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<div class="section" id="module-pymatgen.analysis.magnetism.jahnteller">
<span id="pymatgen-analysis-magnetism-jahnteller-module"></span><h1>pymatgen.analysis.magnetism.jahnteller module<a class="headerlink" href="#module-pymatgen.analysis.magnetism.jahnteller" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer">
<em class="property">class </em><code class="descname">JahnTellerAnalyzer</code><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer" 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>Will attempt to classify if structure <em>may</em> be Jahn-Teller active.</p>
<p>Class currently uses datafile of hard-coded common Jahn-Teller
active ions.</p>
<p>If structure is annotated with magnetic moments, will estimate
if structure may be high-spin or low-spin.</p>
<p>Class aims for more false-positives than false-negatives.</p>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis">
<code class="descname">get_analysis</code><span class="sig-paren">(</span><em>structure</em>, <em>calculate_valences=True</em>, <em>guesstimate_spin=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.get_analysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis_and_structure">
<code class="descname">get_analysis_and_structure</code><span class="sig-paren">(</span><em>structure</em>, <em>calculate_valences=True</em>, <em>guesstimate_spin=False</em>, <em>op_threshold=0.1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.get_analysis_and_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis_and_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Obtain an analysis of a given structure and if it may be Jahn-Teller
active or not. This is a heuristic, and may give false positives and
false negatives (false positives are preferred).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input structure</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>calculate_valences</em>) – whether to attempt to calculate valences or not, structure</p></li>
</ul>
</dd>
</dl>
<p>should have oxidation states to perform analysis
:param guesstimate_spin (bool): whether to guesstimate spin state from magnetic moments
or not, use with caution
:param op_threshold (float): threshold for order parameter above which to consider site
to match an octahedral or tetrahedral motif, since Jahn-Teller structures can often be
quite distorted, this threshold is smaller than one might expect
:return (dict): analysis of structure, with key ‘strength’ which may be ‘none’, ‘strong’,
‘weak’, or ‘unknown’</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_species">
<code class="descname">get_magnitude_of_effect_from_species</code><span class="sig-paren">(</span><em>species</em>, <em>spin_state</em>, <em>motif</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.get_magnitude_of_effect_from_species"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_species" title="Permalink to this definition">¶</a></dt>
<dd><p>Get magnitude of Jahn-Teller effect from provided species, spin state and motife.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – e.g. Fe2+</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>motif</em>) – “high” or “low”</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – “oct” or “tet”</p></li>
</ul>
</dd>
<dt class="field-even">Return (str)</dt>
<dd class="field-even"><p></p></dd>
</dl>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config">
<em class="property">static </em><code class="descname">get_magnitude_of_effect_from_spin_config</code><span class="sig-paren">(</span><em>motif</em>, <em>spin_config</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config" title="Permalink to this definition">¶</a></dt>
<dd><p>Roughly, the magnitude of Jahn-Teller distortion will be:
* in octahedral environments, strong if e_g orbitals
unevenly occupied but weak if t_2g orbitals unevenly
occupied
* in tetrahedral environments always weaker
:param motif (str): “oct” or “tet”
:param spin_config (dict): dict of ‘e’ (e_g) and ‘t’ (t2_g)
with number of electrons in each state</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.is_jahn_teller_active">
<code class="descname">is_jahn_teller_active</code><span class="sig-paren">(</span><em>structure</em>, <em>calculate_valences=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.is_jahn_teller_active"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.is_jahn_teller_active" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.mu_so">
<em class="property">static </em><code class="descname">mu_so</code><span class="sig-paren">(</span><em>species</em>, <em>motif</em>, <em>spin_state</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.mu_so"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.mu_so" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates the spin-only magnetic moment for a
given species. Only supports transition metals.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – str or Species</p></li>
<li><p><strong>motif</strong> – “oct” or “tet”</p></li>
<li><p><strong>spin_state</strong> – “high” or “low”</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>spin-only magnetic moment in Bohr magnetons</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.tag_structure">
<code class="descname">tag_structure</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/jahnteller.html#JahnTellerAnalyzer.tag_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.tag_structure" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
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