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<div class="section" id="module-pymatgen.command_line.bader_caller">
<span id="pymatgen-command-line-bader-caller-module"></span><h1>pymatgen.command_line.bader_caller module<a class="headerlink" href="#module-pymatgen.command_line.bader_caller" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis">
<em class="property">class </em><code class="descname">BaderAnalysis</code><span class="sig-paren">(</span><em>chgcar_filename</em>, <em>potcar_filename=None</em>, <em>chgref_filename=None</em>, <em>parse_atomic_densities=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Bader analysis for a CHGCAR.</p>
<p>Initializes the Bader caller.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</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>) – Optional: the filename of the corresponding
POTCAR file. Used for calculating the charge transfer. If
None, the get_charge_transfer method will raise a ValueError.</p></li>
<li><p><strong>chgref_filename</strong> (<em>str</em>) – Optional. The filename of the reference
CHGCAR, which calculated by AECCAR0 + AECCAR2. (See
<a class="reference external" href="http://theory.cm.utexas.edu/henkelman/code/bader/">http://theory.cm.utexas.edu/henkelman/code/bader/</a> for details.)</p></li>
<li><p><strong>parse_atomic_densities</strong> (<em>bool</em>) – Optional. turns on atomic partition of the charge density
charge densities are atom centered</p></li>
</ul>
</dd>
</dl>
<dl class="classmethod">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.from_path">
<em class="property">classmethod </em><code class="descname">from_path</code><span class="sig-paren">(</span><em>path</em>, <em>suffix=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis.from_path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.from_path" title="Permalink 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</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>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.get_charge">
<code class="descname">get_charge</code><span class="sig-paren">(</span><em>atom_index</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis.get_charge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience method to get the charge on a particular atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>atom_index</strong> – Index of atom.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Charge associated with atom from the Bader analysis.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_transfer">
<code class="descname">get_charge_transfer</code><span class="sig-paren">(</span><em>atom_index</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis.get_charge_transfer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_charge_transfer" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the charge transferred for a particular atom. Requires POTCAR
to be supplied.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>atom_index</strong> – Index of atom.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Charge transfer associated with atom from the Bader analysis.
Given by final charge on atom - nelectrons in POTCAR for
associated atom.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.get_oxidation_state_decorated_structure">
<code class="descname">get_oxidation_state_decorated_structure</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis.get_oxidation_state_decorated_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.get_oxidation_state_decorated_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns an oxidation state decorated structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Returns an oxidation state decorated structure. Requires POTCAR
to be supplied.</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.rebuild_chgcar">
<em class="property">classmethod </em><code class="descname">rebuild_chgcar</code><span class="sig-paren">(</span><em>atomic_densities</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#BaderAnalysis.rebuild_chgcar"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.rebuild_chgcar" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.command_line.bader_caller.BaderAnalysis.summary">
<code class="descname">summary</code><a class="headerlink" href="#pymatgen.command_line.bader_caller.BaderAnalysis.summary" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.command_line.bader_caller.bader_analysis_from_objects">
<code class="descname">bader_analysis_from_objects</code><span class="sig-paren">(</span><em>chgcar</em>, <em>potcar=None</em>, <em>aeccar0=None</em>, <em>aeccar2=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#bader_analysis_from_objects"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.bader_analysis_from_objects" title="Permalink 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</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</dt>
<dd class="field-even"><p>summary dict</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.command_line.bader_caller.bader_analysis_from_path">
<code class="descname">bader_analysis_from_path</code><span class="sig-paren">(</span><em>path</em>, <em>suffix=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/command_line/bader_caller.html#bader_analysis_from_path"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.command_line.bader_caller.bader_analysis_from_path" title="Permalink 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, AECAR0, AECAR2, 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</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</dt>
<dd class="field-even"><p>summary dict</p>
</dd>
</dl>
</dd></dl>
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