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<div class="section" id="module-pymatgen.entries.correction_calculator">
<span id="pymatgen-entries-correction-calculator-module"></span><h1>pymatgen.entries.correction_calculator module<a class="headerlink" href="#module-pymatgen.entries.correction_calculator" title="Permalink to this headline">¶</a></h1>
<p>This module calculates corrections for the species listed below, fitted to the experimental and computed
entries given to the CorrectionCalculator constructor.</p>
<dl class="py class">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator">
<em class="property">class </em><code class="sig-name descname">CorrectionCalculator</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">species</span><span class="p">:</span> <span class="n">Sequence<span class="p">[</span>str<span class="p">]</span></span> <span class="o">=</span> <span class="default_value">'oxide', 'peroxide', 'superoxide', 'S', 'F', 'Cl', 'Br', 'I', 'N', 'Se', 'Si', 'Sb', 'Te', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'W', 'Mo', 'H'</span></em>, <em class="sig-param"><span class="n">max_error</span><span class="p">:</span> <span class="n">float</span> <span class="o">=</span> <span class="default_value">0.1</span></em>, <em class="sig-param"><span class="n">allow_unstable</span><span class="p">:</span> <span class="n">Union<span class="p">[</span>float<span class="p">, </span>bool<span class="p">]</span></span> <span class="o">=</span> <span class="default_value">0.1</span></em>, <em class="sig-param"><span class="n">exclude_polyanions</span><span class="p">:</span> <span class="n">Sequence<span class="p">[</span>str<span class="p">]</span></span> <span class="o">=</span> <span class="default_value">'SO4', 'CO3', 'NO3', 'OCl3', 'SiO4', 'SeO3', 'TiO3', 'TiO4'</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L30-L543"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator" 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>A CorrectionCalculator contains experimental and computed entries which it uses to compute corrections.</p>
<p>It graphs residual errors after applying the computed corrections and creates the MPCompatibility.yaml
file the Correction classes use.</p>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.species">
<code class="sig-name descname">species</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.species" title="Permalink to this definition">¶</a></dt>
<dd><p>list of species that corrections are being calculated for</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.exp_compounds">
<code class="sig-name descname">exp_compounds</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.exp_compounds" title="Permalink to this definition">¶</a></dt>
<dd><p>list of dictionaries which each contain a compound’s formula and experimental data</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.calc_compounds">
<code class="sig-name descname">calc_compounds</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.calc_compounds" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of ComputedEntry objects</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.corrections">
<code class="sig-name descname">corrections</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.corrections" title="Permalink to this definition">¶</a></dt>
<dd><p>list of corrections in same order as species list</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.corrections_std_error">
<code class="sig-name descname">corrections_std_error</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.corrections_std_error" title="Permalink to this definition">¶</a></dt>
<dd><p>list of the variances of the corrections in same order as species list</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.corrections_dict">
<code class="sig-name descname">corrections_dict</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.corrections_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>dictionary of format {‘species’: (value, uncertainty)} for easier correction lookup</p>
</dd></dl>
<p>Initializes a CorrectionCalculator.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – list of species to calculate corrections for</p></li>
<li><p><strong>max_error</strong> – maximum tolerable relative uncertainty in experimental energy.
Compounds with relative uncertainty greater than this value will be excluded from the fit</p></li>
<li><p><strong>allow_unstable</strong> – whether unstable entries are to be included in the fit. If True, all compounds will
be included regardless of their energy above hull. If False or a float, compounds with
energy above hull greater than the given value (defaults to 0.1 eV/atom) will be
excluded</p></li>
<li><p><strong>exclude_polyanions</strong> – a list of polyanions that contain additional sources of error that may negatively
influence the quality of the fitted corrections. Compounds with these polyanions
will be excluded from the fit</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.compute_corrections">
<code class="sig-name descname">compute_corrections</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">exp_entries</span><span class="p">:</span> <span class="n">list</span></em>, <em class="sig-param"><span class="n">calc_entries</span><span class="p">:</span> <span class="n">dict</span></em><span class="sig-paren">)</span> → dict<a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L143-L318"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.compute_corrections" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes the corrections and fills in correction, corrections_std_error, and corrections_dict.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>exp_entries</strong> – list of dictionary objects with the following keys/values:
{“formula”: chemical formula, “exp energy”: formation energy in eV/formula unit,
“uncertainty”: uncertainty in formation energy}</p></li>
<li><p><strong>calc_entries</strong> – dictionary of computed entries, of the form {chemical formula: ComputedEntry}</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>ValueError</strong> – calc_compounds is missing an entry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.compute_from_files">
<code class="sig-name descname">compute_from_files</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">exp_gz</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">comp_gz</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L127-L141"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.compute_from_files" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>exp_gz</strong> – name of .json.gz file that contains experimental data
data in .json.gz file should be a list of dictionary objects with the following keys/values:
{“formula”: chemical formula, “exp energy”: formation energy in eV/formula unit,
“uncertainty”: uncertainty in formation energy}</p></li>
<li><p><strong>comp_gz</strong> – name of .json.gz file that contains computed entries
data in .json.gz file should be a dictionary of {chemical formula: ComputedEntry}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.graph_residual_error">
<code class="sig-name descname">graph_residual_error</code><span class="sig-paren">(</span><span class="sig-paren">)</span> → plotly.graph_objs._figure.Figure<a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L320-L363"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.graph_residual_error" title="Permalink to this definition">¶</a></dt>
<dd><p>Graphs the residual errors for all compounds after applying computed corrections.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.graph_residual_error_per_species">
<code class="sig-name descname">graph_residual_error_per_species</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">specie</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> → plotly.graph_objs._figure.Figure<a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L365-L440"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.graph_residual_error_per_species" title="Permalink to this definition">¶</a></dt>
<dd><p>Graphs the residual errors for each compound that contains specie after applying computed corrections.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>specie</strong> – the specie/group that residual errors are being plotted for</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>ValueError</strong> – the specie is not a valid specie that this class fits corrections for</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.entries.correction_calculator.CorrectionCalculator.make_yaml">
<code class="sig-name descname">make_yaml</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">name</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'MP2020'</span></em><span class="sig-paren">)</span> → None<a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/entries/correction_calculator.py#L442-L543"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.entries.correction_calculator.CorrectionCalculator.make_yaml" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates the _name_Compatibility.yaml that stores corrections as well as _name_CompatibilityUncertainties.yaml
for correction uncertainties.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> – str, alternate name for the created .yaml file.</p></li>
<li><p><strong>Default</strong> – “MP2020”</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
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