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<div class="section" id="module-pymatgen.analysis.defects.defect_compatibility">
<span id="pymatgen-analysis-defects-defect-compatibility-module"></span><h1>pymatgen.analysis.defects.defect_compatibility module<a class="headerlink" href="#module-pymatgen.analysis.defects.defect_compatibility" title="Permalink to this headline">¶</a></h1>
<p>This module implements DefectCompatibility analysis for consideration of
defects</p>
<dl class="py class">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility">
<em class="property">class </em><code class="sig-name descname">DefectCompatibility</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">plnr_avg_var_tol</span><span class="o">=</span><span class="default_value">0.0001</span></em>, <em class="sig-param"><span class="n">plnr_avg_minmax_tol</span><span class="o">=</span><span class="default_value">0.1</span></em>, <em class="sig-param"><span class="n">atomic_site_var_tol</span><span class="o">=</span><span class="default_value">0.005</span></em>, <em class="sig-param"><span class="n">atomic_site_minmax_tol</span><span class="o">=</span><span class="default_value">0.1</span></em>, <em class="sig-param"><span class="n">tot_relax_tol</span><span class="o">=</span><span class="default_value">1.0</span></em>, <em class="sig-param"><span class="n">perc_relax_tol</span><span class="o">=</span><span class="default_value">50.0</span></em>, <em class="sig-param"><span class="n">defect_tot_relax_tol</span><span class="o">=</span><span class="default_value">2.0</span></em>, <em class="sig-param"><span class="n">preferred_cc</span><span class="o">=</span><span class="default_value">'freysoldt'</span></em>, <em class="sig-param"><span class="n">free_chg_cutoff</span><span class="o">=</span><span class="default_value">2.1</span></em>, <em class="sig-param"><span class="n">use_bandfilling</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">use_bandedgeshift</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/defect_compatibility.py#L35-L756"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility" 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>The DefectCompatibility class evaluates corrections and delocalization
metrics on a DefectEntry. It can only parse based on the available
parameters that already exist in the parameters dict of the DefectEntry.</p>
<dl>
<dt>required settings in defect_entry.parameters for various types of analysis/correction:</dt><dd><dl class="simple">
<dt>freysoldt: [ “dielectric”, “axis_grid”, “bulk_planar_averages”, “defect_planar_averages”,</dt><dd><p>“initial_defect_structure”, “defect_frac_sc_coords”]</p>
</dd>
<dt>kumagai: [ “dielectric”, “bulk_atomic_site_averages”, “defect_atomic_site_averages”,</dt><dd><p>“site_matching_indices”, “initial_defect_structure”, “defect_frac_sc_coords”]</p>
</dd>
</dl>
<p>bandfilling: [“eigenvalues”, “kpoint_weights”, “potalign”, “vbm”, “cbm”]
bandshifting: [“hybrid_cbm”, “hybrid_vbm”, “vbm”, “cbm”]
defect relaxation/structure analysis: [“final_defect_structure”, “initial_defect_structure”,</p>
<blockquote>
<div><p>“sampling_radius”, “defect_frac_sc_coords”]</p>
</div></blockquote>
</dd>
</dl>
<p>Initializes the DefectCompatibility class</p>
<p>Each argument helps decide whether a DefectEntry is flagged as compatible or not
:param plnr_avg_var_tol: compatibility tolerance for variance of the sampling region</p>
<blockquote>
<div><p>in the planar averaged electrostatic potential (FreysoldtCorrection)</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plnr_avg_minmax_tol</strong> (<em>float</em>) – compatibility tolerance for max/min difference of the
sampling region in the planar averaged electrostatic potential (FreysoldtCorrection)</p></li>
<li><p><strong>atomic_site_var_tol</strong> (<em>float</em>) – compatibility tolerance for variance of the sampling
region in the atomic site averaged electrostatic potential (KumagaiCorrection)</p></li>
<li><p><strong>atomic_site_minmax_tol</strong> (<em>float</em>) – compatibility tolerance for max/min difference
of the sampling region in the atomic site averaged electrostatic
potential (KumagaiCorrection)</p></li>
<li><p><strong>tot_relax_tol</strong> (<em>float</em>) – compatibility tolerance for total integrated relaxation
amount outside of a given radius from the defect (in Angstrom).
Radius is supplied as ‘sampling_radius’ within parameters of DefectEntry.</p></li>
<li><p><strong>perc_relax_tol</strong> (<em>float</em>) – compatibility tolerance for percentage of total relaxation
outside of a given radius from the defect (percentage amount),
assuming a total integration relaxation greater than 1 Angstrom.
Radius is supplied as ‘sampling_radius’ within parameters of DefectEntry.</p></li>
<li><p><strong>defect_tot_relax_tol</strong> (<em>float</em>) – compatibility tolerance for displacement of defect site
itself (in Angstrom).</p></li>
<li><p><strong>preferred_cc</strong> (<em>str</em>) – Charge correction that is preferred to be used.
If only one is available based on metadata, then that charge correction will be used.
Options are: ‘freysoldt’ and ‘kumagai’</p></li>
<li><p><strong>free_chg_cutoff</strong> (<em>float</em>) – compatibility tolerance for total amount of host band occupation
outside of band edges, given by eigenvalue data. Extra occupation in the CB would be
free electrons, while lost occupation in VB would be free holes.</p></li>
<li><p><strong>use_bandfilling</strong> (<em>bool</em>) – Whether to include BandFillingCorrection or not (assuming
sufficient metadata is supplied to perform BandFillingCorrection).</p></li>
<li><p><strong>use_bandedgeshift</strong> (<em>bool</em>) – Whether to perform a BandEdgeShiftingCorrection or not (assuming
sufficient metadata is supplied to perform BandEdgeShiftingCorrection).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_final_relaxed_structure_delocalized">
<code class="sig-name descname">check_final_relaxed_structure_delocalized</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L635-L756"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_final_relaxed_structure_delocalized" title="Permalink to this definition">¶</a></dt>
<dd><p>NOTE this assumes initial and final structures have sites indexed in same way</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> – </p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_freysoldt_delocalized">
<code class="sig-name descname">check_freysoldt_delocalized</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L530-L581"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_freysoldt_delocalized" title="Permalink to this definition">¶</a></dt>
<dd><p>Check for Freysoldt delocalization.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_kumagai_delocalized">
<code class="sig-name descname">check_kumagai_delocalized</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L583-L633"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.check_kumagai_delocalized" title="Permalink to this definition">¶</a></dt>
<dd><p>Check for Kumagai delocalization.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.delocalization_analysis">
<code class="sig-name descname">delocalization_analysis</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L471-L528"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.delocalization_analysis" title="Permalink to this definition">¶</a></dt>
<dd><dl>
<dt>Do delocalization analysis. To do this, one considers:</dt><dd><ol class="lowerroman simple">
<li><p>sampling region of planar averaged electrostatic potential (freysoldt approach)</p></li>
<li><p>sampling region of atomic site averaged potentials (kumagai approach)</p></li>
</ol>
<p>iii) structural relaxation amount outside of radius considered in kumagai approach (default is wigner seitz
radius)
iv) if defect is not a vacancy type -> track to see how much the defect has moved</p>
</dd>
</dl>
<p>calculations that fail delocalization get “is_compatibile” set to False in parameters
also parameters recieves a “delocalization_meta” with following dict:</p>
<blockquote>
<div><p>plnr_avg = {‘is_compatible’: True/False, ‘metadata’: metadata used for determining this}
atomic_site = {‘is_compatible’: True/False, ‘metadata’: metadata used for determining this}
structure_relax = {‘is_compatible’: True/False, ‘metadata’: metadata used for determining this}
defectsite_relax = {‘is_compatible’: True/False, ‘metadata’: metadata used for determing this}</p>
</div></blockquote>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_all_corrections">
<code class="sig-name descname">perform_all_corrections</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L236-L359"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_all_corrections" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform all corrections for a defect.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_band_edge_shifting">
<em class="property">static </em><code class="sig-name descname">perform_band_edge_shifting</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L450-L469"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_band_edge_shifting" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform band edge shifting correction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_bandfilling">
<em class="property">static </em><code class="sig-name descname">perform_bandfilling</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L422-L448"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_bandfilling" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform bandfilling correction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_freysoldt">
<em class="property">static </em><code class="sig-name descname">perform_freysoldt</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L361-L382"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_freysoldt" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform Freysoldt correction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_kumagai">
<em class="property">static </em><code class="sig-name descname">perform_kumagai</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_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/defect_compatibility.py#L384-L420"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.perform_kumagai" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform Kumagai correction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>defect_entry</strong> (<a class="reference internal" href="pymatgen.analysis.defects.core.html#pymatgen.analysis.defects.core.DefectEntry" title="pymatgen.analysis.defects.core.DefectEntry"><em>DefectEntry</em></a>) – Defect to correct.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Corrected DefectEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.process_entry">
<code class="sig-name descname">process_entry</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">defect_entry</span></em>, <em class="sig-param"><span class="n">perform_corrections</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/defects/defect_compatibility.py#L113-L234"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.defects.defect_compatibility.DefectCompatibility.process_entry" title="Permalink to this definition">¶</a></dt>
<dd><p>Process a given DefectEntry with qualifiers given from initialization of class.
Order of processing is:</p>
<blockquote>
<div><ol class="arabic simple">
<li><p>perform all possible defect corrections with information given</p></li>
</ol>
<p>2) consider delocalization analyses based on qualifier metrics
given initialization of class. If delocalized, flag entry as delocalized
3) update corrections to defect entry and flag as delocalized</p>
</div></blockquote>
<dl class="simple">
<dt>Corrections are applied based on:</dt><dd><ol class="lowerroman simple">
<li><dl class="simple">
<dt>if free charges are more than free_chg_cutoff then will not apply charge correction,</dt><dd><p>because it no longer is applicable</p>
</dd>
</dl>
</li>
<li><p>use charge correction set by preferred_cc</p></li>
<li><p>only use BandFilling correction if use_bandfilling is set to True</p></li>
<li><p>only use BandEdgeShift correction if use_bandedgeshift is set to True</p></li>
</ol>
</dd>
</dl>
</dd></dl>
</dd></dl>
</div>
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