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<li><a class="reference internal" href="#">pymatgen.command_line package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.command_line.bader_caller">pymatgen.command_line.bader_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.data"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.data</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_volume"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.vacuum_volume</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_charge"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.vacuum_charge</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.nelectrons"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.nelectrons</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.chgcar"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.chgcar</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.atomic_densities"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.atomic_densities</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.from_path"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.from_path()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_charge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_decorated_structure"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_charge_decorated_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_transfer"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_charge_transfer()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_decorated_structure"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_decorated_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_oxidation_state_decorated_structure"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_oxidation_state_decorated_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_partial_charge"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.get_partial_charge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.BaderAnalysis.summary"><code class="docutils literal notranslate"><span class="pre">BaderAnalysis.summary</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.bader_analysis_from_objects"><code class="docutils literal notranslate"><span class="pre">bader_analysis_from_objects()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.bader_caller.bader_analysis_from_path"><code class="docutils literal notranslate"><span class="pre">bader_analysis_from_path()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.chargemol_caller">pymatgen.command_line.chargemol_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_bond_order"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.get_bond_order()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.get_charge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge_transfer"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.get_charge_transfer()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_partial_charge"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.get_partial_charge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_property_decorated_structure"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.get_property_decorated_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.summary"><code class="docutils literal notranslate"><span class="pre">ChargemolAnalysis.summary</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.critic2_caller">pymatgen.command_line.critic2_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Analysis"><code class="docutils literal notranslate"><span class="pre">Critic2Analysis</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.get_critical_point_for_site"><code class="docutils literal notranslate"><span class="pre">Critic2Analysis.get_critical_point_for_site()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.get_volume_and_charge_for_site"><code class="docutils literal notranslate"><span class="pre">Critic2Analysis.get_volume_and_charge_for_site()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.structure_graph"><code class="docutils literal notranslate"><span class="pre">Critic2Analysis.structure_graph()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Caller"><code class="docutils literal notranslate"><span class="pre">Critic2Caller</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Caller.from_chgcar"><code class="docutils literal notranslate"><span class="pre">Critic2Caller.from_chgcar()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.Critic2Caller.from_path"><code class="docutils literal notranslate"><span class="pre">Critic2Caller.from_path()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPoint"><code class="docutils literal notranslate"><span class="pre">CriticalPoint</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPoint.ellipticity"><code class="docutils literal notranslate"><span class="pre">CriticalPoint.ellipticity</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPoint.laplacian"><code class="docutils literal notranslate"><span class="pre">CriticalPoint.laplacian</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPoint.type"><code class="docutils literal notranslate"><span class="pre">CriticalPoint.type</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType"><code class="docutils literal notranslate"><span class="pre">CriticalPointType</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType.bond"><code class="docutils literal notranslate"><span class="pre">CriticalPointType.bond</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType.cage"><code class="docutils literal notranslate"><span class="pre">CriticalPointType.cage</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType.nnattr"><code class="docutils literal notranslate"><span class="pre">CriticalPointType.nnattr</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType.nucleus"><code class="docutils literal notranslate"><span class="pre">CriticalPointType.nucleus</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType.ring"><code class="docutils literal notranslate"><span class="pre">CriticalPointType.ring</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.critic2_caller.get_filepath"><code class="docutils literal notranslate"><span class="pre">get_filepath()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.enumlib_caller">pymatgen.command_line.enumlib_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.enumlib_caller.EnumError"><code class="docutils literal notranslate"><span class="pre">EnumError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.enumlib_caller.EnumlibAdaptor"><code class="docutils literal notranslate"><span class="pre">EnumlibAdaptor()</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.enumlib_caller.structures"><code class="docutils literal notranslate"><span class="pre">structures</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.gulp_caller">pymatgen.command_line.gulp_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.BuckinghamPotential"><code class="docutils literal notranslate"><span class="pre">BuckinghamPotential</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpCaller"><code class="docutils literal notranslate"><span class="pre">GulpCaller</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpCaller.run"><code class="docutils literal notranslate"><span class="pre">GulpCaller.run()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpConvergenceError"><code class="docutils literal notranslate"><span class="pre">GulpConvergenceError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpError"><code class="docutils literal notranslate"><span class="pre">GulpError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO"><code class="docutils literal notranslate"><span class="pre">GulpIO</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.buckingham_input"><code class="docutils literal notranslate"><span class="pre">GulpIO.buckingham_input()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.buckingham_potential"><code class="docutils literal notranslate"><span class="pre">GulpIO.buckingham_potential()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.get_energy"><code class="docutils literal notranslate"><span class="pre">GulpIO.get_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.get_relaxed_structure"><code class="docutils literal notranslate"><span class="pre">GulpIO.get_relaxed_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.keyword_line"><code class="docutils literal notranslate"><span class="pre">GulpIO.keyword_line()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.library_line"><code class="docutils literal notranslate"><span class="pre">GulpIO.library_line()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.specie_potential_lines"><code class="docutils literal notranslate"><span class="pre">GulpIO.specie_potential_lines()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.structure_lines"><code class="docutils literal notranslate"><span class="pre">GulpIO.structure_lines()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.tersoff_input"><code class="docutils literal notranslate"><span class="pre">GulpIO.tersoff_input()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.GulpIO.tersoff_potential"><code class="docutils literal notranslate"><span class="pre">GulpIO.tersoff_potential()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.TersoffPotential"><code class="docutils literal notranslate"><span class="pre">TersoffPotential</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.get_energy_buckingham"><code class="docutils literal notranslate"><span class="pre">get_energy_buckingham()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.get_energy_relax_structure_buckingham"><code class="docutils literal notranslate"><span class="pre">get_energy_relax_structure_buckingham()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.gulp_caller.get_energy_tersoff"><code class="docutils literal notranslate"><span class="pre">get_energy_tersoff()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.mcsqs_caller">pymatgen.command_line.mcsqs_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs"><code class="docutils literal notranslate"><span class="pre">Sqs</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs.allsqs"><code class="docutils literal notranslate"><span class="pre">Sqs.allsqs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs.bestsqs"><code class="docutils literal notranslate"><span class="pre">Sqs.bestsqs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs.clusters"><code class="docutils literal notranslate"><span class="pre">Sqs.clusters</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs.directory"><code class="docutils literal notranslate"><span class="pre">Sqs.directory</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.Sqs.objective_function"><code class="docutils literal notranslate"><span class="pre">Sqs.objective_function</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.mcsqs_caller.run_mcsqs"><code class="docutils literal notranslate"><span class="pre">run_mcsqs()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.command_line.vampire_caller">pymatgen.command_line.vampire_caller module</a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller"><code class="docutils literal notranslate"><span class="pre">VampireCaller</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.sgraph"><code class="docutils literal notranslate"><span class="pre">VampireCaller.sgraph</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.unique_site_ids"><code class="docutils literal notranslate"><span class="pre">VampireCaller.unique_site_ids</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.nn_interactions"><code class="docutils literal notranslate"><span class="pre">VampireCaller.nn_interactions</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.ex_params"><code class="docutils literal notranslate"><span class="pre">VampireCaller.ex_params</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.mft_t"><code class="docutils literal notranslate"><span class="pre">VampireCaller.mft_t</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.mat_name"><code class="docutils literal notranslate"><span class="pre">VampireCaller.mat_name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.mat_id_dict"><code class="docutils literal notranslate"><span class="pre">VampireCaller.mat_id_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireCaller.parse_stdout"><code class="docutils literal notranslate"><span class="pre">VampireCaller.parse_stdout()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.command_line.vampire_caller.VampireOutput"><code class="docutils literal notranslate"><span class="pre">VampireOutput</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
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<section id="module-pymatgen.command_line">
<span id="pymatgen-command-line-package"></span><h1>pymatgen.command_line package<a class="headerlink" href="#module-pymatgen.command_line" title="Link to this heading"></a></h1>
<p>This package contains various command line wrappers to programs used in
pymatgen that do not have Python equivalents.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.command_line.bader_caller">
<span id="pymatgen-command-line-bader-caller-module"></span><h2>pymatgen.command_line.bader_caller module<a class="headerlink" href="#module-pymatgen.command_line.bader_caller" title="Link to this heading"></a></h2>
<p>This module implements an interface to the Henkelmann et al.’s excellent
Fortran code for calculating a Bader charge analysis.</p>
<p>This module depends on a compiled bader executable available in the path.
Please download the library at <a class="reference external" href="https://theory.cm.utexas.edu/henkelman/code/bader/">https://theory.cm.utexas.edu/henkelman/code/bader/</a>
and follow the instructions to compile the executable.</p>
<p>If you use this module, please cite:</p>
<p>G. Henkelman, A. Arnaldsson, and H. Jonsson, “A fast and robust algorithm for
Bader decomposition of charge density”, Comput. Mater. Sci. 36, 254-360 (2006).</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BaderAnalysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chgcar_filename</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">potcar_filename</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">chgref_filename</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">cube_filename</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">bader_path</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_atomic_densities</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/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L51-L493"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis" 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>Perform Bader charge analysis for Cube files or VASP outputs.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.data">
<span class="sig-name descname"><span class="pre">data</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.data" title="Link to this definition"></a></dt>
<dd><p>Atomic data parsed from bader analysis.
Each dictionary in the list has the keys:
“atomic_vol”, “min_dist”, “charge”, “x”, “y”, “z”.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[dict]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_volume">
<span class="sig-name descname"><span class="pre">vacuum_volume</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_volume" title="Link to this definition"></a></dt>
<dd><p>Vacuum volume of the Bader analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_charge">
<span class="sig-name descname"><span class="pre">vacuum_charge</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.vacuum_charge" title="Link to this definition"></a></dt>
<dd><p>Vacuum charge of the Bader analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.nelectrons">
<span class="sig-name descname"><span class="pre">nelectrons</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.nelectrons" title="Link to this definition"></a></dt>
<dd><p>Number of electrons of the Bader analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.chgcar">
<span class="sig-name descname"><span class="pre">chgcar</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.chgcar" title="Link to this definition"></a></dt>
<dd><p>Chgcar object associated with input CHGCAR file.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.outputs.Chgcar" title="pymatgen.io.vasp.outputs.Chgcar">Chgcar</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.atomic_densities">
<span class="sig-name descname"><span class="pre">atomic_densities</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.atomic_densities" title="Link to this definition"></a></dt>
<dd><p>List of charge densities for each
atom centered on the atom. Each dictionary has the keys:
“data”, “shift”, “dim”, where “data” is the charge density array,
“shift” is the shift used to center the atomic charge density, and
“dim” is the dimension of the original charge density.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[dict]</p>
</dd>
</dl>
</dd></dl>
<p>Initialize the Bader caller.</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>chgcar_filename</strong> (<em>str</em>) – The filename of the CHGCAR.</p></li>
<li><p><strong>potcar_filename</strong> (<em>str</em>) – The filename of the POTCAR.</p></li>
<li><p><strong>chgref_filename</strong> (<em>str</em>) – The filename of the
reference charge density.</p></li>
<li><p><strong>cube_filename</strong> (<em>str</em><em>, </em><em>optional</em>) – The filename of the cube file.</p></li>
<li><p><strong>bader_path</strong> (<em>str</em><em>, </em><em>optional</em>) – The path to the bader executable.</p></li>
<li><p><strong>parse_atomic_densities</strong> (<em>bool</em><em>, </em><em>optional</em>) – Enable atomic partition of the
charge density. Charge densities are atom centered. Defaults to False.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.from_path">
<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_path</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">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</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><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/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L441-L493"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.from_path" title="Link to this definition"></a></dt>
<dd><p>Convenient constructor that takes in the path name of VASP run
to perform Bader analysis.</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>path</strong> (<em>str</em>) – Name of directory where VASP output files are stored.</p></li>
<li><p><strong>suffix</strong> (<em>str</em>) – specific suffix to look for (e.g. ‘.relax1’ for ‘CHGCAR.relax1.gz’).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>BaderAnalysis</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_charge">
<span class="sig-name descname"><span class="pre">get_charge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L303-L315"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge" title="Link to this definition"></a></dt>
<dd><p>Convenience method to get the charge on a particular atom. This is the “raw”
charge generated by the Bader program, not a partial atomic charge. If the cube file
is a spin-density file, then this will return the spin density per atom with
positive being spin up and negative being spin down.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>atom_index</strong> (<em>int</em>) – Index of atom.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Charge associated with atom from the Bader analysis.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_decorated_structure">
<span class="sig-name descname"><span class="pre">get_charge_decorated_structure</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"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><span class="pre">IStructure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L355-L364"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_decorated_structure" title="Link to this definition"></a></dt>
<dd><p>Get a charge decorated structure.</p>
<p>Note, this assumes that the Bader analysis was correctly performed on a file
with electron densities</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_transfer">
<span class="sig-name descname"><span class="pre">get_charge_transfer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nelect</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L317-L336"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_transfer" title="Link to this definition"></a></dt>
<dd><p>Get the charge transferred for a particular atom. A positive value means
that the site has gained electron density (i.e. exhibits anionic character)
whereas a negative value means the site has lost electron density (i.e. exhibits
cationic character). If the arg nelect is not supplied, then POTCAR must be
supplied to determine nelect.</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>atom_index</strong> (<em>int</em>) – Index of atom.</p></li>
<li><p><strong>nelect</strong> (<em>int</em>) – number of electrons associated with an isolated atom at this index.
For most DFT codes this corresponds to the number of valence electrons
associated with the pseudopotential (e.g. ZVAL for VASP).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Charge transfer associated with atom from the Bader analysis.
Given by bader charge on atom - nelect for associated atom.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_decorated_structure">
<span class="sig-name descname"><span class="pre">get_decorated_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">property_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">average</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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L384-L417"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_decorated_structure" title="Link to this definition"></a></dt>
<dd><p>Get a property-decorated structure from the Bader analysis.</p>
<p>This is distinct from getting charge decorated structure, which assumes
the “standard” Bader analysis of electron densities followed by converting
electron count to charge. The expected way to use this is to call Bader on
a non-charge density file such as a spin density file, electrostatic potential
file, etc., while using the charge density file as the reference (chgref_filename)
so that the partitioning is determined via the charge, but averaging or integrating
is done for another property.</p>
<p>User warning: Bader analysis cannot automatically determine what property is
inside of the file. So if you want to use this for a non-conventional property
like spin, you must ensure that you have the file is for the appropriate
property and you have an appropriate reference file.</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>property_name</strong> (<em>str</em>) – name of the property to assign to the structure, note that
if name is “spin” this is handled as a special case, and the appropriate
spin properties are set on the species in the structure</p></li>
<li><p><strong>average</strong> (<em>bool</em>) – whether or not to return the average of this property, rather
than the total, by dividing by the atomic volume.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>structure with site properties assigned via Bader Analysis</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_oxidation_state_decorated_structure">
<span class="sig-name descname"><span class="pre">get_oxidation_state_decorated_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nelects</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">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">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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L366-L382"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_oxidation_state_decorated_structure" title="Link to this definition"></a></dt>
<dd><p>Get an oxidation state decorated structure based on bader analysis results.
Each site is assigned a charge based on the computed partial atomic charge from bader.</p>
<p>Note, this assumes that the Bader analysis was correctly performed on a file
with electron densities.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>nelects</strong> (<em>list</em><em>[</em><em>int</em><em>]</em>) – number of electrons associated with an isolated atom at this index.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>with bader-analysis-based oxidation states.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure">Structure</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.get_partial_charge">
<span class="sig-name descname"><span class="pre">get_partial_charge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nelect</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L338-L353"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_partial_charge" title="Link to this definition"></a></dt>
<dd><p>Convenience method to get the partial charge on a particular atom. This is
simply the negative value of the charge transferred. A positive value indicates
that the atom has cationic character, whereas a negative value indicates the
site has anionic character.</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>atom_index</strong> (<em>int</em>) – Index of atom.</p></li>
<li><p><strong>nelect</strong> (<em>int</em>) – number of electrons associated with an isolated atom at this index.
For most DFT codes this corresponds to the number of valence electrons
associated with the pseudopotential (e.g. ZVAL for VASP).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Charge associated with atom from the Bader analysis.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.BaderAnalysis.summary">
<em class="property"><span class="k"><span class="pre">property</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">summary</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><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></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/bader_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.summary" title="Link to this definition"></a></dt>
<dd><p>Dict summary of key analysis, e.g. atomic volume, charge, etc.</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.bader_analysis_from_objects">
<span class="sig-name descname"><span class="pre">bader_analysis_from_objects</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chgcar</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.outputs.Chgcar" title="pymatgen.io.vasp.outputs.Chgcar"><span class="pre">Chgcar</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">potcar</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.inputs.Potcar" title="pymatgen.io.vasp.inputs.Potcar"><span class="pre">Potcar</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 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">aeccar0</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.outputs.Chgcar" title="pymatgen.io.vasp.outputs.Chgcar"><span class="pre">Chgcar</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 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">aeccar2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.outputs.Chgcar" title="pymatgen.io.vasp.outputs.Chgcar"><span class="pre">Chgcar</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 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> <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/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L554-L636"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.bader_analysis_from_objects" title="Link to this definition"></a></dt>
<dd><p>Convenience method to run Bader analysis from a set
of pymatgen Chgcar and Potcar objects.</p>
<p>This method will:</p>
<p>1. If aeccar objects are present, constructs a temporary reference
file as AECCAR0 + AECCAR2
2. Runs Bader analysis twice: once for charge, and a second time
for the charge difference (magnetization density).</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>chgcar</strong> – Chgcar object</p></li>
<li><p><strong>potcar</strong> – (optional) Potcar object</p></li>
<li><p><strong>aeccar0</strong> – (optional) Chgcar object from aeccar0 file</p></li>
<li><p><strong>aeccar2</strong> – (optional) Chgcar object from aeccar2 file</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>summary dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.bader_caller.bader_analysis_from_path">
<span class="sig-name descname"><span class="pre">bader_analysis_from_path</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">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</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><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/v2025.6.14/src/pymatgen/core/../command_line/bader_caller.py#L496-L551"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.bader_analysis_from_path" title="Link to this definition"></a></dt>
<dd><p>Convenience method to run Bader analysis on a folder containing
typical VASP output files.</p>
<p>This method will:</p>
<p>1. Look for files CHGCAR, AECCAR0, AECCAR2, POTCAR or their gzipped
counterparts.
2. If AECCAR* files are present, constructs a temporary reference
file as AECCAR0 + AECCAR2
3. Runs Bader analysis twice: once for charge, and a second time
for the charge difference (magnetization density).</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>path</strong> – path to folder to search in</p></li>
<li><p><strong>suffix</strong> – specific suffix to look for (e.g. ‘.relax1’ for ‘CHGCAR.relax1.gz’</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>summary dict</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.chargemol_caller">
<span id="pymatgen-command-line-chargemol-caller-module"></span><h2>pymatgen.command_line.chargemol_caller module<a class="headerlink" href="#module-pymatgen.command_line.chargemol_caller" title="Link to this heading"></a></h2>
<p>This module implements an interface to Thomas Manz’s Chargemol code
<a class="reference external" href="https://sourceforge.net/projects/ddec">https://sourceforge.net/projects/ddec</a> for calculating DDEC3, DDEC6, and CM5 population analyses.</p>
<p>This module depends on a compiled chargemol executable being available in the path.
If you use this module, please cite the following based on which modules you use:</p>
<p>Chargemol:
(1) T. A. Manz and N. Gabaldon Limas, Chargemol program for performing DDEC analysis,
Version 3.5, 2017, ddec.sourceforge.net.</p>
<p>DDEC6 Charges:
(1) T. A. Manz and N. Gabaldon Limas, “Introducing DDEC6 atomic population analysis:
part 1. Charge partitioning theory and methodology,” RSC Adv., 6 (2016) 47771-47801.
(2) N. Gabaldon Limas and T. A. Manz, “Introducing DDEC6 atomic population analysis:
part 2. Computed results for a wide range of periodic and nonperiodic materials,”
(3) N. Gabaldon Limas and T. A. Manz, “Introducing DDEC6 atomic population analysis:
part 4. Efficient parallel computation of net atomic charges, atomic spin moments,
bond orders, and more,” RSC Adv., 8 (2018) 2678-2707.</p>
<p>CM5 Charges:
(1) A.V. Marenich, S.V. Jerome, C.J. Cramer, D.G. Truhlar, “Charge Model 5: An Extension
of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions
in Gaseous and Condensed Phases”, J. Chem. Theory. Comput., 8 (2012) 527-541.</p>
<p>Spin Moments:
(1) T. A. Manz and D. S. Sholl, “Methods for Computing Accurate Atomic Spin Moments for
Collinear and Noncollinear Magnetism in Periodic and Nonperiodic Materials,”
J. Chem. Theory Comput. 7 (2011) 4146-4164.</p>
<p>Bond Orders:
(1) “Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute
bond orders,” RSC Adv., 7 (2017) 45552-45581.</p>
<p>DDEC3 Charges:
(1) T. A. Manz and D. S. Sholl, “Improved Atoms-in-Molecule Charge Partitioning Functional
for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic
and Non-Periodic Materials,” J. Chem. Theory Comput. 8 (2012) 2844-2867.
(2) T. A. Manz and D. S. Sholl, “Chemically Meaningful Atomic Charges that Reproduce the
Electrostatic Potential in Periodic and Nonperiodic Materials,” J. Chem. Theory Comput. 6
(2010) 2455-2468.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ChargemolAnalysis</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">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</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">atomic_densities_path</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">Path</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">run_chargemol</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">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L80-L592"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis" 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>Chargemol analysis for DDEC3, DDEC6, and/or CM5 population analyses,
including the calculation of partial atomic charges, atomic spin moments,
bond orders, and related properties.</p>
<p>Initialize the Chargemol Analysis.</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>path</strong> (<em>str</em>) – Path to the CHGCAR, POTCAR, AECCAR0, and AECCAR files.
The files can be gzipped or not. Default: None (current working directory).</p></li>
<li><p><strong>atomic_densities_path</strong> (<em>str</em><em> | </em><em>None</em>) – Path to the atomic densities directory
required by Chargemol. If None, Pymatgen assumes that this is
defined in a “DDEC6_ATOMIC_DENSITIES_DIR” environment variable.
Only used if run_chargemol is True. Default: None.</p></li>
<li><p><strong>run_chargemol</strong> (<em>bool</em>) – Whether to run the Chargemol analysis. If False,
the existing Chargemol output files will be read from path. Default: True.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_bond_order">
<span class="sig-name descname"><span class="pre">get_bond_order</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index_from</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index_to</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L334-L346"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_bond_order" title="Link to this definition"></a></dt>
<dd><p>Convenience method to get the bond order between two atoms.</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>index_from</strong> (<em>int</em>) – Index of atom to get bond order from.</p></li>
<li><p><strong>index_to</strong> (<em>int</em>) – Index of atom to get bond order to.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>bond order between atoms</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge">
<span class="sig-name descname"><span class="pre">get_charge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nelect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'ddec'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'cm5'</span></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">'ddec'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L286-L316"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge" title="Link to this definition"></a></dt>
<dd><p>Convenience method to get the charge on a particular atom using the same
sign convention as the BaderAnalysis. Note that this is <em>not</em> the partial
atomic charge. This value is nelect (e.g. ZVAL from the POTCAR) + the
charge transferred. If you want the partial atomic charge, use
get_partial_charge().</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>atom_index</strong> (<em>int</em>) – Index of atom to get charge for.</p></li>
<li><p><strong>nelect</strong> (<em>int</em>) – number of electrons associated with an isolated atom at this index.</p></li>
<li><p><strong>electrons</strong> (<em>For most DFT codes this corresponds to the number</em><em> of </em><em>valence</em>)</p></li>
<li><p><strong>None</strong> (<em>associated with the pseudopotential. If</em>)</p></li>
<li><p><strong>automatically</strong> (<em>this value will be</em>)</p></li>
<li><p><strong>POTCAR</strong> (<em>obtained from the</em>) – Default: None.</p></li>
<li><p><strong>charge_type</strong> (<em>str</em>) – Type of charge to use (“ddec” or “cm5”).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>charge on atom_index</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge_transfer">
<span class="sig-name descname"><span class="pre">get_charge_transfer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ddec'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L264-L284"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_charge_transfer" title="Link to this definition"></a></dt>
<dd><p>Get the charge transferred for a particular atom. A positive value means
that the site has gained electron density (i.e. exhibits anionic character)
whereas a negative value means the site has lost electron density (i.e. exhibits
cationic character). This is the same thing as the negative of the partial atomic
charge.</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>atom_index</strong> (<em>int</em>) – Index of atom to get charge transfer for.</p></li>
<li><p><strong>charge_type</strong> (<em>str</em>) – Type of charge to use (“ddec” or “cm5”).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>charge transferred at atom_index</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_partial_charge">
<span class="sig-name descname"><span class="pre">get_partial_charge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'ddec'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'cm5'</span></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">'ddec'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L318-L332"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_partial_charge" title="Link to this definition"></a></dt>
<dd><p>Convenience method to get the partial atomic charge on a particular atom.
This is the value printed in the Chargemol analysis.</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>atom_index</strong> (<em>int</em>) – Index of atom to get charge for.</p></li>
<li><p><strong>charge_type</strong> (<em>str</em>) – Type of charge to use (“ddec” or “cm5”).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_property_decorated_structure">
<span class="sig-name descname"><span class="pre">get_property_decorated_structure</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/chargemol_caller.py#L482-L499"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.get_property_decorated_structure" title="Link to this definition"></a></dt>
<dd><p>Takes CHGCAR’s structure object and updates it with properties
from the Chargemol analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Pymatgen structure with site properties added</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.command_line.chargemol_caller.ChargemolAnalysis.summary">
<em class="property"><span class="k"><span class="pre">property</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">summary</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/chargemol_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.chargemol_caller.ChargemolAnalysis.summary" title="Link to this definition"></a></dt>
<dd><p>A dictionary summary of the Chargemol analysis
{</p>
<blockquote>
<div><dl class="simple">
<dt>“ddec”: {</dt><dd><p>“partial_charges”: list[float],
“spin_moments”: list[float],
“dipoles”: list[float],
“rsquared_moments”: list[float],
“rcubed_moments”: list[float],
“rfourth_moments”: list[float],
“bond_order_dict”: dict</p>
</dd>
</dl>
<p>},
“cm5”: {</p>
<blockquote>
<div><p>“partial_charges”: list[float],</p>
</div></blockquote>
<p>}</p>
</div></blockquote>
<p>}.</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.critic2_caller">
<span id="pymatgen-command-line-critic2-caller-module"></span><h2>pymatgen.command_line.critic2_caller module<a class="headerlink" href="#module-pymatgen.command_line.critic2_caller" title="Link to this heading"></a></h2>
<p>This module implements an interface to the critic2 Bader analysis code.</p>
<p>For most Bader analysis purposes, users are referred to
pymatgen.command_line.bader_caller instead, this module is for advanced
usage requiring identification of critical points in the charge density.</p>
<p>This module depends on a compiled critic2 executable available in the path.
Please follow the instructions at <a class="reference external" href="https://github.com/aoterodelaroza/critic2">https://github.com/aoterodelaroza/critic2</a>
to compile.</p>
<p>New users are <em>strongly</em> encouraged to read the critic2 manual first.</p>
<p>In brief,
* critic2 searches for critical points in charge density
* a critical point can be one of four types: nucleus, bond, ring
or cage
* it does this by seeding locations for likely critical points
and then searching in these regions
* there are two lists of critical points in the output, a list
of non-equivalent points (with in-depth information about the
field at those points), and a full list of points generated
by the appropriate symmetry operations
* connectivity between these points is also provided when
appropriate (e.g. the two nucleus critical points linked to</p>
<blockquote>
<div><p>a bond critical point)</p>
</div></blockquote>
<ul class="simple">
<li><p>critic2 can do many other things besides</p></li>
</ul>
<p>If you use this module, please cite:</p>
<p>A. Otero-de-la-Roza, E. R. Johnson and V. Luaña,
Comput. Phys. Communications 185, 1007-1018 (2014)
(<a class="reference external" href="https://doi.org/10.1016/j.cpc.2013.10.026">https://doi.org/10.1016/j.cpc.2013.10.026</a>)</p>
<p>A. Otero-de-la-Roza, M. A. Blanco, A. Martín Pendás and
V. Luaña, Comput. Phys. Communications 180, 157-166 (2009)
(<a class="reference external" href="https://doi.org/10.1016/j.cpc.2008.07.018">https://doi.org/10.1016/j.cpc.2008.07.018</a>)</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Analysis">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Critic2Analysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stderr</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cpreport</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</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">yt</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</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">zpsp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</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/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L414-L915"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Analysis" 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>Process the standard output from critic2 into pymatgen-compatible objects.</p>
<p>This class is used to store results from the Critic2Caller.</p>
<p>To explore the bond graph, use the “structure_graph”
method, which returns a user-friendly StructureGraph
class with bonding information. By default, this returns
a StructureGraph with edge weights as bond lengths, but
can optionally return a graph with edge weights as any
property supported by the <cite>CriticalPoint</cite> class, such as
bond ellipticity.</p>
<p>This class also provides an interface to explore just the
non-symmetrically-equivalent critical points via the
<cite>critical_points</cite> attribute, and also all critical
points (via nodes dict) and connections between them
(via edges dict). The user should be familiar with critic2
before trying to understand these.</p>
<p>Indexes of nucleus critical points in the nodes dict are the
same as the corresponding sites in structure, with indices of
other critical points arbitrarily assigned.</p>
<p>Only one of (stdout, cpreport) required, with cpreport preferred
since this is a new, native JSON output from critic2.</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>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – associated Structure</p></li>
<li><p><strong>stdout</strong> (<em>str</em><em>, </em><em>optional</em>) – stdout from running critic2 in automatic mode</p></li>
<li><p><strong>stderr</strong> (<em>str</em><em>, </em><em>optional</em>) – stderr from running critic2 in automatic mode</p></li>
<li><p><strong>cpreport</strong> (<em>dict</em><em>, </em><em>optional</em>) – JSON output from CPREPORT command</p></li>
<li><p><strong>yt</strong> (<em>dict</em><em>, </em><em>optional</em>) – JSON output from YT command</p></li>
<li><p><strong>zpsp</strong> (<em>dict</em><em>, </em><em>optional</em>) – Dict of element/symbol name to number of electrons
(ZVAL in VASP pseudopotential), with which to calculate charge transfer.
Optional.</p></li>
<li><p><strong>structure</strong> – Associated Structure.</p></li>
<li><p><strong>stdout</strong> – stdout from running critic2 in automatic mode.</p></li>
<li><p><strong>stderr</strong> – stderr from running critic2 in automatic mode.</p></li>
<li><p><strong>cpreport</strong> – JSON output from CPREPORT command. Either this or stdout required.</p></li>
<li><p><strong>yt</strong> – JSON output from YT command.</p></li>
<li><p><strong>zpsp</strong> – Dict of element/symbol name to number of electrons (ZVAL in VASP pseudopotential),
with which to calculate charge transfer. Optional.</p></li>
</ul>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>ValueError</strong> – If one of cpreport or stdout is not provided.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Analysis.get_critical_point_for_site">
<span class="sig-name descname"><span class="pre">get_critical_point_for_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L611-L619"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.get_critical_point_for_site" 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>n</strong> (<em>int</em>) – Site index.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>CriticalPoint</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Analysis.get_volume_and_charge_for_site">
<span class="sig-name descname"><span class="pre">get_volume_and_charge_for_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L621-L631"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.get_volume_and_charge_for_site" 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>idx</strong> – Site index.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>with “volume” and “charge” keys, or None if YT integration not performed</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Analysis.structure_graph">
<span class="sig-name descname"><span class="pre">structure_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">include_critical_points</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('bond',</span> <span class="pre">'ring',</span> <span class="pre">'cage')</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L495-L609"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Analysis.structure_graph" title="Link to this definition"></a></dt>
<dd><p>A StructureGraph object describing bonding information in the crystal.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>include_critical_points</strong> – add DummySpecies for the critical points themselves, a list of
“nucleus”, “bond”, “ring”, “cage”, set to None to disable</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>StructureGraph</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Caller">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Critic2Caller</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_script</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L80-L310"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Caller" 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>Call critic2 and store standard output for further processing.</p>
<p>Run Critic2 on a given input script.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_script</strong> – string defining the critic2 input</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Caller.from_chgcar">
<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_chgcar</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chgcar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chgcar_ref</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">user_input_settings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_cml</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_json</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">zpsp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L123-L252"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Caller.from_chgcar" title="Link to this definition"></a></dt>
<dd><p>Run Critic2 in automatic mode on a supplied structure, charge
density (chgcar) and reference charge density (chgcar_ref).</p>
<p>The reason for a separate reference field is that in
VASP, the CHGCAR charge density only contains valence
electrons and may be missing substantial charge at
nuclei leading to misleading results. Thus, a reference
field is commonly constructed from the sum of AECCAR0
and AECCAR2 which is the total charge density, but then
the valence charge density is used for the final analysis.</p>
<p>If chgcar_ref is not supplied, chgcar will be used as the
reference field. If chgcar is not supplied, the promolecular
charge density will be used as the reference field – this can
often still give useful results if only topological information
is wanted.</p>
<p>User settings is a dictionary that can contain:
* GRADEPS, float (field units), gradient norm threshold
* CPEPS, float (Bohr units in crystals), minimum distance between</p>
<blockquote>
<div><p>critical points for them to be equivalent</p>
</div></blockquote>
<ul class="simple">
<li><p>NUCEPS, same as CPEPS but specifically for nucleus critical
points (critic2 default is dependent on grid dimensions)</p></li>
<li><p>NUCEPSH, same as NUCEPS but specifically for hydrogen nuclei
since associated charge density can be significantly displaced
from hydrogen nucleus</p></li>
<li><p>EPSDEGEN, float (field units), discard critical point if any
element of the diagonal of the Hessian is below this value,
useful for discarding points in vacuum regions</p></li>
<li><p>DISCARD, float (field units), discard critical points with field
value below this value, useful for discarding points in vacuum
regions</p></li>
<li><p>SEED, list of strings, strategies for seeding points, default
is [‘WS 1’, ‘PAIR 10’] which seeds critical points by
sub-dividing the Wigner-Seitz cell and between every atom pair
closer than 10 Bohr, see critic2 manual for more options</p></li>
</ul>
<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>structure</strong> – Structure to analyze</p></li>
<li><p><strong>chgcar</strong> – Charge density to use for analysis. If None, will
use promolecular density. Should be a Chgcar object or path (string).</p></li>
<li><p><strong>chgcar_ref</strong> – Reference charge density. If None, will use
chgcar as reference. Should be a Chgcar object or path (string).</p></li>
<li><p><strong>user_input_settings</strong> (<em>dict</em>) – as explained above</p></li>
<li><p><strong>write_cml</strong> (<em>bool</em>) – Useful for debug, if True will write all
critical points to a file ‘table.cml’ in the working directory
useful for visualization</p></li>
<li><p><strong>write_json</strong> (<em>bool</em>) – Whether to write out critical points
and YT JSON. YT integration will be performed with this setting.</p></li>
<li><p><strong>zpsp</strong> (<em>dict</em>) – Dict of element/symbol name to number of electrons
(ZVAL in VASP pseudopotential), with which to properly augment core regions
and calculate charge transfer. Optional.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.Critic2Caller.from_path">
<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zpsp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L254-L310"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.Critic2Caller.from_path" title="Link to this definition"></a></dt>
<dd><p>Convenience method to run critic2 analysis on a folder with typical VASP output files.</p>
<p>This method will:</p>
<p>1. Look for files CHGCAR, AECAR0, AECAR2, POTCAR or their gzipped
counterparts.</p>
<p>2. If AECCAR* files are present, constructs a temporary reference
file as AECCAR0 + AECCAR2.</p>
<p>3. Runs critic2 analysis twice: once for charge, and a second time
for the charge difference (magnetization density).</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>path</strong> – path to folder to search in</p></li>
<li><p><strong>suffix</strong> – specific suffix to look for (e.g. ‘.relax1’ for
‘CHGCAR.relax1.gz’)</p></li>
<li><p><strong>zpsp</strong> – manually specify ZPSP if POTCAR not present</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPoint">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CriticalPoint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frac_coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">point_group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multiplicity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field_gradient</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field_hessian</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L346-L411"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPoint" 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>Access information about a critical point and the field values at that point.</p>
<p>Characterize a critical point from a topological
analysis of electron charge density.</p>
<p>Note this class is usually associated with a Structure, so
has information on multiplicity/point group symmetry.</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>index</strong> – index of point</p></li>
<li><p><strong>type</strong> – type of point, given as a string</p></li>
<li><p><strong>coords</strong> – Cartesian coordinates in Angstroms</p></li>
<li><p><strong>frac_coords</strong> – fractional coordinates</p></li>
<li><p><strong>point_group</strong> – point group associated with critical point</p></li>
<li><p><strong>multiplicity</strong> – number of equivalent critical points</p></li>
<li><p><strong>field</strong> – value of field at point (f)</p></li>
<li><p><strong>field_gradient</strong> – gradient of field at point (grad f)</p></li>
<li><p><strong>field_hessian</strong> – hessian of field at point (del^2 f)</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPoint.ellipticity">
<em class="property"><span class="k"><span class="pre">property</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ellipticity</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPoint.ellipticity" title="Link to this definition"></a></dt>
<dd><p>Most meaningful for bond critical points, can be physically interpreted as e.g.
degree of pi-bonding in organic molecules. Consult literature for more info.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>The ellipticity of the field at the critical point.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPoint.laplacian">
<em class="property"><span class="k"><span class="pre">property</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">laplacian</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPoint.laplacian" title="Link to this definition"></a></dt>
<dd><p>The Laplacian of the field at the critical point.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPoint.type">
<em class="property"><span class="k"><span class="pre">property</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">type</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.command_line.critic2_caller.CriticalPointType" title="pymatgen.command_line.critic2_caller.CriticalPointType"><span class="pre">CriticalPointType</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPoint.type" title="Link to this definition"></a></dt>
<dd><p>Instance of CriticalPointType.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CriticalPointType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L313-L321"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Enum</span></code></p>
<p>Enum type for the different varieties of critical point.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType.bond">
<span class="sig-name descname"><span class="pre">bond</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'bond'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType.bond" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType.cage">
<span class="sig-name descname"><span class="pre">cage</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'cage'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType.cage" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType.nnattr">
<span class="sig-name descname"><span class="pre">nnattr</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'nnattr'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType.nnattr" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType.nucleus">
<span class="sig-name descname"><span class="pre">nucleus</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'nucleus'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType.nucleus" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.CriticalPointType.ring">
<span class="sig-name descname"><span class="pre">ring</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'ring'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/critic2_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.CriticalPointType.ring" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.critic2_caller.get_filepath">
<span class="sig-name descname"><span class="pre">get_filepath</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">warning</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/critic2_caller.py#L324-L343"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.critic2_caller.get_filepath" 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>filename</strong> – Filename</p></li>
<li><p><strong>warning</strong> – Warning message</p></li>
<li><p><strong>path</strong> – Path to search</p></li>
<li><p><strong>suffix</strong> – Suffixes to search.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.enumlib_caller">
<span id="pymatgen-command-line-enumlib-caller-module"></span><h2>pymatgen.command_line.enumlib_caller module<a class="headerlink" href="#module-pymatgen.command_line.enumlib_caller" title="Link to this heading"></a></h2>
<p>This module implements an interface to enumlib, Gus Hart’s excellent Fortran
code for enumerating derivative structures.</p>
<p>This module depends on a compiled enumlib with the executables enum.x and
makestr.x available in the path. Please download the library at
<a class="reference external" href="https://github.com/msg-byu/enumlib">https://github.com/msg-byu/enumlib</a> and follow the instructions in the README to
compile these two executables accordingly.</p>
<p>If you use this module, please cite:</p>
<blockquote>
<div><ul class="simple">
<li><p>Gus L. W. Hart and Rodney W. Forcade, “Algorithm for generating derivative</p></li>
</ul>
<p>structures,” Phys. Rev. B 77 224115 (26 June 2008)</p>
<ul class="simple">
<li><p>Gus L. W. Hart and Rodney W. Forcade, “Generating derivative structures from</p></li>
</ul>
<p>multilattices: Application to hcp alloys,” Phys. Rev. B 80 014120 (July 2009)</p>
<ul class="simple">
<li><p>Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, “Generating</p></li>
</ul>
<p>derivative structures at a fixed concentration,” Comp. Mat. Sci. 59
101-107 (March 2012)</p>
<ul class="simple">
<li><p>Wiley S. Morgan, Gus L. W. Hart, Rodney W. Forcade, “Generating derivative</p></li>
</ul>
<p>superstructures for systems with high configurational freedom,” Comp. Mat.
Sci. 136 144-149 (May 2017)</p>
</div></blockquote>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.command_line.enumlib_caller.EnumError">
<em class="property"><span class="k"><span class="pre">exception</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EnumError</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/enumlib_caller.py#L411-L412"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.enumlib_caller.EnumError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">BaseException</span></code></p>
<p>Error subclass for enumeration errors.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.enumlib_caller.EnumlibAdaptor">
<span class="sig-name descname"><span class="pre">EnumlibAdaptor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><span class="pre">IStructure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_cell_size</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>, <em class="sig-param"><span class="n"><span class="pre">max_cell_size</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>, <em class="sig-param"><span class="n"><span class="pre">symm_prec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enum_precision_parameter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refine_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">check_ordered_symmetry</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timeout</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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> <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/v2025.6.14/src/pymatgen/core/../../../.venv/lib/python3.11/site-packages/monty/dev.py#L60-L408"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.enumlib_caller.EnumlibAdaptor" title="Link to this definition"></a></dt>
<dd><p>An adaptor for enumlib.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.enumlib_caller.structures">
<span class="sig-name descname"><span class="pre">structures</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/enumlib_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.enumlib_caller.structures" title="Link to this definition"></a></dt>
<dd><p>all enumerated structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure">Structure</a>]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.gulp_caller">
<span id="pymatgen-command-line-gulp-caller-module"></span><h2>pymatgen.command_line.gulp_caller module<a class="headerlink" href="#module-pymatgen.command_line.gulp_caller" title="Link to this heading"></a></h2>
<p>Interface with command line GULP.
<a class="reference external" href="https://gulp.curtin.edu.au/index.html">https://gulp.curtin.edu.au/index.html</a>
WARNING: you need to have GULP installed on your system.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.BuckinghamPotential">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BuckinghamPotential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bush_lewis_flag</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pot_file</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L648-L726"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.BuckinghamPotential" 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>Generate the Buckingham Potential Table from the bush.lib or lewis.lib.</p>
<p>Ref:
T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle, J. Mater Chem.,
4, 831-837 (1994).
G.V. Lewis and C.R.A. Catlow, J. Phys. C: Solid State Phys., 18,
1149-1161 (1985)</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>bush_lewis_flag</strong> (<em>str</em>) – Flag for using Bush or Lewis potential.</p></li>
<li><p><strong>pot_file</strong> – The potential file, either bush.lib or lewis.lib.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpCaller">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GulpCaller</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmd</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gulp'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L493-L562"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpCaller" 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>Run gulp from command line.</p>
<p>Initialize with the executable if not in the standard path.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>cmd</strong> – Command. Defaults to gulp.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpCaller.run">
<span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gin</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L520-L562"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpCaller.run" title="Link to this definition"></a></dt>
<dd><p>Run GULP using the gin as input.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>gin</strong> – GULP input string</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>GULP output string</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>gout</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpConvergenceError">
<em class="property"><span class="k"><span class="pre">exception</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GulpConvergenceError</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">msg</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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L631-L645"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpConvergenceError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Exception class for GULP.
Raised when proper convergence is not reached in Mott-Littleton
defect energy optimization procedure in GULP.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>msg</strong> (<em>str</em>) – Message.</p>
</dd>
</dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpError">
<em class="property"><span class="k"><span class="pre">exception</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GulpError</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">msg</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L615-L628"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Exception class for GULP.
Raised when the GULP gives an error.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>msg</strong> (<em>str</em>) – Message.</p>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GulpIO</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L98-L490"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO" 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>To generate GULP input and process output.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.buckingham_input">
<span class="sig-name descname"><span class="pre">buckingham_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">keywords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">library</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uc</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">valence_dict</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L232-L249"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.buckingham_input" title="Link to this definition"></a></dt>
<dd><p>Get a GULP input for an oxide structure and buckingham potential
from library.</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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>keywords</strong> – GULP first line keywords.</p></li>
<li><p><strong>library</strong> (<em>Default=None</em>) – File containing the species and potential.</p></li>
<li><p><strong>uc</strong> (<em>Default=True</em>) – Unit Cell Flag.</p></li>
<li><p><strong>valence_dict</strong> – {El: valence}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.buckingham_potential">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">buckingham_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">val_dict</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L251-L318"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.buckingham_potential" title="Link to this definition"></a></dt>
<dd><p>Generate species, buckingham, and spring options for an oxide structure
using the parameters in default libraries.</p>
<dl class="simple">
<dt>Ref:</dt><dd><ol class="arabic simple">
<li><p>G.V. Lewis and C.R.A. Catlow, J. Phys. C: Solid State Phys.,
18, 1149-1161 (1985)</p></li>
<li><p>T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle,
J. Mater Chem., 4, 831-837 (1994)</p></li>
</ol>
</dd>
</dl>
<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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>val_dict</strong> (<em>Needed if structure is not charge neutral</em>) – {El:valence}
dict, where El is element.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.get_energy">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gout</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L377-L394"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.get_energy" 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>gout</strong> (<em>str</em>) – GULP output string.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.get_relaxed_structure">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_relaxed_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gout</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L396-L490"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.get_relaxed_structure" 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>gout</strong> (<em>str</em>) – GULP output string.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>relaxed structure.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure">Structure</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.keyword_line">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">keyword_line</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L101-L111"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.keyword_line" title="Link to this definition"></a></dt>
<dd><p>Check if the input args are proper gulp keywords and
generates the 1st line of gulp input. Full keywords are expected.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>args</strong> – 1st line keywords</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.library_line">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">library_line</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L198-L230"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.library_line" title="Link to this definition"></a></dt>
<dd><p>Specify GULP library file to read species and potential parameters.
If using library don’t specify species and potential
in the input file and vice versa. Make sure the elements of
structure are in the library file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>file_name</strong> – Name of GULP library file</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>GULP input string specifying library option</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.specie_potential_lines">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">specie_potential_lines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">potential</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L175-L196"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.specie_potential_lines" title="Link to this definition"></a></dt>
<dd><p>Generate GULP input species and potential string for pymatgen structure.</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>structure</strong> – pymatgen Structure object</p></li>
<li><p><strong>potential</strong> – String specifying the type of potential used</p></li>
<li><p><strong>kwargs</strong> – Additional parameters related to potential. For
potential == “buckingham”,
anion_shell_flg (default = False):
If True, anions are considered polarizable.
anion_core_chrg=float
anion_shell_chrg=float
cation_shell_flg (default = False):
If True, cations are considered polarizable.
cation_core_chrg=float
cation_shell_chrg=float</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>containing species and potential for GULP input</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.command_line.gulp_caller.GulpIO.structure_lines">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structure_lines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_flg</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frac_flg</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anion_shell_flg</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cation_shell_flg</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">symm_flg</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">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L113-L173"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.structure_lines" title="Link to this definition"></a></dt>
<dd><p>Generate GULP input string corresponding to pymatgen structure.</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>structure</strong> – pymatgen Structure object</p></li>
<li><p><strong>cell_flg</strong> (<em>default = True</em>) – Option to use lattice parameters.</p></li>
<li><p><strong>frac_flg</strong> (<em>default = True</em>) – If True, fractional coordinates
are used. Else, Cartesian coordinates in Angstroms are used.
<strong>**</strong>
GULP convention is to use fractional coordinates for periodic
structures and Cartesian coordinates for non-periodic
structures.
<strong>**</strong></p></li>
<li><p><strong>anion_shell_flg</strong> (<em>default = True</em>) – If True, anions are considered
polarizable.</p></li>
<li><p><strong>cation_shell_flg</strong> (<em>default = False</em>) – If True, cations are
considered polarizable.</p></li>
<li><p><strong>symm_flg</strong> (<em>default = True</em>) – If True, symmetry information is also
written.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>containing structure for GULP input</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.command_line.gulp_caller.GulpIO.tersoff_input">
<span class="sig-name descname"><span class="pre">tersoff_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uc</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="o"><span class="pre">*</span></span><span class="n"><span class="pre">keywords</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L320-L342"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.tersoff_input" title="Link to this definition"></a></dt>
<dd><p>Get a GULP input with Tersoff potential for an oxide structure.</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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>periodic</strong> (<em>Default=False</em>) – Flag denoting whether periodic
boundary conditions are used</p></li>
<li><p><strong>library</strong> (<em>Default=None</em>) – File containing the species and potential.</p></li>
<li><p><strong>uc</strong> (<em>Default=True</em>) – Unit Cell Flag.</p></li>
<li><p><strong>keywords</strong> – GULP first line keywords.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.GulpIO.tersoff_potential">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">tersoff_potential</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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L344-L375"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.GulpIO.tersoff_potential" title="Link to this definition"></a></dt>
<dd><p>Generate the species, Tersoff potential lines for an oxide structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – pymatgen Structure</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.TersoffPotential">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TersoffPotential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pot_file</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L729-L740"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.TersoffPotential" 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>Generate Tersoff Potential Table from “OxideTersoffPotentialentials” file.</p>
<p>Init TersoffPotential.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.get_energy_buckingham">
<span class="sig-name descname"><span class="pre">get_energy_buckingham</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gulp_cmd</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gulp'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keywords</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('optimise',</span> <span class="pre">'conp',</span> <span class="pre">'qok')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valence_dict</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L579-L593"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.get_energy_buckingham" title="Link to this definition"></a></dt>
<dd><p>Compute the energy of a structure using Buckingham potential.</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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>gulp_cmd</strong> – GULP command if not in standard place</p></li>
<li><p><strong>keywords</strong> – GULP first line keywords</p></li>
<li><p><strong>valence_dict</strong> – {El: valence}. Needed if the structure is not charge
neutral.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.get_energy_relax_structure_buckingham">
<span class="sig-name descname"><span class="pre">get_energy_relax_structure_buckingham</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gulp_cmd</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gulp'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keywords</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('optimise',</span> <span class="pre">'conp')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valence_dict</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L596-L612"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.get_energy_relax_structure_buckingham" title="Link to this definition"></a></dt>
<dd><p>Relax a structure and compute the energy using Buckingham potential.</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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>gulp_cmd</strong> – GULP command if not in standard place</p></li>
<li><p><strong>keywords</strong> – GULP first line keywords</p></li>
<li><p><strong>valence_dict</strong> – {El: valence}. Needed if the structure is not charge
neutral.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.gulp_caller.get_energy_tersoff">
<span class="sig-name descname"><span class="pre">get_energy_tersoff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gulp_cmd</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'gulp'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/gulp_caller.py#L565-L576"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.gulp_caller.get_energy_tersoff" title="Link to this definition"></a></dt>
<dd><p>Compute the energy of a structure using Tersoff potential.</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>structure</strong> – pymatgen Structure</p></li>
<li><p><strong>gulp_cmd</strong> – GULP command if not in standard place</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.mcsqs_caller">
<span id="pymatgen-command-line-mcsqs-caller-module"></span><h2>pymatgen.command_line.mcsqs_caller module<a class="headerlink" href="#module-pymatgen.command_line.mcsqs_caller" title="Link to this heading"></a></h2>
<p>Module to call mcsqs, distributed with AT-AT
<a class="reference external" href="https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/">https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/</a>.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Sqs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bestsqs</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><span class="pre">IStructure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">objective_function</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allsqs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clusters</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/mcsqs_caller.py#L23-L30"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Return type for run_mcsqs.</p>
<p>Create new instance of Sqs(bestsqs, objective_function, allsqs, clusters, directory)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs.allsqs">
<span class="sig-name descname"><span class="pre">allsqs</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/mcsqs_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs.allsqs" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs.bestsqs">
<span class="sig-name descname"><span class="pre">bestsqs</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><span class="pre">IStructure</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/mcsqs_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs.bestsqs" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs.clusters">
<span class="sig-name descname"><span class="pre">clusters</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/mcsqs_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs.clusters" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs.directory">
<span class="sig-name descname"><span class="pre">directory</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/mcsqs_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs.directory" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 4</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.Sqs.objective_function">
<span class="sig-name descname"><span class="pre">objective_function</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/mcsqs_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.Sqs.objective_function" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.command_line.mcsqs_caller.run_mcsqs">
<span class="sig-name descname"><span class="pre">run_mcsqs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</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.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><span class="pre">IStructure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">clusters</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">int</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></em>, <em class="sig-param"><span class="n"><span class="pre">scaling</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </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><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>, <em class="sig-param"><span class="n"><span class="pre">search_time</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">60</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</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">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">instances</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">temperature</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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>, <em class="sig-param"><span class="n"><span class="pre">wr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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>, <em class="sig-param"><span class="n"><span class="pre">wn</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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>, <em class="sig-param"><span class="n"><span class="pre">wd</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</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">0.001</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.command_line.mcsqs_caller.Sqs" title="pymatgen.command_line.mcsqs_caller.Sqs"><span class="pre">Sqs</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../../../.venv/lib/python3.11/site-packages/monty/dev.py#L33-L169"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.mcsqs_caller.run_mcsqs" title="Link to this definition"></a></dt>
<dd><p>Helper function for calling mcsqs with different arguments
:param structure: Disordered pymatgen Structure object
:type structure: Structure
:param clusters: Dictionary of cluster interactions with entries in the form</p>
<blockquote>
<div><p>number of atoms: cutoff in angstroms</p>
</div></blockquote>
<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>scaling</strong> (<em>int</em><em> or </em><em>list</em>) – <dl class="simple">
<dt>Scaling factor to determine supercell. Two options are possible:</dt><dd><ol class="loweralpha simple">
<li><p>(preferred) Scales number of atoms, e.g. for a structure with 8 atoms,
scaling=4 would lead to a 32 atom supercell</p></li>
<li><p>A sequence of three scaling factors, e.g. [2, 1, 1], which
specifies that the supercell should have dimensions 2a x b x c</p></li>
</ol>
</dd>
</dl>
<p>Defaults to 1.</p>
</p></li>
<li><p><strong>search_time</strong> (<em>float</em>) – Time spent looking for the ideal SQS in minutes (default: 60)</p></li>
<li><p><strong>directory</strong> (<em>str</em>) – Directory to run mcsqs calculation and store files (default: None
runs calculations in a temp directory)</p></li>
<li><p><strong>instances</strong> (<em>int</em>) – Specifies the number of parallel instances of mcsqs to run
(default: number of cpu cores detected by Python)</p></li>
<li><p><strong>temperature</strong> (<em>float</em>) – Monte Carlo temperature (default: 1), “T” in atat code</p></li>
<li><p><strong>wr</strong> (<em>float</em>) – Weight assigned to range of perfect correlation match in objective
function (default = 1)</p></li>
<li><p><strong>wn</strong> (<em>float</em>) – Multiplicative decrease in weight per additional point in cluster (default: 1)</p></li>
<li><p><strong>wd</strong> (<em>float</em>) – Exponent of decay in weight as function of cluster diameter (default: 0.5)</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – Tolerance for matching correlations (default: 1e-3).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Pymatgen structure SQS of the input structure, the mcsqs objective function,</dt><dd><p>list of all SQS structures, and the directory where calculations are run</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.command_line.vampire_caller">
<span id="pymatgen-command-line-vampire-caller-module"></span><h2>pymatgen.command_line.vampire_caller module<a class="headerlink" href="#module-pymatgen.command_line.vampire_caller" title="Link to this heading"></a></h2>
<p>This module implements an interface to the VAMPIRE code for atomistic
simulations of magnetic materials.</p>
<p>This module depends on a compiled vampire executable available in the path.
Please download at <a class="reference external" href="https://vampire.york.ac.uk/download/">https://vampire.york.ac.uk/download/</a> and
follow the instructions to compile the executable.</p>
<p>If you use this module, please cite:</p>
<p>“Atomistic spin model simulations of magnetic nanomaterials.”
R. F. L. Evans, W. J. Fan, P. Chureemart, T. A. Ostler, M. O. A. Ellis
and R. W. Chantrell. J. Phys.: Condens. Matter 26, 103202 (2014)</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VampireCaller</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ordered_structures</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mc_box_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">equil_timesteps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mc_timesteps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_inputs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avg</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">user_input_settings</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/vampire_caller.py#L39-L402"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller" 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>Run Vampire on a material with magnetic ordering and exchange parameter
information to compute the critical temperature with classical Monte Carlo.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.sgraph">
<span class="sig-name descname"><span class="pre">sgraph</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.sgraph" title="Link to this definition"></a></dt>
<dd><p>Ground state graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.analysis.html#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph">StructureGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.unique_site_ids">
<span class="sig-name descname"><span class="pre">unique_site_ids</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.unique_site_ids" title="Link to this definition"></a></dt>
<dd><p>Maps each site to its unique identifier</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.nn_interactions">
<span class="sig-name descname"><span class="pre">nn_interactions</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.nn_interactions" title="Link to this definition"></a></dt>
<dd><p>{i: j} pairs of NN interactions
between unique sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.ex_params">
<span class="sig-name descname"><span class="pre">ex_params</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.ex_params" title="Link to this definition"></a></dt>
<dd><p>Exchange parameter values (meV/atom)</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.mft_t">
<span class="sig-name descname"><span class="pre">mft_t</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.mft_t" title="Link to this definition"></a></dt>
<dd><p>Mean field theory estimate of critical T</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.mat_name">
<span class="sig-name descname"><span class="pre">mat_name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.mat_name" title="Link to this definition"></a></dt>
<dd><p>Formula unit label for input files</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.mat_id_dict">
<span class="sig-name descname"><span class="pre">mat_id_dict</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/command_line/vampire_caller.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.mat_id_dict" title="Link to this definition"></a></dt>
<dd><p>Maps sites to material id # for vampire
indexing.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<p>user_input_settings is a dictionary that can contain:
* start_t (int): Start MC sim at this temp, defaults to 0 K.
* end_t (int): End MC sim at this temp, defaults to 1500 K.
* temp_increment (int): Temp step size, defaults to 25 K.</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>ordered_structures</strong> (<em>list</em>) – Structure objects with magmoms.</p></li>
<li><p><strong>energies</strong> (<em>list</em>) – Energies of each relaxed magnetic structure.</p></li>
<li><p><strong>mc_box_size</strong> (<em>float</em>) – x=y=z dimensions (nm) of MC simulation box</p></li>
<li><p><strong>equil_timesteps</strong> (<em>int</em>) – number of MC steps for equilibrating</p></li>
<li><p><strong>mc_timesteps</strong> (<em>int</em>) – number of MC steps for averaging</p></li>
<li><p><strong>save_inputs</strong> (<em>bool</em>) – if True, save scratch dir of vampire input files</p></li>
<li><p><strong>hm</strong> (<a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergModel" title="pymatgen.analysis.magnetism.heisenberg.HeisenbergModel"><em>HeisenbergModel</em></a>) – object already fit to low energy
magnetic orderings.</p></li>
<li><p><strong>avg</strong> (<em>bool</em>) – If True, simply use <J> exchange parameter estimate.
If False, attempt to use NN, NNN, etc. interactions.</p></li>
<li><p><strong>user_input_settings</strong> (<em>dict</em>) – optional commands for VAMPIRE Monte Carlo</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireCaller.parse_stdout">
<em class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">parse_stdout</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vamp_stdout</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_mats</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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">tuple</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.6.14/src/pymatgen/core/../command_line/vampire_caller.py#L371-L402"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireCaller.parse_stdout" title="Link to this definition"></a></dt>
<dd><p>Parse stdout from Vampire.</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>vamp_stdout</strong> (<em>txt file</em>) – Vampire ‘output’ file.</p></li>
<li><p><strong>n_mats</strong> (<em>int</em>) – Number of materials in Vampire simulation.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>MSONable vampire output.
critical_temp (float): Calculated critical temp.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>parsed_out (DataFrame)</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.command_line.vampire_caller.VampireOutput">
<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VampireOutput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parsed_out</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nmats</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">critical_temp</span></span><span class="o"><span class="pre">=</span></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/v2025.6.14/src/pymatgen/core/../command_line/vampire_caller.py#L405-L419"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.command_line.vampire_caller.VampireOutput" 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>This class processes results from a Vampire Monte Carlo simulation
and parses the critical temperature.</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>parsed_out</strong> (<em>str</em>) – JSON rep of parsed stdout DataFrame.</p></li>
<li><p><strong>nmats</strong> (<em>int</em>) – Number of distinct materials (1 for each specie and up/down spin).</p></li>
<li><p><strong>critical_temp</strong> (<em>float</em>) – Monte Carlo Tc result.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
</section>
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