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<div class="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 headline">¶</a></h1>
<p>This module defines classes to represent all xas and stitching methods</p>
<dl class="py class">
<dt id="pymatgen.analysis.xas.spectrum.XAS">
<em class="property">class </em><code class="sig-name descname">XAS</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">x</span></em>, <em class="sig-param"><span class="n">y</span></em>, <em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">absorbing_element</span></em>, <em class="sig-param"><span class="n">edge</span><span class="o">=</span><span class="default_value">'K'</span></em>, <em class="sig-param"><span class="n">spectrum_type</span><span class="o">=</span><span class="default_value">'XANES'</span></em>, <em class="sig-param"><span class="n">absorbing_index</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/xas/spectrum.py#L27-L272"><span class="viewcode-link">[source]</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">pymatgen.core.spectrum.Spectrum</span></code></a></p>
<p>Basic XAS object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</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 id="pymatgen.analysis.xas.spectrum.XAS.XLABEL">
<code class="sig-name descname">XLABEL</code><em class="property"> = 'Energy'</em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/xas/spectrum.py"><span class="viewcode-link">[source]</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 id="pymatgen.analysis.xas.spectrum.XAS.YLABEL">
<code class="sig-name descname">YLABEL</code><em class="property"> = 'Intensity'</em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/xas/spectrum.py"><span class="viewcode-link">[source]</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 id="pymatgen.analysis.xas.spectrum.XAS.stitch">
<code class="sig-name descname">stitch</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">other</span><span class="p">:</span> <span class="n"><a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS">pymatgen.analysis.xas.spectrum.XAS</a></span></em>, <em class="sig-param"><span class="n">num_samples</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">500</span></em>, <em class="sig-param"><span class="n">mode</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'XAFS'</span></em><span class="sig-paren">)</span> → <a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS">pymatgen.analysis.xas.spectrum.XAS</a><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/xas/spectrum.py#L113-L272"><span class="viewcode-link">[source]</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</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>str</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</dt>
<dd class="field-even"><p>The stitched spectrum.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>XAS object</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt id="pymatgen.analysis.xas.spectrum.site_weighted_spectrum">
<code class="sig-name descname">site_weighted_spectrum</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">xas_list</span><span class="p">:</span> <span class="n">List<span class="p">[</span>XAS<span class="p">]</span></span></em>, <em class="sig-param"><span class="n">num_samples</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">500</span></em><span class="sig-paren">)</span> → <a class="reference internal" href="#pymatgen.analysis.xas.spectrum.XAS" title="pymatgen.analysis.xas.spectrum.XAS">pymatgen.analysis.xas.spectrum.XAS</a><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/xas/spectrum.py#L275-L342"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>The site-weighted spectrum</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>XAS object</p>
</dd>
</dl>
</dd></dl>
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