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<li><a class="reference internal" href="#">pymatgen.apps.borg package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.apps.borg.hive">pymatgen.apps.borg.hive module</a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone"><code class="docutils literal notranslate"><span class="pre">AbstractDrone</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone.assimilate"><code class="docutils literal notranslate"><span class="pre">AbstractDrone.assimilate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone.get_valid_paths"><code class="docutils literal notranslate"><span class="pre">AbstractDrone.get_valid_paths()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone"><code class="docutils literal notranslate"><span class="pre">GaussianToComputedEntryDrone</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.as_dict"><code class="docutils literal notranslate"><span class="pre">GaussianToComputedEntryDrone.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.assimilate"><code class="docutils literal notranslate"><span class="pre">GaussianToComputedEntryDrone.assimilate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.from_dict"><code class="docutils literal notranslate"><span class="pre">GaussianToComputedEntryDrone.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.get_valid_paths"><code class="docutils literal notranslate"><span class="pre">GaussianToComputedEntryDrone.get_valid_paths()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone"><code class="docutils literal notranslate"><span class="pre">SimpleVaspToComputedEntryDrone</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.as_dict"><code class="docutils literal notranslate"><span class="pre">SimpleVaspToComputedEntryDrone.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.assimilate"><code class="docutils literal notranslate"><span class="pre">SimpleVaspToComputedEntryDrone.assimilate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.from_dict"><code class="docutils literal notranslate"><span class="pre">SimpleVaspToComputedEntryDrone.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone"><code class="docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.as_dict"><code class="docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.assimilate"><code class="docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone.assimilate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.from_dict"><code class="docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.get_valid_paths"><code class="docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone.get_valid_paths()</span></code></a></li>
</ul>
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</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.apps.borg.queen">pymatgen.apps.borg.queen module</a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen"><code class="docutils literal notranslate"><span class="pre">BorgQueen</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen.get_data"><code class="docutils literal notranslate"><span class="pre">BorgQueen.get_data()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen.load_data"><code class="docutils literal notranslate"><span class="pre">BorgQueen.load_data()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen.parallel_assimilate"><code class="docutils literal notranslate"><span class="pre">BorgQueen.parallel_assimilate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen.save_data"><code class="docutils literal notranslate"><span class="pre">BorgQueen.save_data()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.apps.borg.queen.BorgQueen.serial_assimilate"><code class="docutils literal notranslate"><span class="pre">BorgQueen.serial_assimilate()</span></code></a></li>
</ul>
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<li><a class="reference internal" href="#pymatgen.apps.borg.queen.order_assimilation"><code class="docutils literal notranslate"><span class="pre">order_assimilation()</span></code></a></li>
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<section id="module-pymatgen.apps.borg">
<span id="pymatgen-apps-borg-package"></span><h1>pymatgen.apps.borg package<a class="headerlink" href="#module-pymatgen.apps.borg" title="Link to this heading"></a></h1>
<p>The borg package contains modules that assimilate large quantities of data into
pymatgen objects for analysis.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.apps.borg.hive">
<span id="pymatgen-apps-borg-hive-module"></span><h2>pymatgen.apps.borg.hive module<a class="headerlink" href="#module-pymatgen.apps.borg.hive" title="Link to this heading"></a></h2>
<p>This module define the various drones used to assimilate data.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.AbstractDrone">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractDrone</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L33-L73"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.AbstractDrone" 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>, <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract drone class that defines the various methods that must be
implemented by drones. Because of the quirky nature of Python”s
multiprocessing, the intermediate data representations has to be in the
form of python primitives. So all objects that drones work with must be
MSONable. All drones must also implement the standard MSONable as_dict() and
from_dict API.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.AbstractDrone.assimilate">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</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/../apps/borg/hive.py#L42-L54"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.AbstractDrone.assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate data in a directory path into a pymatgen object. Because of
the quirky nature of Python’s multiprocessing, the object must support
pymatgen’s as_dict() for parallel processing.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – directory path</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>An assimilated object</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.AbstractDrone.get_valid_paths">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_valid_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</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/../apps/borg/hive.py#L56-L73"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.AbstractDrone.get_valid_paths" title="Link to this definition"></a></dt>
<dd><p>Check if path contains valid data for assimilation, and then returns
the valid paths. The paths returned can be a list of directory or file
paths, depending on what kind of data you are assimilating. For
example, if you are assimilating VASP runs, you are only interested in
directories containing vasprun.xml files. On the other hand, if you are
interested converting all POSCARs in a directory tree to CIFs for
example, you will want the file paths.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – input path as a tuple generated from os.walk, i.e.,
(parent, subdirs, files).</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of valid dir/file paths for assimilation</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.GaussianToComputedEntryDrone">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GaussianToComputedEntryDrone</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inc_structure</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>, <em class="sig-param"><span class="n"><span class="pre">parameters</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><span class="pre">str</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>, <em class="sig-param"><span class="n"><span class="pre">data</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><span class="pre">str</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>, <em class="sig-param"><span class="n"><span class="pre">file_extensions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">str</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">('.log',)</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/../apps/borg/hive.py#L318-L441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone" title="pymatgen.apps.borg.hive.AbstractDrone"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractDrone</span></code></a></p>
<p>GaussianToEntryDrone assimilates directories containing Gaussian output to
ComputedEntry/ComputedStructureEntry objects. By default, it is assumed
that Gaussian output files have a “.log” extension.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Like the GaussianOutput class, this is still in early beta.</p>
</div>
<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>inc_structure</strong> (<em>bool</em>) – Set to True if you want
ComputedStructureEntries to be returned instead of
ComputedEntries.</p></li>
<li><p><strong>parameters</strong> (<em>list</em>) – Input parameters to include. It has to be one of
the properties supported by the GaussianOutput object. See
pymatgen.io.gaussian.GaussianOutput. The parameters
have to be one of python’s primitive types, i.e., list, dict of
strings and integers. If parameters is None, a default set of
parameters will be set.</p></li>
<li><p><strong>data</strong> (<em>list</em>) – Output data to include. Has to be one of the properties
supported by the GaussianOutput object. The parameters have to
be one of python’s primitive types, i.e. list, dict of strings
and integers. If data is None, a default set will be set.</p></li>
<li><p><strong>file_extensions</strong> (<em>list</em>) – File extensions to be considered as Gaussian output files.
Defaults to just the typical “log” extension.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><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">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L419-L430"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.assimilate">
<span class="sig-name descname"><span class="pre">assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><span class="pre">ComputedStructureEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L374-L404"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate data in a directory path into a ComputedEntry object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – directory path</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>ComputedEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</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">Any</span><span class="p"><span class="pre">]</span></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">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L432-L441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.from_dict" 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"><p><strong>dct</strong> (<em>dict</em>) – Dict Representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>GaussianToComputedEntryDrone</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.get_valid_paths">
<span class="sig-name descname"><span class="pre">get_valid_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</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">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L406-L417"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.GaussianToComputedEntryDrone.get_valid_paths" title="Link to this definition"></a></dt>
<dd><p>Check if path contains files with define extensions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – input path as a tuple generated from os.walk, i.e.,
(parent, subdirs, files).</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of valid dir/file paths for assimilation</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimpleVaspToComputedEntryDrone</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inc_structure</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/../apps/borg/hive.py#L202-L315"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone" title="pymatgen.apps.borg.hive.VaspToComputedEntryDrone"><code class="xref py py-class docutils literal notranslate"><span class="pre">VaspToComputedEntryDrone</span></code></a></p>
<p>A simpler VaspToComputedEntryDrone. Instead of parsing vasprun.xml, it
parses only the INCAR, POTCAR, OSZICAR and KPOINTS files, which are much
smaller and faster to parse. However, much fewer properties are available
compared to the standard VaspToComputedEntryDrone.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>inc_structure</strong> (<em>bool</em>) – Return ComputedStructureEntries (True) instead of
ComputedEntries (False). Structure will be parsed from the CONTCAR.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><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">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L298-L304"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.assimilate">
<span class="sig-name descname"><span class="pre">assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><span class="pre">ComputedStructureEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L221-L296"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate data in a directory path into a ComputedEntry object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – directory path</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>ComputedEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</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">Any</span><span class="p"><span class="pre">]</span></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">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L306-L315"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.SimpleVaspToComputedEntryDrone.from_dict" 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"><p><strong>dct</strong> (<em>dict</em>) – Dict Representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>SimpleVaspToComputedEntryDrone</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.VaspToComputedEntryDrone">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VaspToComputedEntryDrone</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inc_structure</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>, <em class="sig-param"><span class="n"><span class="pre">parameters</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><span class="pre">str</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>, <em class="sig-param"><span class="n"><span class="pre">data</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><span class="pre">str</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/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L76-L199"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone" title="pymatgen.apps.borg.hive.AbstractDrone"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractDrone</span></code></a></p>
<p>VaspToEntryDrone assimilates directories containing VASP output to
ComputedEntry/ComputedStructureEntry objects.</p>
<p>There are some restrictions on the valid directory structures:</p>
<ol class="arabic simple">
<li><p>There can be only one vasp run in each directory.</p></li>
<li><p>Directories designated “relax1”, “relax2” are considered to be 2 parts
of an aflow style run, and only “relax2” is parsed.</p></li>
<li><p>The drone parses only the vasprun.xml file.</p></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>inc_structure</strong> (<em>bool</em>) – Set to True if you want ComputedStructureEntries
to be returned instead of ComputedEntries.</p></li>
<li><p><strong>parameters</strong> (<em>list</em>) – Input parameters to include. It has to be one of
the properties supported by the Vasprun object. See
pymatgen.io.vasp.Vasprun. If parameters is None,
a default set of parameters that are necessary for typical
post-processing will be set.</p></li>
<li><p><strong>data</strong> (<em>list</em>) – Output data to include. Has to be one of the properties
supported by the Vasprun object.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.VaspToComputedEntryDrone.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><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">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L178-L188"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.VaspToComputedEntryDrone.assimilate">
<span class="sig-name descname"><span class="pre">assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><span class="pre">ComputedStructureEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L121-L152"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate data in a directory path into a ComputedEntry object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – directory path</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>ComputedEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.VaspToComputedEntryDrone.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</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">Any</span><span class="p"><span class="pre">]</span></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">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L190-L199"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.from_dict" 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"><p><strong>dct</strong> (<em>dict</em>) – Dict Representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>VaspToComputedEntryDrone</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.hive.VaspToComputedEntryDrone.get_valid_paths">
<span class="sig-name descname"><span class="pre">get_valid_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</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">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></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">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/hive.py#L154-L176"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.hive.VaspToComputedEntryDrone.get_valid_paths" title="Link to this definition"></a></dt>
<dd><p>Check if paths contains vasprun.xml or (POSCAR+OSZICAR).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – input path as a tuple generated from os.walk, i.e.,
(parent, subdirs, files).</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of valid dir/file paths for assimilation</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.apps.borg.queen">
<span id="pymatgen-apps-borg-queen-module"></span><h2>pymatgen.apps.borg.queen module<a class="headerlink" href="#module-pymatgen.apps.borg.queen" title="Link to this heading"></a></h2>
<p>This module defines the BorgQueen class, which manages drones to assimilate
data using Python’s multiprocessing.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BorgQueen</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drone</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone" title="pymatgen.apps.borg.hive.AbstractDrone"><span class="pre">AbstractDrone</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">rootpath</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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">number_of_drones</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">1</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/../apps/borg/queen.py#L24-L112"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen" title="Link 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>The Borg Queen controls the drones to assimilate data in an entire
directory tree. Uses multiprocessing to speed up things considerably. It
also contains convenience methods to save and load data between sessions.</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>drone</strong> (<a class="reference internal" href="#pymatgen.apps.borg.hive.AbstractDrone" title="pymatgen.apps.borg.hive.AbstractDrone"><em>AbstractDrone</em></a>) – An implementation of
AbstractDrone to use for assimilation.</p></li>
<li><p><strong>rootpath</strong> (<em>PathLike</em>) – The root directory to start assimilation. Leave it
as None if you want to do assimilation later, or is using the
BorgQueen to load previously assimilated data.</p></li>
<li><p><strong>number_of_drones</strong> (<em>int</em>) – Number of drones to parallelize over.
Typical machines today have up to four processors. Note that you
won’t see a 100% improvement with two drones over one, but you
will definitely see a significant speedup of at least 50% or so.
If you are running this over a server with far more processors,
the speedup will be even greater.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen.get_data">
<span class="sig-name descname"><span class="pre">get_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L94-L96"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen.get_data" title="Link to this definition"></a></dt>
<dd><p>Get an list of assimilated objects.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen.load_data">
<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L109-L112"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen.load_data" title="Link to this definition"></a></dt>
<dd><p>Load assimilated data from a file.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen.parallel_assimilate">
<span class="sig-name descname"><span class="pre">parallel_assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rootpath</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L60-L78"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen.parallel_assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate the entire subdirectory structure in rootpath.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen.save_data">
<span class="sig-name descname"><span class="pre">save_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L98-L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen.save_data" title="Link to this definition"></a></dt>
<dd><p>Save the assimilated data to a 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>) – filename to save the assimilated data to. Note
that if the filename ends with gz or bz2, the relevant gzip
or bz2 compression will be applied.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.BorgQueen.serial_assimilate">
<span class="sig-name descname"><span class="pre">serial_assimilate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">PathLike</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L80-L92"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.BorgQueen.serial_assimilate" title="Link to this definition"></a></dt>
<dd><p>Assimilate the entire subdirectory structure in rootpath serially.</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.apps.borg.queen.order_assimilation">
<span class="sig-name descname"><span class="pre">order_assimilation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</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">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../apps/borg/queen.py#L115-L123"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.apps.borg.queen.order_assimilation" title="Link to this definition"></a></dt>
<dd><p>Internal helper method for BorgQueen to process assimilation.</p>
</dd></dl>
</section>
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