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<!DOCTYPE html>
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<title>turbomoleio — turbomoleio 1.6.0 documentation</title>
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turbomoleio
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1.6.0
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<p class="caption" role="heading"><span class="caption-text">User guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="datagroups.html">The data group files</a></li>
<li class="toctree-l1"><a class="reference internal" href="coord.html">The coord file</a></li>
<li class="toctree-l1"><a class="reference internal" href="definerunner.html">Running define</a></li>
<li class="toctree-l1"><a class="reference internal" href="output_parsing.html">Outputs parsing</a></li>
<li class="toctree-l1"><a class="reference internal" href="appendix.html">Appendix</a></li>
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<p class="caption" role="heading"><span class="caption-text">Developer guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="developer/introduction.html">Contributing</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer/parsing_logs.html">Output logs parsing</a></li>
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<section id="turbomoleio">
<h1>turbomoleio<a class="headerlink" href="#turbomoleio" title="Link to this heading"></a></h1>
<p>turbomoleio is a python library containing a set of tools for the generation of inputs and parsing of
outputs for <a class="reference external" href="http://www.turbomole.com/">TURBOMOLE</a>, based on the open-source <a class="reference external" href="http://pymatgen.org/">pymatgen</a>
library. turbomoleio is compatible with python version 3.8 and higher. The current version of turbomoleio is
compatible with TURBOMOLE version 7.8. Care is taken to provide backward compatibility for parsing of output
files generated with versions of TURBOMOLE down to 7.3. Full compatibility (i.e. input generation using define)
is only tested for TURBOMOLE version 7.8. The following table summarizes the compatibility (full, including input
generation using define) between TURBOMOLE and turbomoleio versions:</p>
<table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>TURBOMOLE version(s)</p></th>
<th class="head"><p>turbomoleio version(s)</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>7.8 series</p></td>
<td><p>1.6.x series</p></td>
</tr>
<tr class="row-odd"><td><p>7.7 series</p></td>
<td><p>1.5.x series</p></td>
</tr>
<tr class="row-even"><td><p>7.6 series</p></td>
<td><p>1.4.x series</p></td>
</tr>
<tr class="row-odd"><td><p>7.5 series</p></td>
<td><p>1.3.x series</p></td>
</tr>
<tr class="row-even"><td><p>7.4 series</p></td>
<td><p>1.2.x series</p></td>
</tr>
<tr class="row-odd"><td><p>7.3 series</p></td>
<td><p>1.0.x and 1.1.x series</p></td>
</tr>
</tbody>
</table>
<p>The main features of turbomoleio include:</p>
<ul class="simple">
<li><p>generation of the input files with the execution of <code class="docutils literal notranslate"><span class="pre">define</span></code> based on a set of parameters</p></li>
<li><p>an interface for several of the files generated by TURBOMOLE, like for example the <code class="docutils literal notranslate"><span class="pre">control</span></code> and
<code class="docutils literal notranslate"><span class="pre">energy</span></code> files.</p></li>
<li><p>the <code class="docutils literal notranslate"><span class="pre">MoleculeSystem</span></code>, an object that can be used for reading and generating <code class="docutils literal notranslate"><span class="pre">coord</span></code> files,
based on the pymatgen <code class="docutils literal notranslate"><span class="pre">Molecule</span></code> object.</p></li>
<li><p>a <code class="docutils literal notranslate"><span class="pre">Parser</span></code> for the extraction of the most relevant data from the text output of the most common
TURBOMOLE calculations.</p></li>
</ul>
<p>Note that most of the objects have been designed to be <code class="docutils literal notranslate"><span class="pre">MSONable</span></code> (from the <a class="reference external" href="http://guide.materialsvirtuallab.org/monty/">monty</a>
package). This provides a way to naturally store input and output objects in JSON format and MongoDB databases,
enabling their use in connection with the <a class="reference external" href="https://materialsproject.github.io/fireworks/">FireWorks</a> workflow
manager. More details about all the objects available and how to use them can be found in the following user guide.</p>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">User guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="datagroups.html">The data group files</a><ul>
<li class="toctree-l2"><a class="reference internal" href="datagroups.html#the-datagroups-object">The DataGroups object</a><ul>
<li class="toctree-l3"><a class="reference internal" href="datagroups.html#accessing-a-data-group-value">Accessing a data group value</a></li>
<li class="toctree-l3"><a class="reference internal" href="datagroups.html#modifying-a-data-group-value">Modifying a data group value</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="datagroups.html#the-control-object">The Control object</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="coord.html">The coord file</a><ul>
<li class="toctree-l2"><a class="reference internal" href="coord.html#periodic-systems">Periodic systems</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="definerunner.html">Running define</a><ul>
<li class="toctree-l2"><a class="reference internal" href="definerunner.html#the-definerunner-parameters">The DefineRunner parameters</a><ul>
<li class="toctree-l3"><a class="reference internal" href="definerunner.html#validation">Validation</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="output_parsing.html">Outputs parsing</a><ul>
<li class="toctree-l2"><a class="reference internal" href="output_parsing.html#the-log-files">The log files</a><ul>
<li class="toctree-l3"><a class="reference internal" href="output_parsing.html#quick-start">Quick Start</a></li>
<li class="toctree-l3"><a class="reference internal" href="output_parsing.html#overall-structure">Overall Structure</a></li>
<li class="toctree-l3"><a class="reference internal" href="output_parsing.html#data-and-file-objects">Data and File Objects</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="output_parsing.html#the-states-object">The States object</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="appendix.html">Appendix</a><ul>
<li class="toctree-l2"><a class="reference internal" href="api/modules.html">turbomoleio</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/turbomoleio.html">turbomoleio package</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
<section id="contributing-to-turbomoleio">
<h2>Contributing to turbomoleio<a class="headerlink" href="#contributing-to-turbomoleio" title="Link to this heading"></a></h2>
<p>Advanced turbomoleio users might want to contribute new features or increase the amount
of parsed output data. Before doing so they are advised to carefully read the following developer guide.</p>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Developer guide</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="developer/introduction.html">Contributing</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer/parsing_logs.html">Output logs parsing</a><ul>
<li class="toctree-l2"><a class="reference internal" href="developer/parsing_logs.html#parsing-a-new-quantity">Parsing a new quantity</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/parsing_logs.html#parsing-a-new-type-of-log">Parsing a new type of log</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/parsing_logs.html#tests">Tests</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="developer/definerunner.html">Define runner</a><ul>
<li class="toctree-l2"><a class="reference internal" href="developer/definerunner.html#tests">Tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/definerunner.html#validation">Validation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="developer/testing.html">Testing</a><ul>
<li class="toctree-l2"><a class="reference internal" href="developer/testing.html#the-test-suite">The test suite</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/testing.html#unit-tests">Unit tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/testing.html#integration-tests">Integration tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="developer/testing.html#writing-new-tests">Writing new tests</a><ul>
<li class="toctree-l3"><a class="reference internal" href="developer/testing.html#tests-for-output-parsing">Tests for output parsing</a></li>
<li class="toctree-l3"><a class="reference internal" href="developer/testing.html#turbomole-version-change">Turbomole version change</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="developer/versioning.html">Versioning</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer/versioning.html#backward-compatibility">Backward-compatibility</a></li>
</ul>
</div>
</section>
<section id="additional-information">
<h2>Additional information<a class="headerlink" href="#additional-information" title="Link to this heading"></a></h2>
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<p class="caption" role="heading"><span class="caption-text">Additional information</span></p>
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<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-6-0-sep-6-2024">Release 1.6.0 (Sep 6, 2024)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-5-0-mar-27-2024">Release 1.5.0 (Mar 27, 2024)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#developer-changes">Developer changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-4-0-mar-4-2024">Release 1.4.0 (Mar 4, 2024)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-3-0-feb-24-2022">Release 1.3.0 (Feb 24, 2022)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#id1">Developer changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-2-0-feb-16-2022">Release 1.2.0 (Feb 16, 2022)</a></li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-1-1-feb-15-2022">Release 1.1.1 (Feb 15, 2022)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#features-added">Features added</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-1-0-sep-20-2021">Release 1.1.0 (Sep 20, 2021)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#id2">Features added</a></li>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#bug-fixing">Bug fixing</a></li>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#testing-and-development">Testing and development</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-1-0-0-mar-11-2021">Release 1.0.0 (Mar 11, 2021)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="bugs.html">Reporting bugs</a></li>
</ul>
</div>
</section>
<section id="indices-and-tables">
<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Link to this heading"></a></h2>
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<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
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