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<div class="section" id="module-pymatgen.analysis.magnetism.analyzer">
<span id="pymatgen-analysis-magnetism-analyzer-module"></span><h1>pymatgen.analysis.magnetism.analyzer module<a class="headerlink" href="#module-pymatgen.analysis.magnetism.analyzer" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer">
<em class="property">class </em><code class="descname">CollinearMagneticStructureAnalyzer</code><span class="sig-paren">(</span><em>structure: pymatgen.core.structure.Structure</em>, <em>overwrite_magmom_mode: Union[pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode</em>, <em>str] = 'none'</em>, <em>round_magmoms: bool = False</em>, <em>detect_valences: bool = False</em>, <em>make_primitive: bool = True</em>, <em>default_magmoms: bool = None</em>, <em>set_net_positive: bool = True</em>, <em>threshold: float = 0.1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer" 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 class which provides a few helpful methods to analyze
collinear magnetic structures.</p>
<p>If magnetic moments are not defined, moments will be
taken either from default_magmoms.yaml (similar to the
default magmoms in MPRelaxSet, with a few extra definitions)
or from a specie:magmom dict provided by the default_magmoms
kwarg.</p>
<p>Input magmoms can be replaced using the ‘overwrite_magmom_mode’
kwarg. This can be:
* “none” to do nothing,
* “respect_sign” which will overwrite existing magmoms with</p>
<blockquote>
<div><p>those from default_magmoms but will keep sites with positive magmoms
positive, negative magmoms negative and zero magmoms zero,</p>
</div></blockquote>
<ul class="simple">
<li><p>“respect_zeros”, which will give a ferromagnetic structure
(all positive magmoms from default_magmoms) but still keep sites with
zero magmoms as zero,</p></li>
<li><p>“replace_all” which will try to guess initial magmoms for
all sites in the structure irrespective of input structure
(this is most suitable for an initial DFT calculation),</p></li>
<li><p>“replace_all_if_undefined” is the same as “replace_all” but only if
no magmoms are defined in input structure, otherwise it will respect
existing magmoms.</p></li>
<li><p>“normalize” will normalize magmoms to unity, but will respect sign
(used for comparing orderings), magmoms < theshold will be set to zero</p></li>
</ul>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>overwrite_magmom_mode</em>) – default “none”</p></li>
<li><p><strong>(</strong><strong>int</strong><strong> or </strong><strong>bool</strong><strong>)</strong> (<em>round_magmoms</em>) – will round input magmoms to</p></li>
</ul>
</dd>
</dl>
<p>specified number of decimal places if integer is supplied, if set
to a float will try and group magmoms together using a kernel density
estimator of provided width, and extracting peaks of the estimator
:param detect_valences (bool): if True, will attempt to assign valences
to input structure
:param make_primitive (bool): if True, will transform to primitive
magnetic cell
:param default_magmoms (dict): (optional) dict specifying default magmoms
:param set_net_positive (bool): if True, will change sign of magnetic
moments such that the net magnetization is positive. Argument will be
ignored if mode “respect_sign” is used.
:param threshold (float): number (in Bohr magnetons) below which magmoms
will be rounded to zero, default of 0.1 can probably be increased for many
magnetic systems, depending on your application</p>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_exchange_group_info">
<code class="descname">get_exchange_group_info</code><span class="sig-paren">(</span><em>symprec=0.01</em>, <em>angle_tolerance=5.0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.get_exchange_group_info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_exchange_group_info" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the information on the symmetry of the Hamiltonian
describing the exchange energy of the system, taking into
account relative direction of magnetic moments but not their
absolute direction.</p>
<p>This is not strictly accurate (e.g. some/many atoms will
have zero magnetic moments), but defining symmetry this
way is a useful way of keeping track of distinct magnetic
orderings within pymatgen.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symprec</strong> – same as SpacegroupAnalyzer</p></li>
<li><p><strong>angle_tolerance</strong> – same as SpacegroupAnalyzer</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>spacegroup_symbol, international_number</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure">
<code class="descname">get_ferromagnetic_structure</code><span class="sig-paren">(</span><em>make_primitive=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a Structure with all magnetic moments positive
or zero.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure">
<code class="descname">get_nonmagnetic_structure</code><span class="sig-paren">(</span><em>make_primitive=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a Structure without magnetic moments defined.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms">
<code class="descname">get_structure_with_only_magnetic_atoms</code><span class="sig-paren">(</span><em>make_primitive=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a Structure with only magnetic atoms present.
:return: Structure</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_spin">
<code class="descname">get_structure_with_spin</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.get_structure_with_spin"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_spin" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a Structure with species decorated with spin values instead
of using magmom site properties.
:return: Structure</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.is_magnetic">
<code class="descname">is_magnetic</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.is_magnetic" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience property, returns True if any non-zero magmoms present.
:return:</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magmoms">
<code class="descname">magmoms</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magmoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience property, returns magmoms as a numpy array.
:return: np.array</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magnetic_species_and_magmoms">
<code class="descname">magnetic_species_and_magmoms</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magnetic_species_and_magmoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a dict of magnetic species and the magnitude of
their associated magmoms. Will return a set if there are
multiple magmoms per species.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>dict of magnetic species and magmoms</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.matches_ordering">
<code class="descname">matches_ordering</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.matches_ordering"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.matches_ordering" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares the magnetic orderings of one structure with another.
:param other: Structure
:return (bool):</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_magnetic_sites">
<code class="descname">number_of_magnetic_sites</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_magnetic_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of magnetic sites present in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return (int)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites">
<code class="descname">number_of_unique_magnetic_sites</code><span class="sig-paren">(</span><em>symprec=0.001</em>, <em>angle_tolerance=5</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites" 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>(</strong><strong>float</strong><strong>)</strong> (<em>angle_tolerance</em>) – same as in SpacegroupAnalyzer</p></li>
<li><p><strong>(</strong><strong>float</strong><strong>)</strong> – same as in SpacegroupAnalyzer</p></li>
</ul>
</dd>
<dt class="field-even">Return (int)</dt>
<dd class="field-even"><p>Number of symmetrically-distinct magnetic sites present</p>
</dd>
</dl>
<p>in structure.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.ordering">
<code class="descname">ordering</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.ordering" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies heuristics to return a magnetic ordering for a collinear
magnetic structure. Result is not guaranteed for correctness.
:return: Ordering Enum (‘FiM’ is used as the abbreviation for
ferrimagnetic)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.types_of_magnetic_specie">
<code class="descname">types_of_magnetic_specie</code><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.types_of_magnetic_specie" title="Permalink to this definition">¶</a></dt>
<dd><p>Equivalent to Structure.types_of_specie but only returns
magnetic species.
:return: types of Specie</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator">
<em class="property">class </em><code class="descname">MagneticStructureEnumerator</code><span class="sig-paren">(</span><em>structure</em>, <em>default_magmoms=None</em>, <em>strategies=('ferromagnetic'</em>, <em>'antiferromagnetic')</em>, <em>automatic=True</em>, <em>truncate_by_symmetry=True</em>, <em>transformation_kwargs=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#MagneticStructureEnumerator"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator" 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>Combines MagneticStructureAnalyzer and MagOrderingTransformation to
automatically generate a set of transformations for a given structure
and produce a list of plausible magnetic orderings.</p>
<p>This class will try generated different collinear
magnetic orderings for a given input structure.</p>
<p>If the input structure has magnetic moments defined, it
is possible to use these as a hint as to which elements are
magnetic, otherwise magnetic elements will be guessed
(this can be changed using default_magmoms kwarg).</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>default_magmoms</strong> – (optional, defaults provided) dict of</p></li>
</ul>
</dd>
</dl>
<p>magnetic elements to their initial magnetic moments in µB, generally
these are chosen to be high-spin since they can relax to a low-spin
configuration during a DFT electronic configuration</p>
<blockquote>
<div><p>strategies: different ordering strategies to use, choose from:</p>
</div></blockquote>
<p>ferromagnetic, antiferromagnetic, antiferromagnetic_by_motif,
ferrimagnetic_by_motif and ferrimagnetic_by_species (here, “motif”,
means to use a different ordering parameter for symmetry inequivalent
sites)</p>
<blockquote>
<div><p>automatic: if True, will automatically choose sensible strategies
truncate_by_symmetry: if True, will remove very unsymmetrical</p>
</div></blockquote>
<dl class="simple">
<dt>orderings that are likely physically implausible</dt><dd><p>transformation_kwargs: keyword arguments to pass to</p>
</dd>
</dl>
<p>MagOrderingTransformation, to change automatic cell size limits, etc.</p>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator.available_strategies">
<code class="descname">available_strategies</code><em class="property"> = ('ferromagnetic', 'antiferromagnetic', 'ferrimagnetic_by_motif', 'ferrimagnetic_by_species', 'antiferromagnetic_by_motif', 'nonmagnetic')</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator.available_strategies" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering">
<em class="property">class </em><code class="descname">Ordering</code><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#Ordering"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">enum.Enum</span></code></p>
<p>An enumeration.</p>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering.AFM">
<code class="descname">AFM</code><em class="property"> = 'AFM'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering.AFM" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering.FM">
<code class="descname">FM</code><em class="property"> = 'FM'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering.FM" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering.FiM">
<code class="descname">FiM</code><em class="property"> = 'FiM'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering.FiM" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering.NM">
<code class="descname">NM</code><em class="property"> = 'NM'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering.NM" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.Ordering.Unknown">
<code class="descname">Unknown</code><em class="property"> = 'Unknown'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.Ordering.Unknown" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode">
<em class="property">class </em><code class="descname">OverwriteMagmomMode</code><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#OverwriteMagmomMode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">enum.Enum</span></code></p>
<p>An enumeration.</p>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.none">
<code class="descname">none</code><em class="property"> = 'none'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.none" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.normalize">
<code class="descname">normalize</code><em class="property"> = 'normalize'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.normalize" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.replace_all">
<code class="descname">replace_all</code><em class="property"> = 'replace_all'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.replace_all" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_sign">
<code class="descname">respect_sign</code><em class="property"> = 'respect_sign'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_sign" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_zero">
<code class="descname">respect_zero</code><em class="property"> = 'respect_zeros'</em><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_zero" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.magnetism.analyzer.magnetic_deformation">
<code class="descname">magnetic_deformation</code><span class="sig-paren">(</span><em>structure_A</em>, <em>structure_B</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/magnetism/analyzer.html#magnetic_deformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.magnetism.analyzer.magnetic_deformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates ‘magnetic deformation proxy’,
a measure of deformation (norm of finite strain)
between ‘non-magnetic’ (non-spin-polarized) and
ferromagnetic structures.</p>
<p>Adapted from Bocarsly et al. 2017,
doi: 10.1021/acs.chemmater.6b04729</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure_A</strong> – Structure</p></li>
<li><p><strong>structure_B</strong> – Structure</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
</div>
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