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<!DOCTYPE html>
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<title>pymatgen.io.xtb package — pymatgen 2024.3.1 documentation</title>
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<li><a class="reference internal" href="#">pymatgen.io.xtb package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.io.xtb.inputs">pymatgen.io.xtb.inputs module</a><ul>
<li><a class="reference internal" href="#pymatgen.io.xtb.inputs.CRESTInput"><code class="docutils literal notranslate"><span class="pre">CRESTInput</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.io.xtb.inputs.CRESTInput.constrains_template"><code class="docutils literal notranslate"><span class="pre">CRESTInput.constrains_template()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.io.xtb.inputs.CRESTInput.write_input_files"><code class="docutils literal notranslate"><span class="pre">CRESTInput.write_input_files()</span></code></a></li>
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<li><a class="reference internal" href="#pymatgen.io.xtb.outputs.CRESTOutput"><code class="docutils literal notranslate"><span class="pre">CRESTOutput</span></code></a></li>
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<section id="module-pymatgen.io.xtb">
<span id="pymatgen-io-xtb-package"></span><h1>pymatgen.io.xtb package<a class="headerlink" href="#module-pymatgen.io.xtb" title="Link to this heading"></a></h1>
<p>This package implements modules for input and output to and from CREST.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.io.xtb.inputs">
<span id="pymatgen-io-xtb-inputs-module"></span><h2>pymatgen.io.xtb.inputs module<a class="headerlink" href="#module-pymatgen.io.xtb.inputs" title="Link to this heading"></a></h2>
<p>Classes for writing XTB input files.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.xtb.inputs.CRESTInput">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CRESTInput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</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.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">working_dir</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">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords_filename</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><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">'crest_in.xyz'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">constraints</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></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><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2024.3.1/pymatgen/core/../io/xtb/inputs.py#L24-L97"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xtb.inputs.CRESTInput" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>An object representing CREST input files.
Because CREST is controlled through command line flags and external
files, the CRESTInput class mainly consists of methods for containing
and writing external files.</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>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Molecule object</p></li>
<li><p><strong>working_dir</strong> (<em>str</em>) – Directory to write input files to</p></li>
<li><p><strong>coords_filename</strong> (<em>str</em>) – Name of input coordinates file</p></li>
<li><p><strong>constraints</strong> (<em>dict</em>) – Dictionary of common editable parameters for
.constrains file. {“atoms”: [List of 1-indexed atoms to fix],
“force_constant”: float]</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.xtb.inputs.CRESTInput.constrains_template">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">constrains_template</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference_fnm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">constraints</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2024.3.1/pymatgen/core/../io/xtb/inputs.py#L65-L97"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xtb.inputs.CRESTInput.constrains_template" title="Link to this definition"></a></dt>
<dd><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>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Molecule the constraints will be performed on</p></li>
<li><p><strong>reference_fnm</strong> (<em>str</em>) – Name of file containing reference structure in same directory</p></li>
<li><p><strong>constraints</strong> (<em>dict</em>) – Dictionary of common editable parameters for .constrains file.
{“atoms”: [List of 1-indexed atoms to fix], “force_constant”: float]</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>for .constrains file</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.xtb.inputs.CRESTInput.write_input_files">
<span class="sig-name descname"><span class="pre">write_input_files</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2024.3.1/pymatgen/core/../io/xtb/inputs.py#L53-L63"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xtb.inputs.CRESTInput.write_input_files" title="Link to this definition"></a></dt>
<dd><p>Write input files to working directory.</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.io.xtb.outputs">
<span id="pymatgen-io-xtb-outputs-module"></span><h2>pymatgen.io.xtb.outputs module<a class="headerlink" href="#module-pymatgen.io.xtb.outputs" title="Link to this heading"></a></h2>
<p>Parsers for XTB output files and directories.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.xtb.outputs.CRESTOutput">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CRESTOutput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2024.3.1/pymatgen/core/../io/xtb/outputs.py#L24-L167"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.xtb.outputs.CRESTOutput" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Class to parse CREST output files.</p>
<p>Assumes runtype is iMTD-GC [default].</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>output_filename</strong> (<em>str</em>) – Filename to parse</p></li>
<li><p><strong>path</strong> (<em>str</em>) – Path to directory including output_filename and all
other xtb output files (crest_best.xyz, etc.)</p></li>
</ul>
</dd>
</dl>
</dd></dl>
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