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<li><a class="reference internal" href="#">pymatgen.analysis.xas package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.analysis.xas.spectrum">pymatgen.analysis.xas.spectrum module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS"><code class="docutils literal notranslate"><span class="pre">XAS</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.x"><code class="docutils literal notranslate"><span class="pre">XAS.x</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.y"><code class="docutils literal notranslate"><span class="pre">XAS.y</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.absorbing_element"><code class="docutils literal notranslate"><span class="pre">XAS.absorbing_element</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.edge"><code class="docutils literal notranslate"><span class="pre">XAS.edge</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.spectrum_type"><code class="docutils literal notranslate"><span class="pre">XAS.spectrum_type</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.absorbing_index"><code class="docutils literal notranslate"><span class="pre">XAS.absorbing_index</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.zero_negative_intensity"><code class="docutils literal notranslate"><span class="pre">XAS.zero_negative_intensity</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.XLABEL"><code class="docutils literal notranslate"><span class="pre">XAS.XLABEL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.YLABEL"><code class="docutils literal notranslate"><span class="pre">XAS.YLABEL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS.stitch"><code class="docutils literal notranslate"><span class="pre">XAS.stitch()</span></code></a></li>
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<li><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.site_weighted_spectrum"><code class="docutils literal notranslate"><span class="pre">site_weighted_spectrum()</span></code></a></li>
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<section id="module-pymatgen.analysis.xas">
<span id="pymatgen-analysis-xas-package"></span><h1>pymatgen.analysis.xas package<a class="headerlink" href="#module-pymatgen.analysis.xas" title="Link to this heading"></a></h1>
<p>Package for analysis of X-ray Absorption Spectroscopy.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.analysis.xas.spectrum">
<span id="pymatgen-analysis-xas-spectrum-module"></span><h2>pymatgen.analysis.xas.spectrum module<a class="headerlink" href="#module-pymatgen.analysis.xas.spectrum" title="Link to this heading"></a></h2>
<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><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">absorbing_element</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><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge</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">'K'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spectrum_type</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">'XANES'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">absorbing_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><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>, <em class="sig-param"><span class="n"><span class="pre">zero_negative_intensity</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><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/xas/spectrum.py#L31-L223"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.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.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.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>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.x">
<span class="sig-name descname"><span class="pre">x</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.x" title="Link to this definition"></a></dt>
<dd><p>The sequence of energies.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Sequence[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.y">
<span class="sig-name descname"><span class="pre">y</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.y" title="Link to this definition"></a></dt>
<dd><p>The sequence of mu(E).</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Sequence[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.absorbing_element">
<span class="sig-name descname"><span class="pre">absorbing_element</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.absorbing_element" title="Link to this definition"></a></dt>
<dd><p>The absorbing element of the spectrum.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str or .Element</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.edge">
<span class="sig-name descname"><span class="pre">edge</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.edge" title="Link to this definition"></a></dt>
<dd><p>The edge of the spectrum.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.spectrum_type">
<span class="sig-name descname"><span class="pre">spectrum_type</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.spectrum_type" title="Link to this definition"></a></dt>
<dd><p>The type of the spectrum (XANES or EXAFS).</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.absorbing_index">
<span class="sig-name descname"><span class="pre">absorbing_index</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.absorbing_index" title="Link to this definition"></a></dt>
<dd><p>The absorbing index of the spectrum.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xas.spectrum.XAS.zero_negative_intensity">
<span class="sig-name descname"><span class="pre">zero_negative_intensity</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/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.zero_negative_intensity" title="Link to this definition"></a></dt>
<dd><p>Whether to set unphysical negative intensities to zero</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<p>Initialize 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/v2025.1.24/src/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="Link 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/v2025.1.24/src/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="Link 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/v2025.1.24/src/pymatgen/core/../analysis/xas/spectrum.py#L100-L223"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.XAS.stitch" title="Link 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">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/v2025.1.24/src/pymatgen/core/../analysis/xas/spectrum.py#L226-L285"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xas.spectrum.site_weighted_spectrum" title="Link 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>
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