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<title>pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module — pymatgen 2019.5.1 documentation</title>
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<div class="section" id="module-pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder">
<span id="pymatgen-analysis-chemenv-coordination-environments-coordination-geometry-finder-module"></span><h1>pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module<a class="headerlink" href="#module-pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder" title="Permalink to this headline">¶</a></h1>
<p>This module contains the main object used to identify the coordination environments in a given structure.
If you use this module, please cite the following:</p>
<p>David Waroquiers, Xavier Gonze, Gian-Marco Rignanese, Cathrin Welker-Nieuwoudt, Frank Rosowski,
Michael Goebel, Stephan Schenk, Peter Degelmann, Rute Andre, Robert Glaum, and Geoffroy Hautier,
“Statistical analysis of coordination environments in oxides”,
Chem. Mater., 2017, 29 (19), pp 8346–8360,
DOI: 10.1021/acs.chemmater.7b02766</p>
<dl class="class">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry">
<em class="property">class </em><code class="descname">AbstractGeometry</code><span class="sig-paren">(</span><em>central_site=None</em>, <em>bare_coords=None</em>, <em>centering_type='standard'</em>, <em>include_central_site_in_centroid=False</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry" 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>Class used to describe a geometry (perfect or distorted)</p>
<p>Constructor for the abstract geometry
:param central_site: Coordinates of the central site
:param bare_coords: Coordinates of the neighbors of the central site
:param centering_type: How to center the abstract geometry
:param include_central_site_in_centroid: When the centering is on the centroid, the central site is included</p>
<blockquote>
<div><p>if this parameter is set to True.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Raise</dt>
<dd class="field-odd"><p>ValueError if the parameters are not consistent</p>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.cn">
<code class="descname">cn</code><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.cn" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.coordination_number">
<code class="descname">coordination_number</code><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.coordination_number" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.from_cg">
<em class="property">classmethod </em><code class="descname">from_cg</code><span class="sig-paren">(</span><em>cg</em>, <em>centering_type='standard'</em>, <em>include_central_site_in_centroid=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.from_cg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.from_cg" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_csc">
<code class="descname">points_wcs_csc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wcs_csc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_csc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwcc">
<code class="descname">points_wcs_ctwcc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wcs_ctwcc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwcc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwocc">
<code class="descname">points_wcs_ctwocc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wcs_ctwocc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwocc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_csc">
<code class="descname">points_wocs_csc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wocs_csc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_csc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwcc">
<code class="descname">points_wocs_ctwcc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wocs_ctwcc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwcc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwocc">
<code class="descname">points_wocs_ctwocc</code><span class="sig-paren">(</span><em>permutation=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#AbstractGeometry.points_wocs_ctwocc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwocc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder">
<em class="property">class </em><code class="descname">LocalGeometryFinder</code><span class="sig-paren">(</span><em>permutations_safe_override=False</em>, <em>plane_ordering_override=True</em>, <em>debug_level=None</em>, <em>plane_safe_permutations=False</em>, <em>only_symbols=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder" 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>Main class used to find the local environments in a structure</p>
<p>Constructor for the LocalGeometryFinder, initializes the list of coordination geometries
:param permutations_safe_override: If set to True, all permutations are tested (very time-consuming for large
coordination numbers!)
:param plane_ordering_override: If set to False, the ordering of the points in the plane is disabled</p>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORS">
<code class="descname">BVA_DISTANCE_SCALE_FACTORS</code><em class="property"> = {'GGA_relaxed': 1.015, 'LDA_relaxed': 0.995, 'experimental': 1.0}</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORS" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTOR">
<code class="descname">DEFAULT_BVA_DISTANCE_SCALE_FACTOR</code><em class="property"> = 1.0</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTOR" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONS">
<code class="descname">DEFAULT_SPG_ANALYZER_OPTIONS</code><em class="property"> = {'angle_tolerance': 5, 'symprec': 0.001}</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONS" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_STRATEGY">
<code class="descname">DEFAULT_STRATEGY</code><em class="property"> = <pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object></em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_STRATEGY" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.PRESETS">
<code class="descname">PRESETS</code><em class="property"> = {'DEFAULT': {'maximum_distance_factor': 2.0, 'minimum_angle_factor': 0.05, 'optimization': 2, 'voronoi_normalized_angle_tolerance': 0.03, 'voronoi_normalized_distance_tolerance': 0.05}}</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.PRESETS" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_NONE">
<code class="descname">STRUCTURE_REFINEMENT_NONE</code><em class="property"> = 'none'</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_NONE" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_REFINED">
<code class="descname">STRUCTURE_REFINEMENT_REFINED</code><em class="property"> = 'refined'</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_REFINED" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZED">
<code class="descname">STRUCTURE_REFINEMENT_SYMMETRIZED</code><em class="property"> = 'symmetrized'</em><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZED" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_coordination_environments">
<code class="descname">compute_coordination_environments</code><span class="sig-paren">(</span><em>structure</em>, <em>indices=None</em>, <em>only_cations=True</em>, <em>strategy=<pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.MultiWeightsChemenvStrategy object></em>, <em>valences='bond-valence-analysis'</em>, <em>initial_structure_environments=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.compute_coordination_environments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_coordination_environments" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_structure_environments">
<code class="descname">compute_structure_environments</code><span class="sig-paren">(</span><em>excluded_atoms=None</em>, <em>only_atoms=None</em>, <em>only_cations=True</em>, <em>only_indices=None</em>, <em>maximum_distance_factor=2.0</em>, <em>minimum_angle_factor=0.05</em>, <em>max_cn=None</em>, <em>min_cn=None</em>, <em>only_symbols=None</em>, <em>valences='undefined'</em>, <em>additional_conditions=None</em>, <em>info=None</em>, <em>timelimit=None</em>, <em>initial_structure_environments=None</em>, <em>get_from_hints=False</em>, <em>voronoi_normalized_distance_tolerance=0.05</em>, <em>voronoi_normalized_angle_tolerance=0.03</em>, <em>recompute=None</em>, <em>optimization=2</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.compute_structure_environments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_structure_environments" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes and returns the StructureEnvironments object containing all the information about the coordination
environments in the structure
:param excluded_atoms: Atoms for which the coordination geometries does not have to be identified
:param only_atoms: If not set to None, atoms for which the coordination geometries have to be identified
:param only_cations: If set to True, will only compute environments for cations
:param only_indices: If not set to None, will only compute environments the atoms of the given indices
:param maximum_distance_factor: If not set to None, neighbors beyond</p>
<blockquote>
<div><p>maximum_distance_factor*closest_neighbor_distance are not considered</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>minimum_angle_factor</strong> – If not set to None, neighbors for which the angle is lower than
minimum_angle_factor*largest_angle_neighbor are not considered</p></li>
<li><p><strong>max_cn</strong> – maximum coordination number to be considered</p></li>
<li><p><strong>min_cn</strong> – minimum coordination number to be considered</p></li>
<li><p><strong>only_symbols</strong> – if not set to None, consider only coordination environments with the given symbols</p></li>
<li><p><strong>valences</strong> – valences of the atoms</p></li>
<li><p><strong>additional_conditions</strong> – additional conditions to be considered in the bonds (example : only bonds
between cation and anion</p></li>
<li><p><strong>info</strong> – additional info about the calculation</p></li>
<li><p><strong>timelimit</strong> – time limit (in secs) after which the calculation of the StructureEnvironments object stops</p></li>
<li><p><strong>initial_structure_environments</strong> – initial StructureEnvironments object (most probably incomplete)</p></li>
<li><p><strong>get_from_hints</strong> – whether to add neighbors sets from “hints” (e.g. capped environment => test the
neighbors without the cap)</p></li>
<li><p><strong>voronoi_normalized_distance_tolerance</strong> – tolerance for the normalized distance used to distinguish
neighbors sets</p></li>
<li><p><strong>voronoi_normalized_angle_tolerance</strong> – tolerance for the normalized angle used to distinguish
neighbors sets</p></li>
<li><p><strong>recompute</strong> – whether to recompute the sites already computed (when initial_structure_environments
is not None)</p></li>
<li><p><strong>optimization</strong> – optimization algorithm</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The StructureEnvironments object containing all the information about the coordination</p>
</dd>
</dl>
<p>environments in the structure</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures">
<code class="descname">coordination_geometry_symmetry_measures</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>tested_permutations=False</em>, <em>points_perfect=None</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures of a given coordination_geometry for a set of permutations depending on
the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination</p>
<blockquote>
<div><p>geometry, different methods are called.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>coordination_geometry</strong> – Coordination geometry for which the symmetry measures are looked for</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the symmetry measures of a given coordination_geometry for a set of permutations</p>
</dd>
<dt class="field-odd">Raise</dt>
<dd class="field-odd"><p>NotImplementedError if the permutation_setup does not exists</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random">
<code class="descname">coordination_geometry_symmetry_measures_fallback_random</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>NRANDOM=10</em>, <em>points_perfect=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures for a random set of permutations for the coordination geometry
“coordination_geometry”. Fallback implementation for the plane separation algorithms measures
of each permutation</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coordination_geometry</strong> – The coordination geometry to be investigated</p></li>
<li><p><strong>NRANDOM</strong> – Number of random permutations to be tested</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The symmetry measures for the given coordination geometry for each permutation investigated</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane">
<code class="descname">coordination_geometry_symmetry_measures_separation_plane</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>separation_plane_algo</em>, <em>testing=False</em>, <em>tested_permutations=False</em>, <em>points_perfect=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures of the given coordination geometry “coordination_geometry” using separation
facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other …
:param coordination_geometry: The coordination geometry to be investigated
:return: The symmetry measures for the given coordination geometry for each plane and permutation investigated</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim">
<code class="descname">coordination_geometry_symmetry_measures_separation_plane_optim</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>separation_plane_algo</em>, <em>points_perfect=None</em>, <em>nb_set=None</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures of the given coordination geometry “coordination_geometry” using separation
facets to reduce the complexity of the system. Caller to the refined 2POINTS, 3POINTS and other …
:param coordination_geometry: The coordination geometry to be investigated
:return: The symmetry measures for the given coordination geometry for each plane and permutation investigated</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim">
<code class="descname">coordination_geometry_symmetry_measures_sepplane_optim</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>points_perfect=None</em>, <em>nb_set=None</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures of a given coordination_geometry for a set of permutations depending on
the permutation setup. Depending on the parameters of the LocalGeometryFinder and on the coordination</p>
<blockquote>
<div><p>geometry, different methods are called.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>coordination_geometry</strong> – Coordination geometry for which the symmetry measures are looked for</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>the symmetry measures of a given coordination_geometry for a set of permutations</p>
</dd>
<dt class="field-odd">Raise</dt>
<dd class="field-odd"><p>NotImplementedError if the permutation_setup does not exists</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_standard">
<code class="descname">coordination_geometry_symmetry_measures_standard</code><span class="sig-paren">(</span><em>coordination_geometry</em>, <em>algo</em>, <em>points_perfect=None</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.coordination_geometry_symmetry_measures_standard"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_standard" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the symmetry measures for a set of permutations (whose setup depends on the coordination geometry)
for the coordination geometry “coordination_geometry”. Standard implementation looking for the symmetry
measures of each permutation</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>coordination_geometry</strong> – The coordination geometry to be investigated</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The symmetry measures for the given coordination geometry for each permutation investigated</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures">
<code class="descname">get_coordination_symmetry_measures</code><span class="sig-paren">(</span><em>only_minimum=True</em>, <em>all_csms=True</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.get_coordination_symmetry_measures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the continuous symmetry measures of the current local geometry in a dictionary.
:return: the continuous symmetry measures of the current local geometry in a dictionary.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures_optim">
<code class="descname">get_coordination_symmetry_measures_optim</code><span class="sig-paren">(</span><em>only_minimum=True</em>, <em>all_csms=True</em>, <em>nb_set=None</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.get_coordination_symmetry_measures_optim"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures_optim" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the continuous symmetry measures of the current local geometry in a dictionary.
:return: the continuous symmetry measures of the current local geometry in a dictionary.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_structure">
<code class="descname">get_structure</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.get_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the pymatgen Structure that has been setup for the identification of geometries (the initial one
might have been refined/symmetrized using the SpaceGroupAnalyzer).
:return: The pymatgen Structure that has been setup for the identification of geometries (the initial one
might have been refined/symmetrized using the SpaceGroupAnalyzer).</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.set_structure">
<code class="descname">set_structure</code><span class="sig-paren">(</span><em>lattice</em>, <em>species</em>, <em>coords</em>, <em>coords_are_cartesian</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.set_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.set_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up the pymatgen structure for which the coordination geometries have to be identified starting from the
lattice, the species and the coordinates
:param lattice: The lattice of the structure
:param species: The species on the sites
:param coords: The coordinates of the sites
:param coords_are_cartesian: If set to True, the coordinates are given in cartesian coordinates</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_explicit_indices_local_geometry">
<code class="descname">setup_explicit_indices_local_geometry</code><span class="sig-paren">(</span><em>explicit_indices</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_explicit_indices_local_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_explicit_indices_local_geometry" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up explicit indices for the local geometry, for testing purposes
:param explicit_indices: explicit indices for the neighbors (set of numbers
from 0 to CN-1 in a given order)</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_local_geometry">
<code class="descname">setup_local_geometry</code><span class="sig-paren">(</span><em>isite</em>, <em>coords</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_local_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_local_geometry" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up the AbstractGeometry for the local geometry of site with index isite.
:param isite: Index of the site for which the local geometry has to be set up
:param coords: The coordinates of the (local) neighbors</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_ordered_indices_local_geometry">
<code class="descname">setup_ordered_indices_local_geometry</code><span class="sig-paren">(</span><em>coordination</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_ordered_indices_local_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_ordered_indices_local_geometry" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up ordered indices for the local geometry, for testing purposes
:param coordination: coordination of the local geometry</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameter">
<code class="descname">setup_parameter</code><span class="sig-paren">(</span><em>parameter</em>, <em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_parameter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameter" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup of one specific parameter to the given value. The other parameters are unchanged. See setup_parameters
method for the list of possible parameters
:param parameter: Parameter to setup/update
:param value: Value of the parameter</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameters">
<code class="descname">setup_parameters</code><span class="sig-paren">(</span><em>centering_type='standard'</em>, <em>include_central_site_in_centroid=False</em>, <em>bva_distance_scale_factor=None</em>, <em>structure_refinement='refined'</em>, <em>spg_analyzer_options=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_parameters"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup of the parameters for the coordination geometry finder. A reference point for the geometries has to be
chosen. This can be the centroid of the structure (including or excluding the atom for which the coordination
geometry is looked for) or the atom itself. In the ‘standard’ centering_type, the reference point is the central
atom for coordination numbers 1, 2, 3 and 4 and the centroid for coordination numbers > 4.
:param centering_type: Type of the reference point (centering) ‘standard’, ‘centroid’ or ‘central_site’
:param include_central_site_in_centroid: In case centering_type is ‘centroid’, the central site is included if</p>
<blockquote>
<div><p>this value is set to True.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bva_distance_scale_factor</strong> – Scaling factor for the bond valence analyzer (this might be different whether
the structure is an experimental one, an LDA or a GGA relaxed one, or any
other relaxation scheme (where under- or over-estimation of bond lengths
is known).</p></li>
<li><p><strong>structure_refinement</strong> – Refinement of the structure. Can be “none”, “refined” or “symmetrized”.</p></li>
<li><p><strong>spg_analyzer_options</strong> – Options for the SpaceGroupAnalyzer (dictionary specifying “symprec”
and “angle_tolerance”. See pymatgen’s SpaceGroupAnalyzer for more information.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_indices_local_geometry">
<code class="descname">setup_random_indices_local_geometry</code><span class="sig-paren">(</span><em>coordination</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_random_indices_local_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_indices_local_geometry" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up random indices for the local geometry, for testing purposes
:param coordination: coordination of the local geometry</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_structure">
<code class="descname">setup_random_structure</code><span class="sig-paren">(</span><em>coordination</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_random_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a purely random structure with a given coordination.
:param coordination: coordination number for the random structure</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_structure">
<code class="descname">setup_structure</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up the structure for which the coordination geometries have to be identified. The structure is analyzed
with the space group analyzer and a refined structure is used
:param structure: A pymatgen Structure
:param</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_test_perfect_environment">
<code class="descname">setup_test_perfect_environment</code><span class="sig-paren">(</span><em>symbol</em>, <em>randomness=False</em>, <em>max_random_dist=0.1</em>, <em>symbol_type='mp_symbol'</em>, <em>indices='RANDOM'</em>, <em>random_translation='NONE'</em>, <em>random_rotation='NONE'</em>, <em>random_scale='NONE'</em>, <em>points=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.setup_test_perfect_environment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_test_perfect_environment" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.update_nb_set_environments">
<code class="descname">update_nb_set_environments</code><span class="sig-paren">(</span><em>se</em>, <em>isite</em>, <em>cn</em>, <em>inb_set</em>, <em>nb_set</em>, <em>recompute=False</em>, <em>optimization=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#LocalGeometryFinder.update_nb_set_environments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.update_nb_set_environments" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_rotation">
<code class="descname">find_rotation</code><span class="sig-paren">(</span><em>points_distorted</em>, <em>points_perfect</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#find_rotation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_rotation" title="Permalink to this definition">¶</a></dt>
<dd><p>This finds the rotation matrix that aligns the (distorted) set of points “points_distorted” with respect to the
(perfect) set of points “points_perfect” in a least-square sense.
:param points_distorted: List of points describing a given (distorted) polyhedron for which the rotation that</p>
<blockquote>
<div><p>aligns these points in a least-square sense to the set of perfect points “points_perfect”</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>points_perfect</strong> – List of “perfect” points describing a given model polyhedron.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The rotation matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_scaling_factor">
<code class="descname">find_scaling_factor</code><span class="sig-paren">(</span><em>points_distorted</em>, <em>points_perfect</em>, <em>rot</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#find_scaling_factor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_scaling_factor" title="Permalink to this definition">¶</a></dt>
<dd><p>This finds the scaling factor between the (distorted) set of points “points_distorted” and the
(perfect) set of points “points_perfect” in a least-square sense.
:param points_distorted: List of points describing a given (distorted) polyhedron for which the scaling factor has</p>
<blockquote>
<div><p>to be obtained.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>points_perfect</strong> – List of “perfect” points describing a given model polyhedron.</p></li>
<li><p><strong>rot</strong> – The rotation matrix</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The scaling factor between the two structures and the rotated set of (distorted) points.</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.symmetry_measure">
<code class="descname">symmetry_measure</code><span class="sig-paren">(</span><em>points_distorted</em>, <em>points_perfect</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.html#symmetry_measure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.symmetry_measure" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes the continuous symmetry measure of the (distorted) set of points “points_distorted” with respect to the
(perfect) set of points “points_perfect”.
:param points_distorted: List of points describing a given (distorted) polyhedron for which the symmetry measure</p>
<blockquote>
<div><p>has to be computed with respect to the model polyhedron described by the list of points
“points_perfect”.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>points_perfect</strong> – List of “perfect” points describing a given model polyhedron.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The continuous symmetry measure of the distorted polyhedron with respect to the perfect polyhedron</p>
</dd>
</dl>
</dd></dl>
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