forked from materialsproject/pymatgen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pymatgen.analysis.defects.dilute_solution_model.html
233 lines (219 loc) · 12.4 KB
/
pymatgen.analysis.defects.dilute_solution_model.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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>pymatgen.analysis.defects.dilute_solution_model module — pymatgen 2019.5.1 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33990148-1']);
_gaq.push(['_trackPageview']);
</script>
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">pymatgen 2019.5.1 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="module-pymatgen.analysis.defects.dilute_solution_model">
<span id="pymatgen-analysis-defects-dilute-solution-model-module"></span><h1>pymatgen.analysis.defects.dilute_solution_model module<a class="headerlink" href="#module-pymatgen.analysis.defects.dilute_solution_model" title="Permalink to this headline">¶</a></h1>
<dl class="function">
<dt id="pymatgen.analysis.defects.dilute_solution_model.check_input">
<code class="descname">check_input</code><span class="sig-paren">(</span><em>def_list</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/defects/dilute_solution_model.html#check_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.dilute_solution_model.check_input" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.defects.dilute_solution_model.compute_defect_density">
<code class="descname">compute_defect_density</code><span class="sig-paren">(</span><em>structure</em>, <em>e0</em>, <em>vac_defs</em>, <em>antisite_defs</em>, <em>T=800</em>, <em>trial_chem_pot=None</em>, <em>plot_style='highcharts'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/defects/dilute_solution_model.html#compute_defect_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.dilute_solution_model.compute_defect_density" title="Permalink to this definition">¶</a></dt>
<dd><p>Wrapper for the dilute_solution_model.
The computed plot data is prepared based on plot_style.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – pymatgen.core.structure.Structure object representing the
primitive or unitcell of the crystal.</p></li>
<li><p><strong>e0</strong> – The total energy of the undefected system.
This is E0 from VASP calculation.</p></li>
<li><p><strong>vac_defs</strong> – List of vacancy defect parameters in the dictionary format.
The keys of the dict associated with each vacancy defect are
1) site_index, 2) site_specie, 3) site_multiplicity, and
4) energy. 1-3 can be obtained from
pymatgen.analysis.defects.point_defects.Vacancy class.
Site index is expected to start with 1 (fortran index).</p></li>
<li><p><strong>antisite_defs</strong> – List of antisite defect parameters in the dictionary
format. The keys of the dict associated with each antisite defect
are 1) site_index, 2) site_specie, 3) site_multiplicity,
4) substitution_specie, and 5) energy. 1-3 can be obtained
from pymatgen.analysis.defects.point_defects.Vacancy class.</p></li>
<li><p><strong>T</strong> – Temperature in Kelvin</p></li>
<li><p><strong>trial_chem_pot</strong> (<em>optional</em>) – Trial chemical potentials to speedup
the plot generation. Format is {el1:mu1,…}</p></li>
<li><p><strong>plot_style</strong> (<em>string</em>) – Allowed options are
1) highcharts (default)
2) gnuplot</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The plot data is generated and returned in asked format.</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.defects.dilute_solution_model.solute_defect_density">
<code class="descname">solute_defect_density</code><span class="sig-paren">(</span><em>structure</em>, <em>e0</em>, <em>vac_defs</em>, <em>antisite_defs</em>, <em>solute_defs</em>, <em>solute_concen=0.01</em>, <em>T=800</em>, <em>trial_chem_pot=None</em>, <em>plot_style='highchargs'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/defects/dilute_solution_model.html#solute_defect_density"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.dilute_solution_model.solute_defect_density" title="Permalink to this definition">¶</a></dt>
<dd><p>Wrapper for the solute_site_preference_finder.
The computed plot data is prepared based on plot_style.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – pymatgen.core.structure.Structure object representing the
primitive or unitcell of the crystal.</p></li>
<li><p><strong>e0</strong> – The total energy of the undefected system.
This is E0 from VASP calculation.</p></li>
<li><p><strong>vac_defs</strong> – List of vacancy defect parameters in the dictionary format.
The keys of the dict associated with each vacancy defect are
1) site_index, 2) site_specie, 3) site_multiplicity, and
4) energy. 1-3 can be obtained from
pymatgen.analysis.defects.point_defects.Vacancy class.
Site index is expected to start with 1 (fortran index).</p></li>
<li><p><strong>antisite_defs</strong> – List of antisite defect parameters in the dictionary
format. The keys of the dict associated with each antisite defect
are 1) site_index, 2) site_specie, 3) site_multiplicity,
4) substitution_specie, and 5) energy. 1-3 can be obtained
from pymatgen.analysis.defects.point_defects.Vacancy class.</p></li>
<li><p><strong>solute_defs</strong> – List of solute defect parameters in the dictionary
format. Similary to that of antisite defs, wtih solute specie
specified in substitution_specie</p></li>
<li><p><strong>solute_concen</strong> – Solute concentration (in fractional value)</p></li>
<li><p><strong>T</strong> – Temperature in Kelvin</p></li>
<li><p><strong>trial_chem_pot</strong> (<em>optional</em>) – Trial chemical potentials to speedup
the plot generation. Format is {el1:mu1,…}</p></li>
<li><p><strong>plot_style</strong> (<em>string</em>) – Allowed options are
1) highcharts (default)
2) gnuplot</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The plot data is generated and returned in asked format.</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.defects.dilute_solution_model.solute_site_preference_finder">
<code class="descname">solute_site_preference_finder</code><span class="sig-paren">(</span><em>structure</em>, <em>e0</em>, <em>T</em>, <em>vac_defs</em>, <em>antisite_defs</em>, <em>solute_defs</em>, <em>solute_concen=0.01</em>, <em>trial_chem_pot=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/defects/dilute_solution_model.html#solute_site_preference_finder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.dilute_solution_model.solute_site_preference_finder" title="Permalink to this definition">¶</a></dt>
<dd><p>Compute the solute defect densities using dilute solution model.
:param structure: pymatgen.core.structure.Structure object representing the</p>
<blockquote>
<div><p>primitive or unitcell of the crystal.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>e0</strong> – The total energy of the undefected system.
This is E0 from VASP calculation.</p></li>
<li><p><strong>T</strong> – Temperature in Kelvin</p></li>
<li><p><strong>vac_defs</strong> – List of vacancy defect parameters in the dictionary format.
The keys of the dict associated with each vacancy defect are
1) site_index, 2) site_specie, 3) site_multiplicity, and
4) energy. 1-3 can be obtained from
pymatgen.analysis.defects.point_defects.Vacancy class.
Site index is expected to start with 1 (fortran index).</p></li>
<li><p><strong>antisite_defs</strong> – List of antisite defect parameters in the dictionary
format. The keys of the dict associated with each antisite
defect are 1) site_index, 2) site_specie, 3) site_multiplicity,
4) substitution_specie, and 5) energy. 1-3 can be obtained
from pymatgen.analysis.defects.point_defects.Vacancy class.</p></li>
<li><p><strong>solute_defs</strong> – List of solute defect parameters in the dictionary
format. Similary to that of antisite defs, wtih solute specie
specified in substitution_specie</p></li>
<li><p><strong>solute_concen</strong> – Solute concentration (in fractional value)</p></li>
<li><p><strong>trial_chem_pot</strong> – Trial chemical potentials to speedup the plot
generation. Format is {el1:mu1,…}</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The data for plotting the solute defect concentration.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>plot_data</p>
</dd>
</dl>
</dd></dl>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/pymatgen.analysis.defects.dilute_solution_model.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">pymatgen 2019.5.1 documentation</a> »</li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2011, Pymatgen Development Team.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.0.1.
</div>
<div class="footer">This page uses <a href="http://analytics.google.com/">
Google Analytics</a> to collect statistics. You can disable it by blocking
the JavaScript coming from www.google-analytics.com.
<script type="text/javascript">
(function() {
var ga = document.createElement('script');
ga.src = ('https:' == document.location.protocol ?
'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
ga.setAttribute('async', 'true');
document.documentElement.firstChild.appendChild(ga);
})();
</script>
</div>
</body>
</html>