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<section id="module-pymatgen.core.sites">
<span id="pymatgen-core-sites-module"></span><h1>pymatgen.core.sites module<a class="headerlink" href="#module-pymatgen.core.sites" title="Permalink to this heading"></a></h1>
<p>This module defines classes representing non-periodic and periodic sites.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PeriodicSite</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">species</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SpeciesLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">CompositionLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.lattice.html#pymatgen.core.lattice.Lattice" title="pymatgen.core.lattice.Lattice"><span class="pre">Lattice</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_unit_cell</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords_are_cartesian</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_checks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L290-L652"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><code class="xref py py-class docutils literal notranslate"><span class="pre">Site</span></code></a>, <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Extension of generic Site object to periodic systems.
PeriodicSite includes a lattice system.</p>
<p>Create a periodic site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – <p>Species on the site. Can be:
i. A Composition-type object (preferred)
ii. An element / species specified either as a string</p>
<blockquote>
<div><p>symbols, e.g. “Li”, “Fe2+”, “P” or atomic numbers,
e.g., 3, 56, or actual Element or Species objects.</p>
</div></blockquote>
<dl class="simple">
<dt>iii.Dict of elements/species and occupancies, e.g.,</dt><dd><p>{“Fe” : 0.5, “Mn”:0.5}. This allows the setup of
disordered structures.</p>
</dd>
</dl>
</p></li>
<li><p><strong>coords</strong> – Cartesian coordinates of site.</p></li>
<li><p><strong>lattice</strong> – Lattice associated with the site.</p></li>
<li><p><strong>to_unit_cell</strong> – Translates fractional coordinate to the
basic unit cell, i.e. all fractional coordinates satisfy 0
<= a < 1. Defaults to False.</p></li>
<li><p><strong>coords_are_cartesian</strong> – Set to True if you are providing
Cartesian coordinates. Defaults to False.</p></li>
<li><p><strong>properties</strong> – Properties associated with the site as a dict, e.g.
{“magmom”: 5}. Defaults to None.</p></li>
<li><p><strong>skip_checks</strong> – Whether to ignore all the usual checks and just
create the site. Use this if the PeriodicSite is created in a
controlled manner and speed is desired.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.a">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">a</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.a" title="Permalink to this definition"></a></dt>
<dd><p>Fractional a coordinate</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L591-L622"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>JSON-serializable dict representation of PeriodicSite.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>verbosity</strong> (<em>int</em>) – Verbosity level. Default of 0 only includes the
matrix representation. Set to 1 for more details such as
Cartesian coordinates, etc.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.b">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">b</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.b" title="Permalink to this definition"></a></dt>
<dd><p>Fractional b coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.c">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">c</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.c" title="Permalink to this definition"></a></dt>
<dd><p>Fractional c coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.coords">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">coords</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ndarray</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.coords" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian coordinates</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.distance">
<span class="sig-name descname"><span class="pre">distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L568-L582"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.distance" title="Permalink to this definition"></a></dt>
<dd><p>Get distance between two sites assuming periodic boundary conditions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> (<a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><em>PeriodicSite</em></a>) – Other site to get distance from.</p></li>
<li><p><strong>jimage</strong> (<em>3x1 array</em>) – Specific periodic image in terms of lattice
translations, e.g., [1,0,0] implies to take periodic image
that is one a-lattice vector away. If jimage is None,
the image that is nearest to the site is found.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Distance between the two sites</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>distance (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.distance_and_image">
<span class="sig-name descname"><span class="pre">distance_and_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">np.ndarray</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L546-L566"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.distance_and_image" title="Permalink to this definition"></a></dt>
<dd><p>Gets distance and instance between two sites assuming periodic boundary
conditions. If the index jimage of two sites atom j is not specified it
selects the j image nearest to the i atom and returns the distance and
jimage indices in terms of lattice vector translations. If the index
jimage of atom j is specified it returns the distance between the ith
atom and the specified jimage atom, the given jimage is also returned.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> (<a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><em>PeriodicSite</em></a>) – Other site to get distance from.</p></li>
<li><p><strong>jimage</strong> (<em>3x1 array</em>) – Specific periodic image in terms of lattice
translations, e.g., [1,0,0] implies to take periodic image
that is one a-lattice vector away. If jimage is None,
the image that is nearest to the site is found.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>distance and periodic lattice translations
of the other site for which the distance applies.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(distance, jimage)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.distance_and_image_from_frac_coords">
<span class="sig-name descname"><span class="pre">distance_and_image_from_frac_coords</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fcoords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">np.ndarray</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L521-L544"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.distance_and_image_from_frac_coords" title="Permalink to this definition"></a></dt>
<dd><p>Gets distance between site and a fractional coordinate assuming
periodic boundary conditions. If the index jimage of two sites atom j
is not specified it selects the j image nearest to the i atom and
returns the distance and jimage indices in terms of lattice vector
translations. If the index jimage of atom j is specified it returns the
distance between the i atom and the specified jimage atom, the given
jimage is also returned.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>fcoords</strong> (<em>3x1 array</em>) – fcoords to get distance from.</p></li>
<li><p><strong>jimage</strong> (<em>3x1 array</em>) – Specific periodic image in terms of
lattice translations, e.g., [1,0,0] implies to take periodic
image that is one a-lattice vector away. If jimage is None,
the image that is nearest to the site is found.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>distance and periodic lattice translations
of the other site for which the distance applies.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>(distance, jimage)</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.frac_coords">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">frac_coords</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ndarray</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.frac_coords" title="Permalink to this definition"></a></dt>
<dd><p>Fractional coordinates</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L624-L652"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.from_dict" title="Permalink to this definition"></a></dt>
<dd><p>Create PeriodicSite from dict representation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>d</strong> (<em>dict</em>) – dict representation of PeriodicSite</p></li>
<li><p><strong>lattice</strong> – Optional lattice to override lattice specified in d.
Useful for ensuring all sites in a structure share the same
lattice.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PeriodicSite</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.is_periodic_image">
<span class="sig-name descname"><span class="pre">is_periodic_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1e-08</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L489-L508"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.is_periodic_image" title="Permalink to this definition"></a></dt>
<dd><p>Returns True if sites are periodic images of each other.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> (<a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><em>PeriodicSite</em></a>) – Other site</p></li>
<li><p><strong>tolerance</strong> (<em>float</em>) – Tolerance to compare fractional coordinates</p></li>
<li><p><strong>check_lattice</strong> (<em>bool</em>) – Whether to check if the two sites have the
same lattice.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if sites are periodic images of each other.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.lattice">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">lattice</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.lattice.html#pymatgen.core.lattice.Lattice" title="pymatgen.core.lattice.Lattice"><span class="pre">Lattice</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.lattice" title="Permalink to this definition"></a></dt>
<dd><p>Lattice associated with PeriodicSite</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.to_unit_cell">
<span class="sig-name descname"><span class="pre">to_unit_cell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">in_place</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L479-L487"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.to_unit_cell" title="Permalink to this definition"></a></dt>
<dd><p>Move frac coords to within the unit cell.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.x">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">x</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.x" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian x coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.y">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">y</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.y" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian y coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.PeriodicSite.z">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">z</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.z" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian z coordinate</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">species</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SpeciesLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">CompositionLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_checks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L25-L287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>A generalized <em>non-periodic</em> site. This is essentially a composition
at a point in space, with some optional properties associated with it. A
Composition is used to represent the atoms and occupancy, which allows for
disordered site representation. Coords are given in standard Cartesian
coordinates.</p>
<p>Creates a non-periodic Site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – <p>Species on the site. Can be:
i. A Composition-type object (preferred)
ii. An element / species specified either as a string</p>
<blockquote>
<div><p>symbols, e.g. “Li”, “Fe2+”, “P” or atomic numbers,
e.g., 3, 56, or actual Element or Species objects.</p>
</div></blockquote>
<dl class="simple">
<dt>iii.Dict of elements/species and occupancies, e.g.,</dt><dd><p>{“Fe” : 0.5, “Mn”:0.5}. This allows the setup of
disordered structures.</p>
</dd>
</dl>
</p></li>
<li><p><strong>coords</strong> – Cartesian coordinates of site.</p></li>
<li><p><strong>properties</strong> – Properties associated with the site as a dict, e.g.
{“magmom”: 5}. Defaults to None.</p></li>
<li><p><strong>skip_checks</strong> – Whether to ignore all the usual checks and just
create the site. Use this if the Site is created in a controlled
manner and speed is desired.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L246-L267"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>JSON-serializable dict representation for Site.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.distance">
<span class="sig-name descname"><span class="pre">distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L134-L144"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.distance" title="Permalink to this definition"></a></dt>
<dd><p>Get distance between two sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>other</strong> – Other site.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>distance</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.distance_from_point">
<span class="sig-name descname"><span class="pre">distance_from_point</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L146-L156"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.distance_from_point" title="Permalink to this definition"></a></dt>
<dd><p>Returns distance between the site and a point in space.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>pt</strong> – Cartesian coordinates of point.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>distance</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><span class="pre">Site</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py#L269-L287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.from_dict" title="Permalink to this definition"></a></dt>
<dd><p>Create Site from dict representation</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.is_ordered">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_ordered</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.is_ordered" title="Permalink to this definition"></a></dt>
<dd><p>True if site is an ordered site, i.e., with a single species with
occupancy 1.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.position_atol">
<span class="sig-name descname"><span class="pre">position_atol</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-05</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.position_atol" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.specie">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">specie</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.DummySpecies" title="pymatgen.core.periodic_table.DummySpecies"><span class="pre">DummySpecies</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.specie" title="Permalink to this definition"></a></dt>
<dd><p>The Species/Element at the site. Only works for ordered sites. Otherwise
an AttributeError is raised. Use this property sparingly. Robust
design should make use of the property species instead. Note that the
singular of species is also species. So the choice of this variable
name is governed by programmatic concerns as opposed to grammar.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>AttributeError if Site is not ordered.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.species">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">species</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.composition.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.species" title="Permalink to this definition"></a></dt>
<dd><p>The species on the site as a composition, e.g., Fe0.5Mn0.5.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.species_string">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">species_string</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.species_string" title="Permalink to this definition"></a></dt>
<dd><p>String representation of species on the site.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.x">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">x</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.x" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian x coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.y">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">y</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.y" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian y coordinate</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.core.sites.Site.z">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">z</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/sites.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.core.sites.Site.z" title="Permalink to this definition"></a></dt>
<dd><p>Cartesian z coordinate</p>
</dd></dl>
</dd></dl>
</section>
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