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<div class="section" id="module-pymatgen.analysis.defects.core">
<span id="pymatgen-analysis-defects-core-module"></span><h1>pymatgen.analysis.defects.core module<a class="headerlink" href="#module-pymatgen.analysis.defects.core" title="Permalink to this headline">¶</a></h1>
<p>Base classes representing defects.</p>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.Defect">
<em class="property">class </em><code class="sig-name descname">Defect</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">defect_site</span></em>, <em class="sig-param"><span class="n">charge</span><span class="o">=</span><span class="default_value">0.0</span></em>, <em class="sig-param"><span class="n">multiplicity</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L33-L142"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>Abstract class for a single point defect</p>
<p>Initializes an abstract defect</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Pymatgen Structure without any defects</p></li>
<li><p><strong>defect_site</strong> (<a class="reference internal" href="pymatgen.core.sites.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – site for defect within structure
must have same lattice as structure</p></li>
<li><p><strong>charge</strong> – (int or float) defect charge
default is zero, meaning no change to NELECT after defect is created in the structure
(assuming use_structure_charge=True in vasp input set)</p></li>
<li><p><strong>multiplicity</strong> (<em>int</em>) – multiplicity of defect within
the supercell can be supplied by user. if not
specified, then space group symmetry analysis is
used to generate multiplicity.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.bulk_structure">
<em class="property">property </em><code class="sig-name descname">bulk_structure</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.bulk_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the structure without any defects.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.charge">
<em class="property">property </em><code class="sig-name descname">charge</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.charge" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the charge of a defect</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.copy">
<code class="sig-name descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L127-L134"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.copy" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience method to get a copy of the defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>A copy of the Defect.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.defect_composition">
<em class="property">abstract property </em><code class="sig-name descname">defect_composition</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.defect_composition" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the defect composition as a Composition object</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.generate_defect_structure">
<em class="property">abstract </em><code class="sig-name descname">generate_defect_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">supercell</span><span class="o">=</span><span class="default_value">1, 1, 1</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L102-L109"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.generate_defect_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Given structure and defect_site (and type of defect) should return a defect_structure that is charged
:param supercell: supercell integer, vector, or scaling matrix
:type supercell: int, [3x1], or [[]] (3x3)</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.get_multiplicity">
<em class="property">abstract </em><code class="sig-name descname">get_multiplicity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L119-L125"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.get_multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Method to determine multiplicity. For non-Interstitial objects, also confirms that defect_site
is a site in bulk_structure.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.multiplicity">
<em class="property">property </em><code class="sig-name descname">multiplicity</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the multiplicity of a defect site within the structure (needed for concentration analysis)</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.name">
<em class="property">abstract property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a name for this defect</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.set_charge">
<code class="sig-name descname">set_charge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">new_charge</span><span class="o">=</span><span class="default_value">0.0</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L136-L142"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.set_charge" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets the overall charge
:param charge: new charge to set
:type charge: float</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Defect.site">
<em class="property">property </em><code class="sig-name descname">site</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Defect.site" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the defect position as a site object</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.DefectCorrection">
<em class="property">class </em><code class="sig-name descname">DefectCorrection</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L730-L766"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectCorrection" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>A Correction class modeled off the computed entry correction format</p>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectCorrection.correct_entry">
<code class="sig-name descname">correct_entry</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">entry</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L752-L766"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectCorrection.correct_entry" title="Permalink to this definition">¶</a></dt>
<dd><p>Corrects a single entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A DefectEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>An processed entry.</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>CompatibilityError if entry is not compatible.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectCorrection.get_correction">
<em class="property">abstract </em><code class="sig-name descname">get_correction</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">entry</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L735-L750"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectCorrection.get_correction" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns correction for a single entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>entry</strong> – A DefectEntry object.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>A single dictionary with the format
correction_name: energy_correction</p>
</dd>
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>CompatibilityError if entry is not compatible.</strong> – </p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.DefectEntry">
<em class="property">class </em><code class="sig-name descname">DefectEntry</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect</span></em>, <em class="sig-param"><span class="n">uncorrected_energy</span></em>, <em class="sig-param"><span class="n">corrections</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parameters</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">entry_id</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L522-L727"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>An lightweight DefectEntry object containing key computed data
for many defect analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>defect</strong> – A Defect object from pymatgen.analysis.defects.core</p></li>
<li><p><strong>uncorrected_energy</strong> (<em>float</em>) – Energy of the defect entry. Usually the difference between
the final calculated energy for the defect supercell - the perfect
supercell energy</p></li>
<li><p><strong>corrections</strong> (<em>dict</em>) – Dict of corrections for defect formation energy. All values will be summed and
added to the defect formation energy.</p></li>
<li><p><strong>parameters</strong> (<em>dict</em>) – An optional dict of calculation parameters and data to
use with correction schemes
(examples of parameter keys: supercell_size, axis_grid, bulk_planar_averages
defect_planar_averages )</p></li>
<li><p><strong>entry_id</strong> (<em>obj</em>) – An id to uniquely identify this defect, can be any MSONable
type</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.as_dict">
<code class="sig-name descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L566-L579"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Json-serializable dict representation of DefectEntry</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.bulk_structure">
<em class="property">property </em><code class="sig-name descname">bulk_structure</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.bulk_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Structure object of bulk.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.charge">
<em class="property">property </em><code class="sig-name descname">charge</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.charge" title="Permalink to this definition">¶</a></dt>
<dd><p>Charge of defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.copy">
<code class="sig-name descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L640-L648"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.copy" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience method to get a copy of the DefectEntry.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>A copy of the DefectEntry.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.defect_concentration">
<code class="sig-name descname">defect_concentration</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">chemical_potentials</span></em>, <em class="sig-param"><span class="n">temperature</span><span class="o">=</span><span class="default_value">300</span></em>, <em class="sig-param"><span class="n">fermi_level</span><span class="o">=</span><span class="default_value">0.0</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L688-L708"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.defect_concentration" title="Permalink to this definition">¶</a></dt>
<dd><p>Compute the defect concentration for a temperature and Fermi level.
:param temperature: the temperature in K
:param fermi_level: the fermi level in eV (with respect to the VBM)</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>defects concentration in cm^-3</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.energy">
<em class="property">property </em><code class="sig-name descname">energy</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.energy" title="Permalink to this definition">¶</a></dt>
<dd><p><em>Corrected</em> energy of the entry</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.formation_energy">
<code class="sig-name descname">formation_energy</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">chemical_potentials</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">fermi_level</span><span class="o">=</span><span class="default_value">0</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L650-L686"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.formation_energy" title="Permalink to this definition">¶</a></dt>
<dd><dl>
<dt>Compute the formation energy for a defect taking into account a given chemical potential and fermi_level</dt><dd><dl>
<dt>Args:</dt><dd><blockquote>
<div><dl class="simple">
<dt>chemical_potentials (dict): Dictionary of elemental chemical potential values.</dt><dd><p>Keys are Element objects within the defect structure’s composition.
Values are float numbers equal to the atomic chemical potential for that element.</p>
</dd>
</dl>
</div></blockquote>
<dl class="simple">
<dt>fermi_level (float): Value corresponding to the electron chemical potential.</dt><dd><p>If “vbm” is supplied in parameters dict, then fermi_level is referenced to the VBM.
If “vbm” is NOT supplied in parameters dict, then fermi_level is referenced to the
calculation’s absolute Kohn-Sham potential (and should include the vbm value provided
by a band structure calculation)</p>
</dd>
</dl>
</dd>
</dl>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Formation energy value (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.from_dict">
<em class="property">classmethod </em><code class="sig-name descname">from_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">d</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L581-L603"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.from_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstitute a DefectEntry object from a dict representation created using
as_dict().</p>
<blockquote>
<div><dl class="simple">
<dt>Args:</dt><dd><p>d (dict): dict representation of DefectEntry.</p>
</dd>
<dt>Returns:</dt><dd><p>DefectEntry object</p>
</dd>
</dl>
</div></blockquote>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.multiplicity">
<em class="property">property </em><code class="sig-name descname">multiplicity</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Multiplicity of defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.name">
<em class="property">property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Defect name</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.DefectEntry.site">
<em class="property">property </em><code class="sig-name descname">site</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.DefectEntry.site" title="Permalink to this definition">¶</a></dt>
<dd><p>Site of defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.Interstitial">
<em class="property">class </em><code class="sig-name descname">Interstitial</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">defect_site</span></em>, <em class="sig-param"><span class="n">charge</span><span class="o">=</span><span class="default_value">0.0</span></em>, <em class="sig-param"><span class="n">site_name</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">multiplicity</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L335-L457"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Interstitial" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.defects.core.Defect" title="pymatgen.analysis.defects.core.Defect"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.analysis.defects.core.Defect</span></code></a></p>
<p>Subclass of Defect to capture essential information for a single Interstitial defect structure.</p>
<p>Initializes an interstial defect.
:param structure: Pymatgen Structure without any defects
:param defect_site: the site for the interstitial
:type defect_site: Site
:param charge: (int or float) defect charge</p>
<blockquote>
<div><p>default is zero, meaning no change to NELECT after defect is created in the structure
(assuming use_structure_charge=True in vasp input set)</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site_name</strong> – allows user to give a unique name to defect, since Wyckoff symbol/multiplicity
is sometimes insufficient to categorize the defect type.
default is no name beyond multiplicity.</p></li>
<li><p><strong>multiplicity</strong> (<em>int</em>) – <p>multiplicity of defect within
the supercell can be supplied by user. if not
specified, then space group symmetry is used
to generator interstitial sublattice</p>
<p>NOTE: multiplicity generation will not work for
interstitial complexes,
where multiplicity may depend on additional
factors (ex. orientation etc.)
If defect is not a complex, then this
process will yield the correct multiplicity,
provided that the defect does not undergo
significant relaxation.</p>
</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Interstitial.defect_composition">
<em class="property">property </em><code class="sig-name descname">defect_composition</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Interstitial.defect_composition" title="Permalink to this definition">¶</a></dt>
<dd><p>Defect composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Interstitial.generate_defect_structure">
<code class="sig-name descname">generate_defect_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">supercell</span><span class="o">=</span><span class="default_value">1, 1, 1</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L381-L418"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Interstitial.generate_defect_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns Defective Interstitial structure, decorated with charge
If bulk structure had any site properties, all of these properties are
removed in the resulting defect structure</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>supercell</strong> (<em>int</em><em>, </em><em>[</em><em>3x1</em><em>]</em><em>, or </em><em>[</em><em>[</em><em>]</em><em>] </em><em>(</em><em>3x3</em><em>)</em>) – supercell integer, vector, or scaling matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Interstitial.get_multiplicity">
<code class="sig-name descname">get_multiplicity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L420-L446"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Interstitial.get_multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the multiplicity of a defect site within the structure (needed for concentration analysis)</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Interstitial.name">
<em class="property">property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Interstitial.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a name for this defect</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.Substitution">
<em class="property">class </em><code class="sig-name descname">Substitution</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">defect_site</span></em>, <em class="sig-param"><span class="n">charge</span><span class="o">=</span><span class="default_value">0.0</span></em>, <em class="sig-param"><span class="n">multiplicity</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L221-L332"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Substitution" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.defects.core.Defect" title="pymatgen.analysis.defects.core.Defect"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.analysis.defects.core.Defect</span></code></a></p>
<p>Subclass of Defect to capture essential information for a single Substitution defect structure.</p>
<p>Initializes an abstract defect</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Pymatgen Structure without any defects</p></li>
<li><p><strong>defect_site</strong> (<a class="reference internal" href="pymatgen.core.sites.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – site for defect within structure
must have same lattice as structure</p></li>
<li><p><strong>charge</strong> – (int or float) defect charge
default is zero, meaning no change to NELECT after defect is created in the structure
(assuming use_structure_charge=True in vasp input set)</p></li>
<li><p><strong>multiplicity</strong> (<em>int</em>) – multiplicity of defect within
the supercell can be supplied by user. if not
specified, then space group symmetry analysis is
used to generate multiplicity.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Substitution.defect_composition">
<em class="property">property </em><code class="sig-name descname">defect_composition</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Substitution.defect_composition" title="Permalink to this definition">¶</a></dt>
<dd><p>Composition of defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Substitution.generate_defect_structure">
<code class="sig-name descname">generate_defect_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">supercell</span><span class="o">=</span><span class="default_value">1, 1, 1</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L245-L291"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Substitution.generate_defect_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns Defective Substitution structure, decorated with charge.
If bulk structure had any site properties, all of these properties are
removed in the resulting defect structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>supercell</strong> (<em>int</em><em>, </em><em>[</em><em>3x1</em><em>]</em><em>, or </em><em>[</em><em>[</em><em>]</em><em>] </em><em>(</em><em>3x3</em><em>)</em>) – supercell integer, vector, or scaling matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Substitution.get_multiplicity">
<code class="sig-name descname">get_multiplicity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L293-L315"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Substitution.get_multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the multiplicity of a defect site within the structure (needed for concentration analysis)
and confirms that defect_site is a site in bulk_structure.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Substitution.name">
<em class="property">property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Substitution.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a name for this defect</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.defects.core.Vacancy">
<em class="property">class </em><code class="sig-name descname">Vacancy</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">defect_site</span></em>, <em class="sig-param"><span class="n">charge</span><span class="o">=</span><span class="default_value">0.0</span></em>, <em class="sig-param"><span class="n">multiplicity</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L145-L218"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Vacancy" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.defects.core.Defect" title="pymatgen.analysis.defects.core.Defect"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.analysis.defects.core.Defect</span></code></a></p>
<p>Subclass of Defect to capture essential information for a single Vacancy defect structure.</p>
<p>Initializes an abstract defect</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Pymatgen Structure without any defects</p></li>
<li><p><strong>defect_site</strong> (<a class="reference internal" href="pymatgen.core.sites.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – site for defect within structure
must have same lattice as structure</p></li>
<li><p><strong>charge</strong> – (int or float) defect charge
default is zero, meaning no change to NELECT after defect is created in the structure
(assuming use_structure_charge=True in vasp input set)</p></li>
<li><p><strong>multiplicity</strong> (<em>int</em>) – multiplicity of defect within
the supercell can be supplied by user. if not
specified, then space group symmetry analysis is
used to generate multiplicity.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Vacancy.defect_composition">
<em class="property">property </em><code class="sig-name descname">defect_composition</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Vacancy.defect_composition" title="Permalink to this definition">¶</a></dt>
<dd><p>Composition of defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>Returns</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Vacancy.generate_defect_structure">
<code class="sig-name descname">generate_defect_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">supercell</span><span class="o">=</span><span class="default_value">1, 1, 1</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L159-L187"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Vacancy.generate_defect_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns Defective Vacancy structure, decorated with charge
:param supercell: supercell integer, vector, or scaling matrix
:type supercell: int, [3x1], or [[]] (3x3)</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Vacancy.get_multiplicity">
<code class="sig-name descname">get_multiplicity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L189-L211"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Vacancy.get_multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the multiplicity of a defect site within the structure (needed for concentration analysis)
and confirms that defect_site is a site in bulk_structure.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.core.Vacancy.name">
<em class="property">property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.Vacancy.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a name for this defect</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt id="pymatgen.analysis.defects.core.create_saturated_interstitial_structure">
<code class="sig-name descname">create_saturated_interstitial_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">interstitial_def</span></em>, <em class="sig-param"><span class="n">dist_tol</span><span class="o">=</span><span class="default_value">0.1</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/core.py#L460-L519"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.core.create_saturated_interstitial_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>this takes a Interstitial defect object and generates the
sublattice for it based on the structure’s space group.
Useful for understanding multiplicity of an interstitial
defect in thermodynamic analysis.</p>
<dl class="simple">
<dt>NOTE: if large relaxation happens to interstitial or</dt><dd><p>defect involves a complex then there may be additional
degrees of freedom that need to be considered for
the multiplicity.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>dist_tol</strong> – changing distance tolerance of saturated structure,
allowing for possibly overlapping sites
but ensuring space group is maintained</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Structure object decorated with interstitial site equivalents</p>
</dd>
</dl>
</dd></dl>
</div>
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