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<div class="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 headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.core.sites.PeriodicSite">
<em class="property">class </em><code class="descname">PeriodicSite</code><span class="sig-paren">(</span><em>atoms_n_occu</em>, <em>coords</em>, <em>lattice</em>, <em>to_unit_cell=False</em>, <em>coords_are_cartesian=False</em>, <em>properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite"><span class="viewcode-link">[source]</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">pymatgen.core.sites.Site</span></code></a>, <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.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</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atoms_n_occu</strong> – <p>Species on the site. Can be:</p>
<ol class="lowerroman simple">
<li><p>A sequence of element / specie specified either as string
symbols, e.g. [“Li”, “Fe2+”, “P”, …] or atomic numbers,
e.g., (3, 56, …) or actual Element or Specie objects.</p></li>
<li><p>List of dict of elements/species and occupancies, e.g.,
[{“Fe” : 0.5, “Mn”:0.5}, …]. This allows the setup of
disordered structures.</p></li>
</ol>
</p></li>
<li><p><strong>coords</strong> (<em>3x1 array</em><em> or </em><em>sequence</em>) – Coordinates of site as fractional
or cartesian coordinates.</p></li>
<li><p><strong>lattice</strong> – Lattice associated with the site</p></li>
<li><p><strong>to_unit_cell</strong> (<em>bool</em>) – 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> (<em>bool</em>) – Set to True if you are providing
cartesian coordinates. Defaults to False.</p></li>
<li><p><strong>properties</strong> (<em>dict</em>) – Properties associated with the PeriodicSite,
e.g., {“magmom”:5}. Defaults to None.</p></li>
</ul>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.a">
<code class="descname">a</code><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="method">
<dt id="pymatgen.core.sites.PeriodicSite.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><em>verbosity=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.as_dict"><span class="viewcode-link">[source]</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</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="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.b">
<code class="descname">b</code><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="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.c">
<code class="descname">c</code><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="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.coords">
<code class="descname">coords</code><a class="headerlink" href="#pymatgen.core.sites.PeriodicSite.coords" title="Permalink to this definition">¶</a></dt>
<dd><p>Fractional coordinates</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.sites.PeriodicSite.distance">
<code class="descname">distance</code><span class="sig-paren">(</span><em>other</em>, <em>jimage=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.distance"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>Distance between the two sites</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>distance (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.sites.PeriodicSite.distance_and_image">
<code class="descname">distance_and_image</code><span class="sig-paren">(</span><em>other</em>, <em>jimage=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.distance_and_image"><span class="viewcode-link">[source]</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</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</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</dt>
<dd class="field-odd"><p>(distance, jimage)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.sites.PeriodicSite.distance_and_image_from_frac_coords">
<code class="descname">distance_and_image_from_frac_coords</code><span class="sig-paren">(</span><em>fcoords</em>, <em>jimage=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.distance_and_image_from_frac_coords"><span class="viewcode-link">[source]</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</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</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</dt>
<dd class="field-odd"><p>(distance, jimage)</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.frac_coords">
<code class="descname">frac_coords</code><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="classmethod">
<dt id="pymatgen.core.sites.PeriodicSite.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em>, <em>lattice=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.from_dict"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>PeriodicSite</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.sites.PeriodicSite.is_periodic_image">
<code class="descname">is_periodic_image</code><span class="sig-paren">(</span><em>other</em>, <em>tolerance=1e-08</em>, <em>check_lattice=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.is_periodic_image"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>True if sites are periodic images of each other.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.lattice">
<code class="descname">lattice</code><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="method">
<dt id="pymatgen.core.sites.PeriodicSite.to_unit_cell">
<code class="descname">to_unit_cell</code><span class="sig-paren">(</span><em>in_place=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#PeriodicSite.to_unit_cell"><span class="viewcode-link">[source]</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 cell.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.x">
<code class="descname">x</code><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="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.y">
<code class="descname">y</code><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="attribute">
<dt id="pymatgen.core.sites.PeriodicSite.z">
<code class="descname">z</code><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="class">
<dt id="pymatgen.core.sites.Site">
<em class="property">class </em><code class="descname">Site</code><span class="sig-paren">(</span><em>atoms_n_occu</em>, <em>coords</em>, <em>properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#Site"><span class="viewcode-link">[source]</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">collections.abc.Hashable</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.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>Create a <em>non-periodic</em> site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atoms_n_occu</strong> – <p>Species on the site. Can be:
i. A Composition object (preferred)
ii. An element / specie 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 Specie 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>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.core.sites.Site.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#Site.as_dict"><span class="viewcode-link">[source]</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="method">
<dt id="pymatgen.core.sites.Site.distance">
<code class="descname">distance</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#Site.distance"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><p><strong>other</strong> – Other site.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Distance (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.sites.Site.distance_from_point">
<code class="descname">distance_from_point</code><span class="sig-paren">(</span><em>pt</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#Site.distance_from_point"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><p><strong>pt</strong> – Cartesian coordinates of point.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Distance (float)</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.core.sites.Site.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/sites.html#Site.from_dict"><span class="viewcode-link">[source]</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="attribute">
<dt id="pymatgen.core.sites.Site.is_ordered">
<code class="descname">is_ordered</code><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="attribute">
<dt id="pymatgen.core.sites.Site.position_atol">
<code class="descname">position_atol</code><em class="property"> = 1e-05</em><a class="headerlink" href="#pymatgen.core.sites.Site.position_atol" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.Site.specie">
<code class="descname">specie</code><a class="headerlink" href="#pymatgen.core.sites.Site.specie" title="Permalink to this definition">¶</a></dt>
<dd><p>The Specie/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_and_occu instead.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>AttributeError if Site is not ordered.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.Site.species">
<code class="descname">species</code><a class="headerlink" href="#pymatgen.core.sites.Site.species" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.Site.species_and_occu">
<code class="descname">species_and_occu</code><a class="headerlink" href="#pymatgen.core.sites.Site.species_and_occu" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.sites.Site.species_string">
<code class="descname">species_string</code><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="attribute">
<dt id="pymatgen.core.sites.Site.x">
<code class="descname">x</code><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="attribute">
<dt id="pymatgen.core.sites.Site.y">
<code class="descname">y</code><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="attribute">
<dt id="pymatgen.core.sites.Site.z">
<code class="descname">z</code><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>
</div>
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