a></dt>
<dd><p>Get auxiliary basis info for a list of species.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>basis_type</strong> (<em>dict</em>) – <p>dict of auxiliary basis sets to use. i.e:
basis_type = {‘Si’: ‘cFIT’, ‘O’: ‘cpFIT’}. Basis type needs to
exist for that species.</p>
<dl class="simple">
<dt>Basis types:</dt><dd><p>FIT
cFIT
pFIT
cpFIT
GTH-def2
aug-{FIT,cFIT,pFIT,cpFIT, GTH-def2}</p>
</dd>
</dl>
</p></li>
<li><p><strong>default_basis_type</strong> (<em>str</em>) – </p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt id="pymatgen.io.cp2k.utils.get_basis_and_potential">
<code class="sig-name descname">get_basis_and_potential</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">species</span></em>, <em class="sig-param"><span class="n">d</span></em>, <em class="sig-param"><span class="n">cardinality</span><span class="o">=</span><span class="default_value">'DZVP'</span></em>, <em class="sig-param"><span class="n">functional</span><span class="o">=</span><span class="default_value">'PBE'</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/io/cp2k/utils.py#L110-L180"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.cp2k.utils.get_basis_and_potential" title="Permalink to this definition">¶</a></dt>
<dd><p>Given a specie and a potential/basis type, this function accesses the available basis sets and potentials.
Generally, the GTH potentials are used with the GTH basis sets.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – (list) list of species for which to get the potential/basis strings</p></li>
<li><p><strong>d</strong> – (dict) a dictionary specifying how bases and/or potentials should be assigned to species
E.g. {‘Si’: {‘cardinality’: ‘DZVP’, ‘sr’: True}, ‘O’: {‘cardinality’: ‘TZVP’}}</p></li>
<li><p><strong>functional</strong> – (str) functional type. Default: ‘PBE’</p></li>
<li><p><strong>basis_type</strong> – (str) the basis set type. Default: ‘MOLOPT’</p></li>
<li><p><strong>cardinality</strong> – (str) basis set cardinality. Default: ‘DZVP’</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>{‘potential’: potential, ‘basis’: basis}…}</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>(dict) of the form {‘specie’</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt id="pymatgen.io.cp2k.utils.get_unique_site_indices">
<code class="sig-name descname">get_unique_site_indices</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/io/cp2k/utils.py#L225-L256"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.cp2k.utils.get_unique_site_indices" title="Permalink to this definition">¶</a></dt>
<dd><p>Get unique site indices for a structure according to site properties. Whatever site-property has the most
unique values is used for indexing.</p>
<p>For example, if you have magnetic CoO with half Co atoms having a positive moment, and the other
half having a negative moment. Then this function will create a dict of sites for Co_1, Co_2, O.</p>
<p>This creates unique sites, based on site properties, but does not have anything to do with turning
those site properties into CP2K input parameters.</p>
</dd></dl>
<dl class="py function">
<dt id="pymatgen.io.cp2k.utils.natural_keys">
<code class="sig-name descname">natural_keys</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">text</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/io/cp2k/utils.py#L97-L107"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.cp2k.utils.natural_keys" title="Permalink to this definition">¶</a></dt>
<dd><p>Sort text by numbers coming after an underscore with natural number
convention,
Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12]</p>
</dd></dl>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2011, Pymatgen Development Team
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
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>