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<section id="module-pymatgen.io.xr">
<span id="pymatgen-io-xr-module"></span><h1>pymatgen.io.xr module<a class="headerlink" href="#module-pymatgen.io.xr" title="Permalink to this heading"></a></h1>
<p>This module provides input and output mechanisms
for the xr file format, which is a modified CSSR
file format and, for example, used in GULP.
In particular, the module makes it easy
to remove shell positions from relaxations
that employed core-shell models.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.xr.Xr">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Xr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/xr.py#L29-L167"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xr.Xr" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Basic object for working with xr files.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<em>Structure/IStructure</em>) – Structure object to create the
Xr object.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.xr.Xr.from_file">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thresh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/xr.py#L148-L167"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xr.Xr.from_file" title="Permalink to this definition"></a></dt>
<dd><p>Reads an xr-formatted file to create an Xr 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>filename</strong> (<em>str</em>) – name of file to read from.</p></li>
<li><p><strong>use_cores</strong> (<em>bool</em>) – use core positions and discard shell
positions if set to True (default). Otherwise,
use shell positions and discard core positions.</p></li>
<li><p><strong>thresh</strong> (<em>float</em>) – relative threshold for consistency check
between cell parameters (lengths and angles) from
header information and cell vectors, respectively.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Xr object corresponding to the input</dt><dd><p>file.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>xr (<a class="reference internal" href="#pymatgen.io.xr.Xr" title="pymatgen.io.xr.Xr">Xr</a>)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.xr.Xr.from_string">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">string</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thresh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/xr.py#L73-L146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xr.Xr.from_string" title="Permalink to this definition"></a></dt>
<dd><p>Creates an Xr object from a string representation.</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>string</strong> (<em>str</em>) – string representation of an Xr object.</p></li>
<li><p><strong>use_cores</strong> (<em>bool</em>) – use core positions and discard shell
positions if set to True (default). Otherwise,
use shell positions and discard core positions.</p></li>
<li><p><strong>thresh</strong> (<em>float</em>) – relative threshold for consistency check
between cell parameters (lengths and angles) from
header information and cell vectors, respectively.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Xr object corresponding to the input</dt><dd><p>string representation.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>xr (<a class="reference internal" href="#pymatgen.io.xr.Xr" title="pymatgen.io.xr.Xr">Xr</a>)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.xr.Xr.write_file">
<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/xr.py#L63-L71"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xr.Xr.write_file" title="Permalink to this definition"></a></dt>
<dd><p>Write out an xr file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> (<em>str</em>) – name of the file to write to.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
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