-
Notifications
You must be signed in to change notification settings - Fork 836
/
pymatgen.analysis.xas.spectrum.html
265 lines (237 loc) · 19.1 KB
/
pymatgen.analysis.xas.spectrum.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
<!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.analysis.xas.spectrum 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.analysis.xas.spectrum.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.analysis.adsorption module" href="pymatgen.analysis.adsorption.html" />
<link rel="prev" title="pymatgen.analysis.xas package" href="pymatgen.analysis.xas.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 current"><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"><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.analysis.html">pymatgen.analysis namespace</a></li>
<li class="breadcrumb-item"><a href="pymatgen.analysis.xas.html">pymatgen.analysis.xas package</a></li>
<li class="breadcrumb-item active">pymatgen.analysis.xas.spectrum module</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.analysis.xas.spectrum.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.analysis.xas.spectrum">
<span id="pymatgen-analysis-xas-spectrum-module"></span><h1>pymatgen.analysis.xas.spectrum module<a class="headerlink" href="#module-pymatgen.analysis.xas.spectrum" title="Permalink to this heading"></a></h1>
<p>This module defines classes to represent all xas and stitching methods</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">XAS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absorbing_element</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'K'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spectrum_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'XANES'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absorbing_index</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/../analysis/xas/spectrum.py#L26-L223"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.spectrum.html#pymatgen.core.spectrum.Spectrum" title="pymatgen.core.spectrum.Spectrum"><code class="xref py py-class docutils literal notranslate"><span class="pre">Spectrum</span></code></a></p>
<p>Basic XAS object.</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>x</strong> – A sequence of x-ray energies in eV</p></li>
<li><p><strong>y</strong> – A sequence of mu(E)</p></li>
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure associated with the spectrum</p></li>
<li><p><strong>absorbing_element</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a>) – Element associated with the spectrum</p></li>
<li><p><strong>edge</strong> (<em>str</em>) – Absorption edge associated with the spectrum</p></li>
<li><p><strong>spectrum_type</strong> (<em>str</em>) – ‘XANES’ or ‘EXAFS’</p></li>
<li><p><strong>absorbing_index</strong> (<em>None</em><em> or </em><em>int</em>) – If None, the spectrum is assumed to be a
site-weighted spectrum, which is comparable to experimental one.
Otherwise, it indicates that the absorbing_index for a site-wise spectrum.</p></li>
</ul>
</dd>
</dl>
<p>Initializes a spectrum object.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.XLABEL">
<span class="sig-name descname"><span class="pre">XLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Energy'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/xas/spectrum.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS.XLABEL" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.YLABEL">
<span class="sig-name descname"><span class="pre">YLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Intensity'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/analysis/xas/spectrum.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS.YLABEL" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.stitch">
<span class="sig-name descname"><span class="pre">stitch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS"><span class="pre">XAS</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_samples</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">500</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'XAFS'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'L23'</span></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">'XAFS'</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.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS"><span class="pre">XAS</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/xas/spectrum.py#L97-L223"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS.stitch" title="Permalink to this definition"></a></dt>
<dd><p>Stitch XAS objects to get the full XAFS spectrum or L23 edge XANES
spectrum depending on the mode.</p>
<ol class="arabic">
<li><dl>
<dt>Use XAFS mode for stitching XANES and EXAFS with same absorption edge.</dt><dd><p>The stitching will be performed based on wavenumber, k.
for k <= 3, XAS(k) = XAS[XANES(k)]
for 3 < k < max(xanes_k), will interpolate according to</p>
<blockquote>
<div><p>XAS(k)=f(k)*mu[XANES(k)]+(1-f(k))*mu[EXAFS(k)]
where f(k)=cos^2((pi/2) (k-3)/(max(xanes_k)-3)</p>
</div></blockquote>
<p>for k > max(xanes_k), XAS(k) = XAS[EXAFS(k)]</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Use L23 mode for stitching L2 and L3 edge XANES for elements with</dt><dd><p>atomic number <=30.</p>
</dd>
</dl>
</li>
</ol>
<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>other</strong> – Another XAS object.</p></li>
<li><p><strong>num_samples</strong> (<em>int</em>) – Number of samples for interpolation.</p></li>
<li><p><strong>mode</strong> (<em>"XAFS"</em><em> | </em><em>"L23"</em>) – Either XAFS mode for stitching XANES and EXAFS
or L23 mode for stitching L2 and L3.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The stitched spectrum.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>XAS object</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.site_weighted_spectrum">
<span class="sig-name descname"><span class="pre">site_weighted_spectrum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">xas_list</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><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS"><span class="pre">pymatgen.analysis.xas.spectrum.XAS</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_samples</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">500</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.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS"><span class="pre">XAS</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../analysis/xas/spectrum.py#L226-L284"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.site_weighted_spectrum" title="Permalink to this definition"></a></dt>
<dd><p>Obtain site-weighted XAS object based on site multiplicity for each
absorbing index and its corresponding site-wise spectrum.</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>xas_list</strong> (<em>[</em><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS"><em>XAS</em></a><em>]</em>) – List of XAS object to be weighted</p></li>
<li><p><strong>num_samples</strong> (<em>int</em>) – Number of samples for interpolation</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The site-weighted spectrum</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>XAS object</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>