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<div class="section" id="module-pymatgen.analysis.adsorption">
<span id="pymatgen-analysis-adsorption-module"></span><h1>pymatgen.analysis.adsorption module<a class="headerlink" href="#module-pymatgen.analysis.adsorption" title="Permalink to this headline">¶</a></h1>
<p>This module provides classes used to enumerate surface sites
and to find adsorption sites on slabs</p>
<dl class="class">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder">
<em class="property">class </em><code class="descname">AdsorbateSiteFinder</code><span class="sig-paren">(</span><em>slab</em>, <em>selective_dynamics=False</em>, <em>height=0.9</em>, <em>mi_vec=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder" 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>This class finds adsorbate sites on slabs and generates
adsorbate structures according to user-defined criteria.
The algorithm for finding sites is essentially as follows:</p>
<blockquote>
<div><ol class="arabic simple">
<li><dl class="simple">
<dt>Determine “surface sites” by finding those within</dt><dd><p>a height threshold along the miller index of the
highest site</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Create a network of surface sites using the Delaunay</dt><dd><p>triangulation of the surface sites</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Assign on-top, bridge, and hollow adsorption sites</dt><dd><p>at the nodes, edges, and face centers of the Del.
Triangulation</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Generate structures from a molecule positioned at</dt><dd><p>these sites</p>
</dd>
</dl>
</li>
</ol>
</div></blockquote>
<p>Create an AdsorbateSiteFinder object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab</strong> (<a class="reference internal" href="pymatgen.core.surface.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – slab object for which to find adsorbate sites</p></li>
<li><p><strong>selective_dynamics</strong> (<em>bool</em>) – flag for whether to assign
non-surface sites as fixed for selective dynamics</p></li>
<li><p><strong>height</strong> (<em>float</em>) – height criteria for selection of surface sites</p></li>
<li><p><strong>mi_vec</strong> (<em>3-D array-like</em>) – vector corresponding to the vector
concurrent with the miller index, this enables use with
slabs that have been reoriented, but the miller vector
must be supplied manually</p></li>
<li><p><strong>top_surface</strong> (<em>bool</em>) – Which surface to adsorb, True for the surface
above the center of mass, False for the surface below
center of mass</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.add_adsorbate">
<code class="descname">add_adsorbate</code><span class="sig-paren">(</span><em>molecule</em>, <em>ads_coord</em>, <em>repeat=None</em>, <em>reorient=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.add_adsorbate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.add_adsorbate" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds an adsorbate at a particular coordinate. Adsorbate
represented by a Molecule object, and is positioned relative
to the input adsorbate coordinate.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule object representing the adsorbate</p></li>
<li><p><strong>ads_coord</strong> (<em>array</em>) – coordinate of adsorbate position</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – input for making a supercell of slab
prior to placing the adsorbate</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether to reorient the molecule to
have its z-axis concurrent with miller index</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.adsorb_both_surfaces">
<code class="descname">adsorb_both_surfaces</code><span class="sig-paren">(</span><em>molecule</em>, <em>repeat=None</em>, <em>min_lw=5.0</em>, <em>reorient=True</em>, <em>find_args={}</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.adsorb_both_surfaces"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.adsorb_both_surfaces" title="Permalink to this definition">¶</a></dt>
<dd><p>Function that generates all adsorption structures for a given
molecular adsorbate on both surfaces of a slab. This is useful
for calculating surface energy where both surfaces need to be
equivalent or if we want to calculate nonpolar systems.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule corresponding to adsorbate</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – repeat argument for supercell generation</p></li>
<li><p><strong>min_lw</strong> (<em>float</em>) – minimum length and width of the slab, only used
if repeat is None</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether or not to reorient adsorbate
along the miller index</p></li>
<li><p><strong>find_args</strong> (<em>dict</em>) – dictionary of arguments to be passed to the
call to self.find_adsorption_sites, e.g. {“distance”:2.0}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_selective_dynamics">
<code class="descname">assign_selective_dynamics</code><span class="sig-paren">(</span><em>slab</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.assign_selective_dynamics"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_selective_dynamics" title="Permalink to this definition">¶</a></dt>
<dd><p>Helper function to assign selective dynamics site_properties
based on surface, subsurface site properties</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>slab</strong> (<a class="reference internal" href="pymatgen.core.surface.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – slab for which to assign selective dynamics</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_site_properties">
<code class="descname">assign_site_properties</code><span class="sig-paren">(</span><em>slab</em>, <em>height=0.9</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.assign_site_properties"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_site_properties" title="Permalink to this definition">¶</a></dt>
<dd><p>Assigns site properties.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.ensemble_center">
<code class="descname">ensemble_center</code><span class="sig-paren">(</span><em>site_list</em>, <em>indices</em>, <em>cartesian=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.ensemble_center"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.ensemble_center" title="Permalink to this definition">¶</a></dt>
<dd><p>Finds the center of an ensemble of sites selected from
a list of sites. Helper method for the find_adsorption_sites
algorithm.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site_list</strong> (<em>list of sites</em>) – list of sites</p></li>
<li><p><strong>indices</strong> (<em>list of ints</em>) – list of ints from which to select
sites from site list</p></li>
<li><p><strong>cartesian</strong> (<em>bool</em>) – whether to get average fractional or
cartesian coordinate</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_adsorption_sites">
<code class="descname">find_adsorption_sites</code><span class="sig-paren">(</span><em>distance=2.0, put_inside=True, symm_reduce=0.01, near_reduce=0.01, positions=['ontop', 'bridge', 'hollow'], no_obtuse_hollow=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.find_adsorption_sites"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_adsorption_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>Finds surface sites according to the above algorithm. Returns
a list of corresponding cartesian coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>distance</strong> (<em>float</em>) – distance from the coordinating ensemble
of atoms along the miller index for the site (i. e.
the distance from the slab itself)</p></li>
<li><p><strong>put_inside</strong> (<em>bool</em>) – whether to put the site inside the cell</p></li>
<li><p><strong>symm_reduce</strong> (<em>float</em>) – symm reduction threshold</p></li>
<li><p><strong>near_reduce</strong> (<em>float</em>) – near reduction threshold</p></li>
<li><p><strong>positions</strong> (<em>list</em>) – <p>which positions to include in the site finding
“ontop”: sites on top of surface sites
“bridge”: sites at edges between surface sites in Delaunay</p>
<blockquote>
<div><p>triangulation of surface sites in the miller plane</p>
</div></blockquote>
<p>”hollow”: sites at centers of Delaunay triangulation faces
“subsurface”: subsurface positions projected into miller plane</p>
</p></li>
<li><p><strong>no_obtuse_hollow</strong> (<em>bool</em>) – flag to indicate whether to include
obtuse triangular ensembles in hollow sites</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_surface_sites_by_height">
<code class="descname">find_surface_sites_by_height</code><span class="sig-paren">(</span><em>slab</em>, <em>height=0.9</em>, <em>xy_tol=0.05</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.find_surface_sites_by_height"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_surface_sites_by_height" title="Permalink to this definition">¶</a></dt>
<dd><p>This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site_list</strong> (<em>list</em>) – list of sites from which to select surface sites</p></li>
<li><p><strong>height</strong> (<em>float</em>) – threshold in angstroms of distance from topmost
site in slab along the slab c-vector to include in surface
site determination</p></li>
<li><p><strong>xy_tol</strong> (<em>float</em>) – if supplied, will remove any sites which are
within a certain distance in the miller plane.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>list of sites selected to be within a threshold of the highest</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.from_bulk_and_miller">
<em class="property">classmethod </em><code class="descname">from_bulk_and_miller</code><span class="sig-paren">(</span><em>structure</em>, <em>miller_index</em>, <em>min_slab_size=8.0</em>, <em>min_vacuum_size=10.0</em>, <em>max_normal_search=None</em>, <em>center_slab=True</em>, <em>selective_dynamics=False</em>, <em>undercoord_threshold=0.09</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.from_bulk_and_miller"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.from_bulk_and_miller" title="Permalink to this definition">¶</a></dt>
<dd><p>This method constructs the adsorbate site finder from a bulk
structure and a miller index, which allows the surface sites
to be determined from the difference in bulk and slab coordination,
as opposed to the height threshold.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure from which slab
input to the ASF is constructed</p></li>
<li><p><strong>miller_index</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – miller index to be used</p></li>
<li><p><strong>min_slab_size</strong> (<em>float</em>) – min slab size for slab generation</p></li>
<li><p><strong>min_vacuum_size</strong> (<em>float</em>) – min vacuum size for slab generation</p></li>
<li><p><strong>max_normal_search</strong> (<em>int</em>) – max normal search for slab generation</p></li>
<li><p><strong>center_slab</strong> (<em>bool</em>) – whether to center slab in slab generation</p></li>
<li><p><strong>dynamics</strong> (<em>selective</em>) – whether to assign surface sites
to selective dynamics</p></li>
<li><p><strong>undercoord_threshold</strong> (<em>float</em>) – threshold of “undercoordation”
to use for the assignment of surface sites. Default is
0.1, for which surface sites will be designated if they
are 10% less coordinated than their bulk counterpart</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_adsorption_structures">
<code class="descname">generate_adsorption_structures</code><span class="sig-paren">(</span><em>molecule</em>, <em>repeat=None</em>, <em>min_lw=5.0</em>, <em>reorient=True</em>, <em>find_args={}</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.generate_adsorption_structures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_adsorption_structures" title="Permalink to this definition">¶</a></dt>
<dd><p>Function that generates all adsorption structures for a given
molecular adsorbate. Can take repeat argument or minimum
length/width of precursor slab as an input</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule corresponding to adsorbate</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – repeat argument for supercell generation</p></li>
<li><p><strong>min_lw</strong> (<em>float</em>) – minimum length and width of the slab, only used
if repeat is None</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether or not to reorient adsorbate
along the miller index</p></li>
<li><p><strong>find_args</strong> (<em>dict</em>) – dictionary of arguments to be passed to the
call to self.find_adsorption_sites, e.g. {“distance”:2.0}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_substitution_structures">
<code class="descname">generate_substitution_structures</code><span class="sig-paren">(</span><em>atom</em>, <em>target_species=[]</em>, <em>sub_both_sides=False</em>, <em>range_tol=0.01</em>, <em>dist_from_surf=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.generate_substitution_structures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_substitution_structures" title="Permalink to this definition">¶</a></dt>
<dd><dl class="simple">
<dt>Function that performs substitution-type doping on the surface and</dt><dd><p>returns all possible configurations where one dopant is substituted
per surface. Can substitute one surface or both.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atom</strong> (<em>str</em>) – atom corresponding to substitutional dopant</p></li>
<li><p><strong>sub_both_sides</strong> (<em>bool</em>) – If true, substitute an equivalent
site on the other surface</p></li>
<li><p><strong>target_species</strong> (<em>list</em>) – List of specific species to substitute</p></li>
<li><p><strong>range_tol</strong> (<em>float</em>) – Find viable substitution sites at a specific
distance from the surface +- this tolerance</p></li>
<li><p><strong>dist_from_surf</strong> (<em>float</em>) – Distance from the surface to find viable
substitution sites, defaults to 0 to substitute at the surface</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.get_extended_surface_mesh">
<code class="descname">get_extended_surface_mesh</code><span class="sig-paren">(</span><em>repeat=(5</em>, <em>5</em>, <em>1)</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.get_extended_surface_mesh"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.get_extended_surface_mesh" title="Permalink to this definition">¶</a></dt>
<dd><p>Gets an extended surface mesh for to use for adsorption
site finding by constructing supercell of surface sites</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>repeat</strong> (<em>3-tuple</em>) – repeat for getting extended surface mesh</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.near_reduce">
<code class="descname">near_reduce</code><span class="sig-paren">(</span><em>coords_set</em>, <em>threshold=0.0001</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.near_reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.near_reduce" title="Permalink to this definition">¶</a></dt>
<dd><p>Prunes coordinate set for coordinates that are within
threshold</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coords_set</strong> (<em>Nx3 array-like</em>) – list or array of coordinates</p></li>
<li><p><strong>threshold</strong> (<em>float</em>) – threshold value for distance</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.subsurface_sites">
<code class="descname">subsurface_sites</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.subsurface_sites"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.subsurface_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>convenience method to return list of subsurface sites</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.surface_sites">
<code class="descname">surface_sites</code><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.surface_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>convenience method to return a list of surface sites</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.symm_reduce">
<code class="descname">symm_reduce</code><span class="sig-paren">(</span><em>coords_set</em>, <em>threshold=1e-06</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#AdsorbateSiteFinder.symm_reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.symm_reduce" title="Permalink to this definition">¶</a></dt>
<dd><p>Reduces the set of adsorbate sites by finding removing
symmetrically equivalent duplicates</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coords_set</strong> – coordinate set in cartesian coordinates</p></li>
<li><p><strong>threshold</strong> – tolerance for distance equivalence, used
as input to in_coord_list_pbc for dupl. checking</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.adsorption.get_mi_vec">
<code class="descname">get_mi_vec</code><span class="sig-paren">(</span><em>slab</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#get_mi_vec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.get_mi_vec" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience function which returns the unit vector aligned
with the miller index.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.adsorption.get_rot">
<code class="descname">get_rot</code><span class="sig-paren">(</span><em>slab</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#get_rot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.get_rot" title="Permalink to this definition">¶</a></dt>
<dd><p>Gets the transformation to rotate the z axis into the miller index</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.adsorption.plot_slab">
<code class="descname">plot_slab</code><span class="sig-paren">(</span><em>slab</em>, <em>ax</em>, <em>scale=0.8</em>, <em>repeat=5</em>, <em>window=1.5</em>, <em>draw_unit_cell=True</em>, <em>decay=0.2</em>, <em>adsorption_sites=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#plot_slab"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.plot_slab" title="Permalink to this definition">¶</a></dt>
<dd><p>Function that helps visualize the slab in a 2-D plot, for
convenient viewing of output of AdsorbateSiteFinder.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab</strong> (<em>slab</em>) – Slab object to be visualized</p></li>
<li><p><strong>ax</strong> (<em>axes</em>) – matplotlib axes with which to visualize</p></li>
<li><p><strong>scale</strong> (<em>float</em>) – radius scaling for sites</p></li>
<li><p><strong>repeat</strong> (<em>int</em>) – number of repeating unit cells to visualize</p></li>
<li><p><strong>window</strong> (<em>float</em>) – window for setting the axes limits, is essentially
a fraction of the unit cell limits</p></li>
<li><p><strong>draw_unit_cell</strong> (<em>bool</em>) – flag indicating whether or not to draw cell</p></li>
<li><p><strong>decay</strong> (<em>float</em>) – how the alpha-value decays along the z-axis</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.adsorption.put_coord_inside">
<code class="descname">put_coord_inside</code><span class="sig-paren">(</span><em>lattice</em>, <em>cart_coordinate</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#put_coord_inside"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.put_coord_inside" title="Permalink to this definition">¶</a></dt>
<dd><p>converts a cartesian coordinate such that it is inside the unit cell.</p>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.adsorption.reorient_z">
<code class="descname">reorient_z</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/adsorption.html#reorient_z"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.reorient_z" title="Permalink to this definition">¶</a></dt>
<dd><p>reorients a structure such that the z axis is concurrent with the
normal to the A-B plane</p>
</dd></dl>
</div>
</div>
</div>
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