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<h1>Source code for pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies</h1><div class="highlight"><pre>
<span></span><span class="c1"># coding: utf-8</span>
<span class="c1"># Copyright (c) Pymatgen Development Team.</span>
<span class="c1"># Distributed under the terms of the MIT License.</span>
<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">division</span><span class="p">,</span> <span class="n">unicode_literals</span>
<span class="sd">"""</span>
<span class="sd">This module provides so-called "strategies" to determine the coordination environments of an atom in a structure.</span>
<span class="sd">Some strategies can favour larger or smaller environments. Some strategies uniquely identifies the environments while</span>
<span class="sd">some others can identify the environment as a "mix" of several environments, each of which is assigned with a given</span>
<span class="sd">fraction. The choice of the strategy depends on the purpose of the user.</span>
<span class="sd">"""</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">"David Waroquiers"</span>
<span class="n">__copyright__</span> <span class="o">=</span> <span class="s2">"Copyright 2012, The Materials Project"</span>
<span class="n">__credits__</span> <span class="o">=</span> <span class="s2">"Geoffroy Hautier"</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">"2.0"</span>
<span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">"David Waroquiers"</span>
<span class="n">__email__</span> <span class="o">=</span> <span class="s2">"david.waroquiers@gmail.com"</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">"Feb 20, 2016"</span>
<span class="kn">import</span> <span class="nn">abc</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">from</span> <span class="nn">monty.json</span> <span class="k">import</span> <span class="n">MSONable</span>
<span class="kn">from</span> <span class="nn">pymatgen.symmetry.analyzer</span> <span class="k">import</span> <span class="n">SpacegroupAnalyzer</span>
<span class="kn">from</span> <span class="nn">pymatgen.core.operations</span> <span class="k">import</span> <span class="n">SymmOp</span>
<span class="kn">from</span> <span class="nn">pymatgen.core.sites</span> <span class="k">import</span> <span class="n">PeriodicSite</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">scipy.stats</span> <span class="k">import</span> <span class="n">gmean</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.coordination_environments.coordination_geometries</span> <span class="k">import</span> <span class="n">UNCLEAR_ENVIRONMENT_SYMBOL</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.coordination_geometry_utils</span> <span class="k">import</span> <span class="n">get_lower_and_upper_f</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.func_utils</span> <span class="k">import</span> <span class="n">CSMFiniteRatioFunction</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.func_utils</span> <span class="k">import</span> <span class="n">CSMInfiniteRatioFunction</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.func_utils</span> <span class="k">import</span> <span class="n">DeltaCSMRatioFunction</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.func_utils</span> <span class="k">import</span> <span class="n">RatioFunction</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.chemenv_errors</span> <span class="k">import</span> <span class="n">EquivalentSiteSearchError</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.coordination_environments.coordination_geometries</span> <span class="k">import</span> <span class="n">AllCoordinationGeometries</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.utils.defs_utils</span> <span class="k">import</span> <span class="n">AdditionalConditions</span>
<span class="kn">from</span> <span class="nn">six</span> <span class="k">import</span> <span class="n">with_metaclass</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.chemenv.coordination_environments.voronoi</span> <span class="k">import</span> <span class="n">DetailedVoronoiContainer</span>
<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">OrderedDict</span>
<span class="n">module_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span>
<span class="n">MPSYMBOL_TO_CN</span> <span class="o">=</span> <span class="n">AllCoordinationGeometries</span><span class="p">()</span><span class="o">.</span><span class="n">get_symbol_cn_mapping</span><span class="p">()</span>
<span class="n">ALLCG</span> <span class="o">=</span> <span class="n">AllCoordinationGeometries</span><span class="p">()</span>
<div class="viewcode-block" id="StrategyOption"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption">[docs]</a><span class="k">class</span> <span class="nc">StrategyOption</span><span class="p">(</span><span class="n">with_metaclass</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABCMeta</span><span class="p">,</span> <span class="n">MSONable</span><span class="p">)):</span>
<span class="n">allowed_values</span> <span class="o">=</span> <span class="kc">None</span>
<div class="viewcode-block" id="StrategyOption.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption.as_dict">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> A JSON serializable dict representation of this strategy option.</span>
<span class="sd"> """</span>
<span class="k">pass</span></div></div>
<div class="viewcode-block" id="DistanceCutoffFloat"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat">[docs]</a><span class="k">class</span> <span class="nc">DistanceCutoffFloat</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">StrategyOption</span><span class="p">):</span>
<span class="n">allowed_values</span> <span class="o">=</span> <span class="s1">'Real number between 1.0 and +infinity'</span>
<span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">):</span>
<span class="n">flt</span> <span class="o">=</span> <span class="nb">float</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">)</span>
<span class="k">if</span> <span class="n">flt</span> <span class="o"><</span> <span class="mf">1.0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Distance cutoff should be between 1.0 and +infinity"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">flt</span>
<div class="viewcode-block" id="DistanceCutoffFloat.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s1">'@module'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s1">'@class'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s1">'value'</span><span class="p">:</span> <span class="bp">self</span><span class="p">}</span></div>
<div class="viewcode-block" id="DistanceCutoffFloat.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceCutoffFloat.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">'value'</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="AngleCutoffFloat"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat">[docs]</a><span class="k">class</span> <span class="nc">AngleCutoffFloat</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">StrategyOption</span><span class="p">):</span>
<span class="n">allowed_values</span> <span class="o">=</span> <span class="s1">'Real number between 0.0 and 1.0'</span>
<span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">):</span>
<span class="n">flt</span> <span class="o">=</span> <span class="nb">float</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">)</span>
<span class="k">if</span> <span class="n">flt</span> <span class="o"><</span> <span class="mf">0.0</span> <span class="ow">or</span> <span class="n">flt</span> <span class="o">></span> <span class="mf">1.0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Angle cutoff should be between 0.0 and 1.0"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">flt</span>
<div class="viewcode-block" id="AngleCutoffFloat.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s1">'@module'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s1">'@class'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s1">'value'</span><span class="p">:</span> <span class="bp">self</span><span class="p">}</span></div>
<div class="viewcode-block" id="AngleCutoffFloat.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">'value'</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="CSMFloat"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat">[docs]</a><span class="k">class</span> <span class="nc">CSMFloat</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">StrategyOption</span><span class="p">):</span>
<span class="n">allowed_values</span> <span class="o">=</span> <span class="s1">'Real number between 0.0 and 100.0'</span>
<span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">):</span>
<span class="n">flt</span> <span class="o">=</span> <span class="nb">float</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">myfloat</span><span class="p">)</span>
<span class="k">if</span> <span class="n">flt</span> <span class="o"><</span> <span class="mf">0.0</span> <span class="ow">or</span> <span class="n">flt</span> <span class="o">></span> <span class="mf">100.0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Continuous symmetry measure limits should be between 0.0 and 100.0"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">flt</span>
<div class="viewcode-block" id="CSMFloat.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s1">'@module'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s1">'@class'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s1">'value'</span><span class="p">:</span> <span class="bp">self</span><span class="p">}</span></div>
<div class="viewcode-block" id="CSMFloat.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">'value'</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="AdditionalConditionInt"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt">[docs]</a><span class="k">class</span> <span class="nc">AdditionalConditionInt</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">StrategyOption</span><span class="p">):</span>
<span class="n">allowed_values</span> <span class="o">=</span> <span class="s1">'Integer amongst :</span><span class="se">\n</span><span class="s1">'</span>
<span class="k">for</span> <span class="n">integer</span><span class="p">,</span> <span class="n">description</span> <span class="ow">in</span> <span class="n">AdditionalConditions</span><span class="o">.</span><span class="n">CONDITION_DESCRIPTION</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">allowed_values</span> <span class="o">+=</span> <span class="s1">' - </span><span class="si">{:d}</span><span class="s1"> for "</span><span class="si">{}</span><span class="s1">"</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">integer</span><span class="p">,</span> <span class="n">description</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">integer</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">integer</span><span class="p">)</span> <span class="o">!=</span> <span class="n">integer</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Additional condition </span><span class="si">{}</span><span class="s2"> is not an integer"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">integer</span><span class="p">)))</span>
<span class="n">intger</span> <span class="o">=</span> <span class="nb">int</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">integer</span><span class="p">)</span>
<span class="k">if</span> <span class="n">intger</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">AdditionalConditions</span><span class="o">.</span><span class="n">ALL</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Additional condition </span><span class="si">{:d}</span><span class="s2"> is not allowed"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">integer</span><span class="p">))</span>
<span class="k">return</span> <span class="n">intger</span>
<div class="viewcode-block" id="AdditionalConditionInt.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s1">'@module'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s1">'@class'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s1">'value'</span><span class="p">:</span> <span class="bp">self</span><span class="p">}</span></div>
<div class="viewcode-block" id="AdditionalConditionInt.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">'value'</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="AbstractChemenvStrategy"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy">[docs]</a><span class="k">class</span> <span class="nc">AbstractChemenvStrategy</span><span class="p">(</span><span class="n">with_metaclass</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABCMeta</span><span class="p">,</span> <span class="n">MSONable</span><span class="p">)):</span>
<span class="sd">"""</span>
<span class="sd"> Class used to define a Chemenv strategy for the neighbors and coordination environment to be applied to a</span>
<span class="sd"> StructureEnvironments object</span>
<span class="sd"> """</span>
<span class="n">AC</span> <span class="o">=</span> <span class="n">AdditionalConditions</span><span class="p">()</span>
<span class="n">STRATEGY_OPTIONS</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
<span class="n">STRATEGY_DESCRIPTION</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">STRATEGY_INFO_FIELDS</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">DEFAULT_SYMMETRY_MEASURE_TYPE</span> <span class="o">=</span> <span class="s1">'csm_wcs_ctwcc'</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">DEFAULT_SYMMETRY_MEASURE_TYPE</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Abstract constructor for the all chemenv strategies.</span>
<span class="sd"> :param structure_environments: StructureEnvironments object containing all the information on the</span>
<span class="sd"> coordination of the sites in a structure</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">if</span> <span class="n">structure_environments</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">set_structure_environments</span><span class="p">(</span><span class="n">structure_environments</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span> <span class="o">=</span> <span class="n">symmetry_measure_type</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">symmetry_measure_type</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span>
<div class="viewcode-block" id="AbstractChemenvStrategy.set_structure_environments"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.set_structure_environments">[docs]</a> <span class="k">def</span> <span class="nf">set_structure_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span> <span class="o">=</span> <span class="n">structure_environments</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">voronoi</span><span class="p">,</span> <span class="n">DetailedVoronoiContainer</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Voronoi Container not of type "DetailedVoronoiContainer"'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">prepare_symmetries</span><span class="p">()</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.prepare_symmetries"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.prepare_symmetries">[docs]</a> <span class="k">def</span> <span class="nf">prepare_symmetries</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">spg_analyzer</span> <span class="o">=</span> <span class="n">SpacegroupAnalyzer</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">symops</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">spg_analyzer</span><span class="o">.</span><span class="n">get_symmetry_operations</span><span class="p">()</span>
<span class="k">except</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">symops</span> <span class="o">=</span> <span class="p">[]</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.equivalent_site_index_and_transform"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.equivalent_site_index_and_transform">[docs]</a> <span class="k">def</span> <span class="nf">equivalent_site_index_and_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">psite</span><span class="p">):</span>
<span class="c1"># Get the index of the site in the unit cell of which the PeriodicSite psite is a replica.</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">isite</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">psite</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">uc_psite</span> <span class="o">=</span> <span class="n">psite</span><span class="o">.</span><span class="n">to_unit_cell</span>
<span class="n">isite</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">uc_psite</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">for</span> <span class="n">isite2</span><span class="p">,</span> <span class="n">site2</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="p">):</span>
<span class="k">if</span> <span class="n">psite</span><span class="o">.</span><span class="n">is_periodic_image</span><span class="p">(</span><span class="n">site2</span><span class="p">):</span>
<span class="n">isite</span> <span class="o">=</span> <span class="n">isite2</span>
<span class="k">break</span>
<span class="c1"># Get the translation between psite and its corresponding site in the unit cell (Translation I)</span>
<span class="n">thissite</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span>
<span class="n">dthissite</span> <span class="o">=</span> <span class="n">psite</span><span class="o">.</span><span class="n">frac_coords</span> <span class="o">-</span> <span class="n">thissite</span><span class="o">.</span><span class="n">frac_coords</span>
<span class="c1"># Get the translation between the equivalent site for which the neighbors have been computed and the site in</span>
<span class="c1"># the unit cell that corresponds to psite (Translation II)</span>
<span class="n">equivsite</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]]</span><span class="o">.</span><span class="n">to_unit_cell</span>
<span class="c1">#equivsite = self.structure_environments.structure[self.structure_environments.sites_map[isite]]</span>
<span class="n">dequivsite</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]]</span><span class="o">.</span><span class="n">frac_coords</span>
<span class="o">-</span> <span class="n">equivsite</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">)</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
<span class="c1"># Find the symmetry that applies the site in the unit cell to the equivalent site, as well as the translation</span>
<span class="c1"># that gets back the site to the unit cell (Translation III)</span>
<span class="c1">#TODO: check that these tolerances are needed, now that the structures are refined before analyzing environments</span>
<span class="n">tolerances</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1e-8</span><span class="p">,</span> <span class="mf">1e-7</span><span class="p">,</span> <span class="mf">1e-6</span><span class="p">,</span> <span class="mf">1e-5</span><span class="p">,</span> <span class="mf">1e-4</span><span class="p">]</span>
<span class="k">for</span> <span class="n">tolerance</span> <span class="ow">in</span> <span class="n">tolerances</span><span class="p">:</span>
<span class="k">for</span> <span class="n">symop</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">symops</span><span class="p">:</span>
<span class="n">newsite</span> <span class="o">=</span> <span class="n">PeriodicSite</span><span class="p">(</span><span class="n">equivsite</span><span class="o">.</span><span class="n">_species</span><span class="p">,</span> <span class="n">symop</span><span class="o">.</span><span class="n">operate</span><span class="p">(</span><span class="n">equivsite</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">),</span> <span class="n">equivsite</span><span class="o">.</span><span class="n">_lattice</span><span class="p">)</span>
<span class="k">if</span> <span class="n">newsite</span><span class="o">.</span><span class="n">is_periodic_image</span><span class="p">(</span><span class="n">thissite</span><span class="p">,</span> <span class="n">tolerance</span><span class="o">=</span><span class="n">tolerance</span><span class="p">):</span>
<span class="n">mysym</span> <span class="o">=</span> <span class="n">symop</span>
<span class="n">dthissite2</span> <span class="o">=</span> <span class="n">thissite</span><span class="o">.</span><span class="n">frac_coords</span> <span class="o">-</span> <span class="n">newsite</span><span class="o">.</span><span class="n">frac_coords</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span>
<span class="n">symops</span> <span class="o">=</span> <span class="p">[</span><span class="n">SymmOp</span><span class="o">.</span><span class="n">from_rotation_and_translation</span><span class="p">()]</span>
<span class="k">for</span> <span class="n">symop</span> <span class="ow">in</span> <span class="n">symops</span><span class="p">:</span>
<span class="n">newsite</span> <span class="o">=</span> <span class="n">PeriodicSite</span><span class="p">(</span><span class="n">equivsite</span><span class="o">.</span><span class="n">_species</span><span class="p">,</span> <span class="n">symop</span><span class="o">.</span><span class="n">operate</span><span class="p">(</span><span class="n">equivsite</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">),</span> <span class="n">equivsite</span><span class="o">.</span><span class="n">_lattice</span><span class="p">)</span>
<span class="c1">#if newsite.is_periodic_image(thissite):</span>
<span class="k">if</span> <span class="n">newsite</span><span class="o">.</span><span class="n">is_periodic_image</span><span class="p">(</span><span class="n">thissite</span><span class="p">,</span> <span class="n">tolerance</span><span class="o">=</span><span class="n">tolerance</span><span class="p">):</span>
<span class="n">mysym</span> <span class="o">=</span> <span class="n">symop</span>
<span class="n">dthissite2</span> <span class="o">=</span> <span class="n">thissite</span><span class="o">.</span><span class="n">frac_coords</span> <span class="o">-</span> <span class="n">newsite</span><span class="o">.</span><span class="n">frac_coords</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">found</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">EquivalentSiteSearchError</span><span class="p">(</span><span class="n">psite</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">],</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span> <span class="o">+</span> <span class="n">dthissite2</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.get_site_neighbors"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_neighbors">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">get_site_neighbors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Applies the strategy to the structure_environments object in order to get the neighbors of a given site.</span>
<span class="sd"> :param site: Site for which the neighbors are looked for</span>
<span class="sd"> :param structure_environments: StructureEnvironments object containing all the information needed to get the</span>
<span class="sd"> neighbors of the site</span>
<span class="sd"> :return: The list of neighbors of the site. For complex strategies, where one allows multiple solutions, this</span>
<span class="sd"> can return a list of list of neighbors</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">uniquely_determines_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Returns True if the strategy leads to a unique coordination environment, False otherwise.</span>
<span class="sd"> :return: True if the strategy leads to a unique coordination environment, False otherwise.</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span>
<div class="viewcode-block" id="AbstractChemenvStrategy.get_site_coordination_environment"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environment">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">get_site_coordination_environment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Applies the strategy to the structure_environments object in order to define the coordination environment of</span>
<span class="sd"> a given site.</span>
<span class="sd"> :param site: Site for which the coordination environment is looked for</span>
<span class="sd"> :return: The coordination environment of the site. For complex strategies, where one allows multiple</span>
<span class="sd"> solutions, this can return a list of coordination environments for the site</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.get_site_coordination_environments"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environments">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">get_site_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Applies the strategy to the structure_environments object in order to define the coordination environment of</span>
<span class="sd"> a given site.</span>
<span class="sd"> :param site: Site for which the coordination environment is looked for</span>
<span class="sd"> :return: The coordination environment of the site. For complex strategies, where one allows multiple</span>
<span class="sd"> solutions, this can return a list of coordination environments for the site</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.get_site_coordination_environments_fractions"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environments_fractions">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">get_site_coordination_environments_fractions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ordered</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_fraction</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">return_maps</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">return_strategy_dict_info</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Applies the strategy to the structure_environments object in order to define the coordination environment of</span>
<span class="sd"> a given site.</span>
<span class="sd"> :param site: Site for which the coordination environment is looked for</span>
<span class="sd"> :return: The coordination environment of the site. For complex strategies, where one allows multiple</span>
<span class="sd"> solutions, this can return a list of coordination environments for the site</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.get_site_ce_fractions_and_neighbors"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_ce_fractions_and_neighbors">[docs]</a> <span class="k">def</span> <span class="nf">get_site_ce_fractions_and_neighbors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">full_ce_info</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">strategy_info</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Applies the strategy to the structure_environments object in order to get coordination environments, their</span>
<span class="sd"> fraction, csm, geometry_info, and neighbors</span>
<span class="sd"> :param site: Site for which the above information is seeked</span>
<span class="sd"> :return: The list of neighbors of the site. For complex strategies, where one allows multiple solutions, this</span>
<span class="sd"> can return a list of list of neighbors</span>
<span class="sd"> """</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">geoms_and_maps_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_site_coordination_environments_fractions</span><span class="p">(</span><span class="n">site</span><span class="o">=</span><span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span>
<span class="n">dequivsite</span><span class="o">=</span><span class="n">dequivsite</span><span class="p">,</span>
<span class="n">dthissite</span><span class="o">=</span><span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="n">mysym</span><span class="p">,</span>
<span class="n">return_maps</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">return_strategy_dict_info</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">geoms_and_maps_list</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">site_nbs_sets</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">neighbors_sets</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span>
<span class="n">ce_and_neighbors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">fractions_dict</span> <span class="ow">in</span> <span class="n">geoms_and_maps_list</span><span class="p">:</span>
<span class="n">ce_map</span> <span class="o">=</span> <span class="n">fractions_dict</span><span class="p">[</span><span class="s1">'ce_map'</span><span class="p">]</span>
<span class="n">ce_nb_set</span> <span class="o">=</span> <span class="n">site_nbs_sets</span><span class="p">[</span><span class="n">ce_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">ce_map</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
<span class="n">neighbors</span> <span class="o">=</span> <span class="p">[{</span><span class="s1">'site'</span><span class="p">:</span> <span class="n">nb_site_and_index</span><span class="p">[</span><span class="s1">'site'</span><span class="p">],</span>
<span class="s1">'index'</span><span class="p">:</span> <span class="n">nb_site_and_index</span><span class="p">[</span><span class="s1">'index'</span><span class="p">]}</span>
<span class="k">for</span> <span class="n">nb_site_and_index</span> <span class="ow">in</span> <span class="n">ce_nb_set</span><span class="o">.</span><span class="n">neighb_sites_and_indices</span><span class="p">]</span>
<span class="n">fractions_dict</span><span class="p">[</span><span class="s1">'neighbors'</span><span class="p">]</span> <span class="o">=</span> <span class="n">neighbors</span>
<span class="n">ce_and_neighbors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fractions_dict</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ce_and_neighbors</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.set_option"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.set_option">[docs]</a> <span class="k">def</span> <span class="nf">set_option</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">option_name</span><span class="p">,</span> <span class="n">option_value</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">option_name</span><span class="p">,</span> <span class="n">option_value</span><span class="p">)</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.setup_options"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.setup_options">[docs]</a> <span class="k">def</span> <span class="nf">setup_options</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">all_options_dict</span><span class="p">):</span>
<span class="k">for</span> <span class="n">option_name</span><span class="p">,</span> <span class="n">option_value</span> <span class="ow">in</span> <span class="n">all_options_dict</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="bp">self</span><span class="o">.</span><span class="n">set_option</span><span class="p">(</span><span class="n">option_name</span><span class="p">,</span> <span class="n">option_value</span><span class="p">)</span></div>
<span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Equality method that should be implemented for any strategy</span>
<span class="sd"> :param other: strategy to be compared with the current one</span>
<span class="sd"> :return:</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">out</span> <span class="o">=</span> <span class="s1">' Chemenv Strategy "</span><span class="si">{}</span><span class="s1">"</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
<span class="n">out</span> <span class="o">+=</span> <span class="s1">' </span><span class="si">{}</span><span class="se">\n\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s1">'='</span><span class="o">*</span><span class="p">(</span><span class="mi">19</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)))</span>
<span class="n">out</span> <span class="o">+=</span> <span class="s1">' Description :</span><span class="se">\n</span><span class="s1"> </span><span class="si">{}</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s1">'-'</span><span class="o">*</span><span class="mi">13</span><span class="p">)</span>
<span class="n">out</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">STRATEGY_DESCRIPTION</span>
<span class="n">out</span> <span class="o">+=</span> <span class="s1">'</span><span class="se">\n\n</span><span class="s1">'</span>
<span class="n">out</span> <span class="o">+=</span> <span class="s1">' Options :</span><span class="se">\n</span><span class="s1"> </span><span class="si">{}</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s1">'-'</span><span class="o">*</span><span class="mi">9</span><span class="p">)</span>
<span class="k">for</span> <span class="n">option_name</span><span class="p">,</span> <span class="n">option_dict</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">STRATEGY_OPTIONS</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">out</span> <span class="o">+=</span> <span class="s1">' - </span><span class="si">{}</span><span class="s1"> : </span><span class="si">{}</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">option_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">option_name</span><span class="p">)))</span>
<span class="k">return</span> <span class="n">out</span>
<div class="viewcode-block" id="AbstractChemenvStrategy.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.as_dict">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Bson-serializable dict representation of the SimplestChemenvStrategy object.</span>
<span class="sd"> :return: Bson-serializable dict representation of the SimplestChemenvStrategy object.</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div>
<div class="viewcode-block" id="AbstractChemenvStrategy.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the</span>
<span class="sd"> SimpleAbundanceChemenvStrategy object created using the as_dict method.</span>
<span class="sd"> :param d: dict representation of the SimpleAbundanceChemenvStrategy object</span>
<span class="sd"> :return: StructureEnvironments object</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">()</span></div></div>
<div class="viewcode-block" id="SimplestChemenvStrategy"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy">[docs]</a><span class="k">class</span> <span class="nc">SimplestChemenvStrategy</span><span class="p">(</span><span class="n">AbstractChemenvStrategy</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Simplest ChemenvStrategy using fixed angle and distance parameters for the definition of neighbors in the</span>
<span class="sd"> Voronoi approach. The coordination environment is then given as the one with the lowest continuous symmetry measure</span>
<span class="sd"> """</span>
<span class="c1"># Default values for the distance and angle cutoffs</span>
<span class="n">DEFAULT_DISTANCE_CUTOFF</span> <span class="o">=</span> <span class="mf">1.4</span>
<span class="n">DEFAULT_ANGLE_CUTOFF</span> <span class="o">=</span> <span class="mf">0.3</span>
<span class="n">DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF</span> <span class="o">=</span> <span class="mf">10.0</span>
<span class="n">DEFAULT_ADDITIONAL_CONDITION</span> <span class="o">=</span> <span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">AC</span><span class="o">.</span><span class="n">ONLY_ACB</span>
<span class="n">STRATEGY_OPTIONS</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'distance_cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'type'</span><span class="p">:</span> <span class="n">DistanceCutoffFloat</span><span class="p">,</span> <span class="s1">'internal'</span><span class="p">:</span> <span class="s1">'_distance_cutoff'</span><span class="p">,</span>
<span class="s1">'default'</span><span class="p">:</span> <span class="n">DEFAULT_DISTANCE_CUTOFF</span><span class="p">}</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'angle_cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'type'</span><span class="p">:</span> <span class="n">AngleCutoffFloat</span><span class="p">,</span> <span class="s1">'internal'</span><span class="p">:</span> <span class="s1">'_angle_cutoff'</span><span class="p">,</span>
<span class="s1">'default'</span><span class="p">:</span> <span class="n">DEFAULT_ANGLE_CUTOFF</span><span class="p">}</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'additional_condition'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'type'</span><span class="p">:</span> <span class="n">AdditionalConditionInt</span><span class="p">,</span>
<span class="s1">'internal'</span><span class="p">:</span> <span class="s1">'_additional_condition'</span><span class="p">,</span>
<span class="s1">'default'</span><span class="p">:</span> <span class="n">DEFAULT_ADDITIONAL_CONDITION</span><span class="p">}</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'continuous_symmetry_measure_cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'type'</span><span class="p">:</span> <span class="n">CSMFloat</span><span class="p">,</span>
<span class="s1">'internal'</span><span class="p">:</span> <span class="s1">'_continuous_symmetry_measure_cutoff'</span><span class="p">,</span>
<span class="s1">'default'</span><span class="p">:</span> <span class="n">DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF</span><span class="p">}</span>
<span class="n">STRATEGY_DESCRIPTION</span> <span class="o">=</span> <span class="s1">' Simplest ChemenvStrategy using fixed angle and distance parameters </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' for the definition of neighbors in the Voronoi approach. </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' The coordination environment is then given as the one with the </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' lowest continuous symmetry measure.'</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">distance_cutoff</span><span class="o">=</span><span class="n">DEFAULT_DISTANCE_CUTOFF</span><span class="p">,</span>
<span class="n">angle_cutoff</span><span class="o">=</span><span class="n">DEFAULT_ANGLE_CUTOFF</span><span class="p">,</span> <span class="n">additional_condition</span><span class="o">=</span><span class="n">DEFAULT_ADDITIONAL_CONDITION</span><span class="p">,</span>
<span class="n">continuous_symmetry_measure_cutoff</span><span class="o">=</span><span class="n">DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF</span><span class="p">,</span>
<span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">DEFAULT_SYMMETRY_MEASURE_TYPE</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Constructor for this SimplestChemenvStrategy.</span>
<span class="sd"> :param distance_cutoff: Distance cutoff used</span>
<span class="sd"> :param angle_cutoff: Angle cutoff used</span>
<span class="sd"> """</span>
<span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">,</span> <span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">symmetry_measure_type</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance_cutoff</span> <span class="o">=</span> <span class="n">distance_cutoff</span>
<span class="bp">self</span><span class="o">.</span><span class="n">angle_cutoff</span> <span class="o">=</span> <span class="n">angle_cutoff</span>
<span class="bp">self</span><span class="o">.</span><span class="n">additional_condition</span> <span class="o">=</span> <span class="n">additional_condition</span>
<span class="bp">self</span><span class="o">.</span><span class="n">continuous_symmetry_measure_cutoff</span> <span class="o">=</span> <span class="n">continuous_symmetry_measure_cutoff</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">uniquely_determines_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="kc">True</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">distance_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span>
<span class="nd">@distance_cutoff</span><span class="o">.</span><span class="n">setter</span>
<span class="k">def</span> <span class="nf">distance_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">distance_cutoff</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span> <span class="o">=</span> <span class="n">DistanceCutoffFloat</span><span class="p">(</span><span class="n">distance_cutoff</span><span class="p">)</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">angle_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span>
<span class="nd">@angle_cutoff</span><span class="o">.</span><span class="n">setter</span>
<span class="k">def</span> <span class="nf">angle_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">angle_cutoff</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span> <span class="o">=</span> <span class="n">AngleCutoffFloat</span><span class="p">(</span><span class="n">angle_cutoff</span><span class="p">)</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">additional_condition</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span>
<span class="nd">@additional_condition</span><span class="o">.</span><span class="n">setter</span>
<span class="k">def</span> <span class="nf">additional_condition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">additional_condition</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="o">=</span> <span class="n">AdditionalConditionInt</span><span class="p">(</span><span class="n">additional_condition</span><span class="p">)</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">continuous_symmetry_measure_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_continuous_symmetry_measure_cutoff</span>
<span class="nd">@continuous_symmetry_measure_cutoff</span><span class="o">.</span><span class="n">setter</span>
<span class="k">def</span> <span class="nf">continuous_symmetry_measure_cutoff</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">continuous_symmetry_measure_cutoff</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_continuous_symmetry_measure_cutoff</span> <span class="o">=</span> <span class="n">CSMFloat</span><span class="p">(</span><span class="n">continuous_symmetry_measure_cutoff</span><span class="p">)</span>
<div class="viewcode-block" id="SimplestChemenvStrategy.get_site_neighbors"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_neighbors">[docs]</a> <span class="k">def</span> <span class="nf">get_site_neighbors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span><span class="c1">#, neighbors_map=None):</span>
<span class="c1">#if neighbors_map is not None:</span>
<span class="c1"># return self.structure_environments.voronoi.get_neighbors(isite=isite, neighbors_map=neighbors_map)</span>
<span class="k">if</span> <span class="n">isite</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">ce</span><span class="p">,</span> <span class="n">cn_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_site_coordination_environment</span><span class="p">(</span><span class="n">site</span><span class="o">=</span><span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span>
<span class="n">dequivsite</span><span class="o">=</span><span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="n">mysym</span><span class="p">,</span>
<span class="n">return_map</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">nb_set</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">neighbors_sets</span><span class="p">[</span><span class="n">isite</span><span class="p">][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
<span class="n">eqsite_ps</span> <span class="o">=</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">neighb_sites</span>
<span class="n">coordinated_neighbors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">ips</span><span class="p">,</span> <span class="n">ps</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">eqsite_ps</span><span class="p">):</span>
<span class="n">coords</span> <span class="o">=</span> <span class="n">mysym</span><span class="o">.</span><span class="n">operate</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">frac_coords</span> <span class="o">+</span> <span class="n">dequivsite</span><span class="p">)</span> <span class="o">+</span> <span class="n">dthissite</span>
<span class="n">ps_site</span> <span class="o">=</span> <span class="n">PeriodicSite</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">_species</span><span class="p">,</span> <span class="n">coords</span><span class="p">,</span> <span class="n">ps</span><span class="o">.</span><span class="n">_lattice</span><span class="p">)</span>
<span class="n">coordinated_neighbors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ps_site</span><span class="p">)</span>
<span class="k">return</span> <span class="n">coordinated_neighbors</span></div>
<div class="viewcode-block" id="SimplestChemenvStrategy.get_site_coordination_environment"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environment">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">return_map</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">if</span> <span class="n">isite</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">neighbors_normalized_distances</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">voronoi</span><span class="o">.</span><span class="n">neighbors_normalized_distances</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span>
<span class="n">neighbors_normalized_angles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">voronoi</span><span class="o">.</span><span class="n">neighbors_normalized_angles</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span>
<span class="n">idist</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">for</span> <span class="n">iwd</span><span class="p">,</span> <span class="n">wd</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">neighbors_normalized_distances</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance_cutoff</span> <span class="o">>=</span> <span class="n">wd</span><span class="p">[</span><span class="s1">'min'</span><span class="p">]:</span>
<span class="n">idist</span> <span class="o">=</span> <span class="n">iwd</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">iang</span> <span class="o">=</span> <span class="kc">None</span>
<span class="k">for</span> <span class="n">iwa</span><span class="p">,</span> <span class="n">wa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">neighbors_normalized_angles</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">angle_cutoff</span> <span class="o"><=</span> <span class="n">wa</span><span class="p">[</span><span class="s1">'max'</span><span class="p">]:</span>
<span class="n">iang</span> <span class="o">=</span> <span class="n">iwa</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">idist</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">iang</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Distance or angle parameter not found ...'</span><span class="p">)</span>
<span class="n">my_cn</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">my_inb_set</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">for</span> <span class="n">cn</span><span class="p">,</span> <span class="n">nb_sets</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">neighbors_sets</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">for</span> <span class="n">inb_set</span><span class="p">,</span> <span class="n">nb_set</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nb_sets</span><span class="p">):</span>
<span class="n">sources</span> <span class="o">=</span> <span class="p">[</span><span class="n">src</span> <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">sources</span>
<span class="k">if</span> <span class="n">src</span><span class="p">[</span><span class="s1">'origin'</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'dist_ang_ac_voronoi'</span> <span class="ow">and</span> <span class="n">src</span><span class="p">[</span><span class="s1">'ac'</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">additional_condition</span><span class="p">]</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">sources</span><span class="p">:</span>
<span class="k">if</span> <span class="n">src</span><span class="p">[</span><span class="s1">'idp'</span><span class="p">]</span> <span class="o">==</span> <span class="n">idist</span> <span class="ow">and</span> <span class="n">src</span><span class="p">[</span><span class="s1">'iap'</span><span class="p">]</span> <span class="o">==</span> <span class="n">iang</span><span class="p">:</span>
<span class="n">my_cn</span> <span class="o">=</span> <span class="n">cn</span>
<span class="n">my_inb_set</span> <span class="o">=</span> <span class="n">inb_set</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">found</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">found</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">cn_map</span> <span class="o">=</span> <span class="p">(</span><span class="n">my_cn</span><span class="p">,</span> <span class="n">my_inb_set</span><span class="p">)</span>
<span class="n">ce</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">ce_list</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
<span class="k">if</span> <span class="n">ce</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">coord_geoms</span> <span class="o">=</span> <span class="n">ce</span><span class="o">.</span><span class="n">coord_geoms</span>
<span class="k">if</span> <span class="n">return_map</span><span class="p">:</span>
<span class="k">if</span> <span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">cn_map</span>
<span class="k">return</span> <span class="p">(</span><span class="n">ce</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">),</span> <span class="n">cn_map</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="n">ce</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">)</span></div>
<div class="viewcode-block" id="SimplestChemenvStrategy.get_site_coordination_environments_fractions"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environments_fractions">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environments_fractions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ordered</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">min_fraction</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">return_maps</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">return_strategy_dict_info</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">if</span> <span class="n">isite</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">dequivsite</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">dthissite</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">mysym</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">site_nb_sets</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">neighbors_sets</span><span class="p">[</span><span class="n">isite</span><span class="p">]</span>
<span class="k">if</span> <span class="n">site_nb_sets</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">ce_and_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_site_coordination_environment</span><span class="p">(</span><span class="n">site</span><span class="o">=</span><span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="n">dequivsite</span><span class="p">,</span>
<span class="n">dthissite</span><span class="o">=</span><span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="n">mysym</span><span class="p">,</span>
<span class="n">return_map</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ce_and_map</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">ce</span><span class="p">,</span> <span class="n">ce_map</span> <span class="o">=</span> <span class="n">ce_and_map</span>
<span class="k">if</span> <span class="n">ce</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">ce_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'ce_symbol'</span><span class="p">:</span> <span class="s1">'UNKNOWN:</span><span class="si">{:d}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">ce_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="s1">'ce_dict'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'ce_fraction'</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">}</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">ce_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'ce_symbol'</span><span class="p">:</span> <span class="n">ce</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">'ce_dict'</span><span class="p">:</span> <span class="n">ce</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">'ce_fraction'</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">}</span>
<span class="k">if</span> <span class="n">return_maps</span><span class="p">:</span>
<span class="n">ce_dict</span><span class="p">[</span><span class="s1">'ce_map'</span><span class="p">]</span> <span class="o">=</span> <span class="n">ce_map</span>
<span class="k">if</span> <span class="n">return_strategy_dict_info</span><span class="p">:</span>
<span class="n">ce_dict</span><span class="p">[</span><span class="s1">'strategy_info'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">fractions_info_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">ce_dict</span><span class="p">]</span>
<span class="k">return</span> <span class="n">fractions_info_list</span></div>
<div class="viewcode-block" id="SimplestChemenvStrategy.get_site_coordination_environments"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environments">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">return_maps</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">get_site_coordination_environment</span><span class="p">(</span><span class="n">site</span><span class="o">=</span><span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="n">dequivsite</span><span class="p">,</span>
<span class="n">dthissite</span><span class="o">=</span><span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="n">mysym</span><span class="p">,</span> <span class="n">return_map</span><span class="o">=</span><span class="n">return_maps</span><span class="p">)]</span></div>
<div class="viewcode-block" id="SimplestChemenvStrategy.add_strategy_visualization_to_subplot"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.add_strategy_visualization_to_subplot">[docs]</a> <span class="k">def</span> <span class="nf">add_strategy_visualization_to_subplot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subplot</span><span class="p">,</span> <span class="n">visualization_options</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">plot_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="n">subplot</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span><span class="p">,</span> <span class="s1">'o'</span><span class="p">,</span> <span class="n">mec</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mfc</span><span class="o">=</span><span class="s1">'w'</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">12</span><span class="p">)</span>
<span class="n">subplot</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span><span class="p">,</span> <span class="s1">'x'</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">12</span><span class="p">)</span></div>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_distance_cutoff</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_angle_cutoff</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_continuous_symmetry_measure_cutoff</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">_continuous_symmetry_measure_cutoff</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">symmetry_measure_type</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">symmetry_measure_type</span><span class="p">)</span>
<div class="viewcode-block" id="SimplestChemenvStrategy.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Bson-serializable dict representation of the SimplestChemenvStrategy object.</span>
<span class="sd"> :return: Bson-serializable dict representation of the SimplestChemenvStrategy object.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">{</span><span class="s2">"@module"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s2">"@class"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s2">"distance_cutoff"</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_distance_cutoff</span><span class="p">),</span>
<span class="s2">"angle_cutoff"</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_angle_cutoff</span><span class="p">),</span>
<span class="s2">"additional_condition"</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span><span class="p">),</span>
<span class="s2">"continuous_symmetry_measure_cutoff"</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_continuous_symmetry_measure_cutoff</span><span class="p">),</span>
<span class="s2">"symmetry_measure_type"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">}</span></div>
<div class="viewcode-block" id="SimplestChemenvStrategy.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reconstructs the SimplestChemenvStrategy object from a dict representation of the SimplestChemenvStrategy object</span>
<span class="sd"> created using the as_dict method.</span>
<span class="sd"> :param d: dict representation of the SimplestChemenvStrategy object</span>
<span class="sd"> :return: StructureEnvironments object</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">distance_cutoff</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"distance_cutoff"</span><span class="p">],</span> <span class="n">angle_cutoff</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"angle_cutoff"</span><span class="p">],</span>
<span class="n">additional_condition</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"additional_condition"</span><span class="p">],</span>
<span class="n">continuous_symmetry_measure_cutoff</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"continuous_symmetry_measure_cutoff"</span><span class="p">],</span>
<span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"symmetry_measure_type"</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy">[docs]</a><span class="k">class</span> <span class="nc">SimpleAbundanceChemenvStrategy</span><span class="p">(</span><span class="n">AbstractChemenvStrategy</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Simple ChemenvStrategy using the neighbors that are the most "abundant" in the grid of angle and distance</span>
<span class="sd"> parameters for the definition of neighbors in the Voronoi approach.</span>
<span class="sd"> The coordination environment is then given as the one with the lowest continuous symmetry measure</span>
<span class="sd"> """</span>
<span class="n">DEFAULT_MAX_DIST</span> <span class="o">=</span> <span class="mf">2.0</span>
<span class="n">DEFAULT_ADDITIONAL_CONDITION</span> <span class="o">=</span> <span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">AC</span><span class="o">.</span><span class="n">ONLY_ACB</span>
<span class="n">STRATEGY_OPTIONS</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'additional_condition'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'type'</span><span class="p">:</span> <span class="n">AdditionalConditionInt</span><span class="p">,</span>
<span class="s1">'internal'</span><span class="p">:</span> <span class="s1">'_additional_condition'</span><span class="p">,</span>
<span class="s1">'default'</span><span class="p">:</span> <span class="n">DEFAULT_ADDITIONAL_CONDITION</span><span class="p">}</span>
<span class="n">STRATEGY_OPTIONS</span><span class="p">[</span><span class="s1">'surface_calculation_type'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">STRATEGY_DESCRIPTION</span> <span class="o">=</span> <span class="s1">' Simple Abundance ChemenvStrategy using the most "abundant" neighbors map </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' for the definition of neighbors in the Voronoi approach. </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' The coordination environment is then given as the one with the </span><span class="se">\n</span><span class="s1">'</span> \
<span class="s1">' lowest continuous symmetry measure.'</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">additional_condition</span><span class="o">=</span><span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">AC</span><span class="o">.</span><span class="n">ONLY_ACB</span><span class="p">,</span>
<span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">DEFAULT_SYMMETRY_MEASURE_TYPE</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Constructor for the SimpleAbundanceChemenvStrategy.</span>
<span class="sd"> :param structure_environments: StructureEnvironments object containing all the information on the</span>
<span class="sd"> coordination of the sites in a structure</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'SimpleAbundanceChemenvStrategy not yet implemented'</span><span class="p">)</span>
<span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">,</span> <span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">symmetry_measure_type</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="o">=</span> <span class="n">additional_condition</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">uniquely_determines_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="kc">True</span>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy.get_site_neighbors"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.get_site_neighbors">[docs]</a> <span class="k">def</span> <span class="nf">get_site_neighbors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">):</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">cn_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_map</span><span class="p">(</span><span class="n">isite</span><span class="p">)</span>
<span class="n">eqsite_ps</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">unique_coordinated_neighbors</span><span class="p">(</span><span class="n">isite</span><span class="p">,</span> <span class="n">cn_map</span><span class="o">=</span><span class="n">cn_map</span><span class="p">))</span>
<span class="n">coordinated_neighbors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">ips</span><span class="p">,</span> <span class="n">ps</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">eqsite_ps</span><span class="p">):</span>
<span class="n">coords</span> <span class="o">=</span> <span class="n">mysym</span><span class="o">.</span><span class="n">operate</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">frac_coords</span> <span class="o">+</span> <span class="n">dequivsite</span><span class="p">)</span> <span class="o">+</span> <span class="n">dthissite</span>
<span class="n">ps_site</span> <span class="o">=</span> <span class="n">PeriodicSite</span><span class="p">(</span><span class="n">ps</span><span class="o">.</span><span class="n">_species</span><span class="p">,</span> <span class="n">coords</span><span class="p">,</span> <span class="n">ps</span><span class="o">.</span><span class="n">_lattice</span><span class="p">)</span>
<span class="n">coordinated_neighbors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ps_site</span><span class="p">)</span>
<span class="k">return</span> <span class="n">coordinated_neighbors</span></div>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy.get_site_coordination_environment"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.get_site_coordination_environment">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">return_map</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">if</span> <span class="n">isite</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">cn_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_map</span><span class="p">(</span><span class="n">isite</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cn_map</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">coord_geoms</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span>
<span class="n">ce_list</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
<span class="k">if</span> <span class="n">return_map</span><span class="p">:</span>
<span class="k">if</span> <span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">cn_map</span>
<span class="k">return</span> <span class="n">coord_geoms</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">),</span> <span class="n">cn_map</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="n">coord_geoms</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">)</span></div>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy.get_site_coordination_environments"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.get_site_coordination_environments">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">return_maps</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">get_site_coordination_environment</span><span class="p">(</span><span class="n">site</span><span class="o">=</span><span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="n">dequivsite</span><span class="p">,</span>
<span class="n">dthissite</span><span class="o">=</span><span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="n">mysym</span><span class="p">,</span> <span class="n">return_map</span><span class="o">=</span><span class="n">return_maps</span><span class="p">)]</span></div>
<span class="k">def</span> <span class="nf">_get_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">):</span>
<span class="n">maps_and_surfaces</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_maps_surfaces</span><span class="p">(</span><span class="n">isite</span><span class="p">)</span>
<span class="k">if</span> <span class="n">maps_and_surfaces</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">surface_max</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">imax</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="k">for</span> <span class="n">ii</span><span class="p">,</span> <span class="n">map_and_surface</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">maps_and_surfaces</span><span class="p">):</span>
<span class="n">all_additional_conditions</span> <span class="o">=</span> <span class="p">[</span><span class="n">ac</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">for</span> <span class="n">ac</span> <span class="ow">in</span> <span class="n">map_and_surface</span><span class="p">[</span><span class="s1">'parameters_indices'</span><span class="p">]]</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="ow">in</span> <span class="n">all_additional_conditions</span> <span class="ow">and</span> <span class="n">map_and_surface</span><span class="p">[</span><span class="s1">'surface'</span><span class="p">]</span> <span class="o">></span> <span class="n">surface_max</span><span class="p">:</span>
<span class="n">surface_max</span> <span class="o">=</span> <span class="n">map_and_surface</span><span class="p">[</span><span class="s1">'surface'</span><span class="p">]</span>
<span class="n">imax</span> <span class="o">=</span> <span class="n">ii</span>
<span class="k">return</span> <span class="n">maps_and_surfaces</span><span class="p">[</span><span class="n">imax</span><span class="p">][</span><span class="s1">'map'</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">_get_maps_surfaces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">,</span> <span class="n">surface_calculation_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">surface_calculation_type</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">surface_calculation_type</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'distance_parameter'</span><span class="p">:</span> <span class="p">(</span><span class="s1">'initial_normalized'</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
<span class="s1">'angle_parameter'</span><span class="p">:</span> <span class="p">(</span><span class="s1">'initial_normalized'</span><span class="p">,</span> <span class="kc">None</span><span class="p">)}</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">voronoi</span><span class="o">.</span><span class="n">maps_and_surfaces</span><span class="p">(</span><span class="n">isite</span><span class="o">=</span><span class="n">isite</span><span class="p">,</span>
<span class="n">surface_calculation_type</span><span class="o">=</span><span class="n">surface_calculation_type</span><span class="p">,</span>
<span class="n">max_dist</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">DEFAULT_MAX_DIST</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">additional_condition</span><span class="p">)</span>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Bson-serializable dict representation of the SimpleAbundanceChemenvStrategy object.</span>
<span class="sd"> :return: Bson-serializable dict representation of the SimpleAbundanceChemenvStrategy object.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">{</span><span class="s2">"@module"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s2">"@class"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s2">"additional_condition"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span><span class="p">}</span></div>
<div class="viewcode-block" id="SimpleAbundanceChemenvStrategy.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the</span>
<span class="sd"> SimpleAbundanceChemenvStrategy object created using the as_dict method.</span>
<span class="sd"> :param d: dict representation of the SimpleAbundanceChemenvStrategy object</span>
<span class="sd"> :return: StructureEnvironments object</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">additional_condition</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"additional_condition"</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="TargettedPenaltiedAbundanceChemenvStrategy"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargettedPenaltiedAbundanceChemenvStrategy">[docs]</a><span class="k">class</span> <span class="nc">TargettedPenaltiedAbundanceChemenvStrategy</span><span class="p">(</span><span class="n">SimpleAbundanceChemenvStrategy</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Simple ChemenvStrategy using the neighbors that are the most "abundant" in the grid of angle and distance</span>
<span class="sd"> parameters for the definition of neighbors in the Voronoi approach, with a bias for a given list of target</span>
<span class="sd"> environments. This can be useful in the case of, e.g. connectivity search of some given environment.</span>
<span class="sd"> The coordination environment is then given as the one with the lowest continuous symmetry measure</span>
<span class="sd"> """</span>
<span class="n">DEFAULT_TARGET_ENVIRONMENTS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'O:6'</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">truncate_dist_ang</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">additional_condition</span><span class="o">=</span><span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">AC</span><span class="o">.</span><span class="n">ONLY_ACB</span><span class="p">,</span>
<span class="n">max_nabundant</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">target_environments</span><span class="o">=</span><span class="n">DEFAULT_TARGET_ENVIRONMENTS</span><span class="p">,</span> <span class="n">target_penalty_type</span><span class="o">=</span><span class="s1">'max_csm'</span><span class="p">,</span>
<span class="n">max_csm</span><span class="o">=</span><span class="mf">5.0</span><span class="p">,</span> <span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">AbstractChemenvStrategy</span><span class="o">.</span><span class="n">DEFAULT_SYMMETRY_MEASURE_TYPE</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'TargettedPenaltiedAbundanceChemenvStrategy not yet implemented'</span><span class="p">)</span>
<span class="n">SimpleAbundanceChemenvStrategy</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">,</span>
<span class="n">additional_condition</span><span class="o">=</span><span class="n">additional_condition</span><span class="p">,</span>
<span class="n">symmetry_measure_type</span><span class="o">=</span><span class="n">symmetry_measure_type</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_nabundant</span> <span class="o">=</span> <span class="n">max_nabundant</span>
<span class="bp">self</span><span class="o">.</span><span class="n">target_environments</span> <span class="o">=</span> <span class="n">target_environments</span>
<span class="bp">self</span><span class="o">.</span><span class="n">target_penalty_type</span> <span class="o">=</span> <span class="n">target_penalty_type</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_csm</span> <span class="o">=</span> <span class="n">max_csm</span>
<div class="viewcode-block" id="TargettedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargettedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment">[docs]</a> <span class="k">def</span> <span class="nf">get_site_coordination_environment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">,</span> <span class="n">isite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dequivsite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dthissite</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mysym</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">return_map</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="k">if</span> <span class="n">isite</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="p">[</span><span class="n">isite</span><span class="p">,</span> <span class="n">dequivsite</span><span class="p">,</span> <span class="n">dthissite</span><span class="p">,</span> <span class="n">mysym</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_site_index_and_transform</span><span class="p">(</span><span class="n">site</span><span class="p">)</span>
<span class="n">cn_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_map</span><span class="p">(</span><span class="n">isite</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cn_map</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">None</span>
<span class="n">chemical_environments</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">ce_list</span>
<span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">cn_map</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
<span class="k">if</span> <span class="n">return_map</span><span class="p">:</span>
<span class="k">if</span> <span class="n">chemical_environments</span><span class="o">.</span><span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">chemical_environments</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">cn_map</span>
<span class="k">return</span> <span class="n">chemical_environments</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">),</span> <span class="n">cn_map</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">chemical_environments</span><span class="o">.</span><span class="n">coord_geoms</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">cn_map</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="n">chemical_environments</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">)</span></div>
<span class="k">def</span> <span class="nf">_get_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">):</span>
<span class="n">maps_and_surfaces</span> <span class="o">=</span> <span class="n">SimpleAbundanceChemenvStrategy</span><span class="o">.</span><span class="n">_get_maps_surfaces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">)</span>
<span class="k">if</span> <span class="n">maps_and_surfaces</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">SimpleAbundanceChemenvStrategy</span><span class="o">.</span><span class="n">_get_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">)</span>
<span class="n">current_map</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">current_target_env_csm</span> <span class="o">=</span> <span class="mf">100.0</span>
<span class="n">surfaces</span> <span class="o">=</span> <span class="p">[</span><span class="n">map_and_surface</span><span class="p">[</span><span class="s1">'surface'</span><span class="p">]</span> <span class="k">for</span> <span class="n">map_and_surface</span> <span class="ow">in</span> <span class="n">maps_and_surfaces</span><span class="p">]</span>
<span class="n">order</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">surfaces</span><span class="p">)[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">target_cgs</span> <span class="o">=</span> <span class="p">[</span><span class="n">AllCoordinationGeometries</span><span class="p">()</span><span class="o">.</span><span class="n">get_geometry_from_mp_symbol</span><span class="p">(</span><span class="n">mp_symbol</span><span class="p">)</span>
<span class="k">for</span> <span class="n">mp_symbol</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_environments</span><span class="p">]</span>
<span class="n">target_cns</span> <span class="o">=</span> <span class="p">[</span><span class="n">cg</span><span class="o">.</span><span class="n">coordination_number</span> <span class="k">for</span> <span class="n">cg</span> <span class="ow">in</span> <span class="n">target_cgs</span><span class="p">]</span>
<span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">min</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">maps_and_surfaces</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_nabundant</span><span class="p">])):</span>
<span class="n">my_map_and_surface</span> <span class="o">=</span> <span class="n">maps_and_surfaces</span><span class="p">[</span><span class="n">order</span><span class="p">[</span><span class="n">ii</span><span class="p">]]</span>
<span class="n">mymap</span> <span class="o">=</span> <span class="n">my_map_and_surface</span><span class="p">[</span><span class="s1">'map'</span><span class="p">]</span>
<span class="n">cn</span> <span class="o">=</span> <span class="n">mymap</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">if</span> <span class="n">cn</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">target_cns</span> <span class="ow">or</span> <span class="n">cn</span> <span class="o">></span> <span class="mi">12</span> <span class="ow">or</span> <span class="n">cn</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">continue</span>
<span class="n">all_conditions</span> <span class="o">=</span> <span class="p">[</span><span class="n">params</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">for</span> <span class="n">params</span> <span class="ow">in</span> <span class="n">my_map_and_surface</span><span class="p">[</span><span class="s1">'parameters_indices'</span><span class="p">]]</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">all_conditions</span><span class="p">:</span>
<span class="k">continue</span>
<span class="n">cg</span><span class="p">,</span> <span class="n">cgdict</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">ce_list</span>
<span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_environments</span><span class="o">.</span><span class="n">sites_map</span><span class="p">[</span><span class="n">isite</span><span class="p">]]</span>
<span class="p">[</span><span class="n">mymap</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">mymap</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span><span class="o">.</span><span class="n">minimum_geometry</span><span class="p">(</span><span class="n">symmetry_measure_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_symmetry_measure_type</span><span class="p">))</span>
<span class="k">if</span> <span class="p">(</span><span class="n">cg</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_environments</span> <span class="ow">and</span> <span class="n">cgdict</span><span class="p">[</span><span class="s1">'symmetry_measure'</span><span class="p">]</span> <span class="o"><=</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_csm</span> <span class="ow">and</span>
<span class="n">cgdict</span><span class="p">[</span><span class="s1">'symmetry_measure'</span><span class="p">]</span> <span class="o"><</span> <span class="n">current_target_env_csm</span><span class="p">):</span>
<span class="n">current_map</span> <span class="o">=</span> <span class="n">mymap</span>
<span class="n">current_target_env_csm</span> <span class="o">=</span> <span class="n">cgdict</span><span class="p">[</span><span class="s1">'symmetry_measure'</span><span class="p">]</span>
<span class="k">if</span> <span class="n">current_map</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">current_map</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">SimpleAbundanceChemenvStrategy</span><span class="o">.</span><span class="n">_get_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isite</span><span class="p">)</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">uniquely_determines_coordination_environments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="kc">True</span>
<div class="viewcode-block" id="TargettedPenaltiedAbundanceChemenvStrategy.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargettedPenaltiedAbundanceChemenvStrategy.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object.</span>
<span class="sd"> :return: Bson-serializable dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">{</span><span class="s2">"@module"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s2">"@class"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s2">"additional_condition"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span><span class="p">,</span>
<span class="s2">"max_nabundant"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_nabundant</span><span class="p">,</span>
<span class="s2">"target_environments"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_environments</span><span class="p">,</span>
<span class="s2">"target_penalty_type"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_penalty_type</span><span class="p">,</span>
<span class="s2">"max_csm"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_csm</span><span class="p">}</span></div>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_additional_condition</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">additional_condition</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_nabundant</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">max_nabundant</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">target_environments</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">target_environments</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">target_penalty_type</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">target_penalty_type</span> <span class="ow">and</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_csm</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">max_csm</span><span class="p">)</span>
<div class="viewcode-block" id="TargettedPenaltiedAbundanceChemenvStrategy.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargettedPenaltiedAbundanceChemenvStrategy.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reconstructs the TargettedPenaltiedAbundanceChemenvStrategy object from a dict representation of the</span>
<span class="sd"> TargettedPenaltiedAbundanceChemenvStrategy object created using the as_dict method.</span>
<span class="sd"> :param d: dict representation of the TargettedPenaltiedAbundanceChemenvStrategy object</span>
<span class="sd"> :return: TargettedPenaltiedAbundanceChemenvStrategy object</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">additional_condition</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"additional_condition"</span><span class="p">],</span>
<span class="n">max_nabundant</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"max_nabundant"</span><span class="p">],</span>
<span class="n">target_environments</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"target_environments"</span><span class="p">],</span>
<span class="n">target_penalty_type</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"target_penalty_type"</span><span class="p">],</span>
<span class="n">max_csm</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">"max_csm"</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="NbSetWeight"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight">[docs]</a><span class="k">class</span> <span class="nc">NbSetWeight</span><span class="p">(</span><span class="n">with_metaclass</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABCMeta</span><span class="p">,</span> <span class="n">MSONable</span><span class="p">)):</span>
<div class="viewcode-block" id="NbSetWeight.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight.as_dict">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> A JSON serializable dict representation of this neighbors set weight.</span>
<span class="sd"> """</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="NbSetWeight.weight"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NbSetWeight.weight">[docs]</a> <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
<span class="k">def</span> <span class="nf">weight</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">,</span> <span class="n">cn_map</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">additional_info</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">pass</span></div></div>
<div class="viewcode-block" id="AngleNbSetWeight"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight">[docs]</a><span class="k">class</span> <span class="nc">AngleNbSetWeight</span><span class="p">(</span><span class="n">NbSetWeight</span><span class="p">):</span>
<span class="n">SHORT_NAME</span> <span class="o">=</span> <span class="s1">'AngleWeight'</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aa</span><span class="o">=</span><span class="mf">1.0</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">=</span> <span class="n">aa</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="mf">1.0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aw</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angle_sum</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aw</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angle_sumn</span>
<div class="viewcode-block" id="AngleNbSetWeight.weight"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.weight">[docs]</a> <span class="k">def</span> <span class="nf">weight</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">,</span> <span class="n">structure_environments</span><span class="p">,</span> <span class="n">cn_map</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">additional_info</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">aw</span><span class="p">(</span><span class="n">nb_set</span><span class="o">=</span><span class="n">nb_set</span><span class="p">)</span></div>
<div class="viewcode-block" id="AngleNbSetWeight.angle_sum"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.angle_sum">[docs]</a> <span class="k">def</span> <span class="nf">angle_sum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">nb_set</span><span class="o">.</span><span class="n">angles</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mf">4.0</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span></div>
<div class="viewcode-block" id="AngleNbSetWeight.angle_sumn"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.angle_sumn">[docs]</a> <span class="k">def</span> <span class="nf">angle_sumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">angle_sum</span><span class="p">(</span><span class="n">nb_set</span><span class="o">=</span><span class="n">nb_set</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span><span class="p">)</span></div>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">aa</span>
<span class="k">def</span> <span class="nf">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span>
<div class="viewcode-block" id="AngleNbSetWeight.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s2">"@module"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s2">"@class"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s2">"aa"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span>
<span class="p">}</span></div>
<div class="viewcode-block" id="AngleNbSetWeight.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dd</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">aa</span><span class="o">=</span><span class="n">dd</span><span class="p">[</span><span class="s1">'aa'</span><span class="p">])</span></div></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight">[docs]</a><span class="k">class</span> <span class="nc">NormalizedAngleDistanceNbSetWeight</span><span class="p">(</span><span class="n">NbSetWeight</span><span class="p">):</span>
<span class="n">SHORT_NAME</span> <span class="o">=</span> <span class="s1">'NormAngleDistWeight'</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">average_type</span><span class="p">,</span> <span class="n">aa</span><span class="p">,</span> <span class="n">bb</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">average_type</span> <span class="o">=</span> <span class="n">average_type</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">average_type</span> <span class="o">==</span> <span class="s1">'geometric'</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gweight</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">average_type</span> <span class="o">==</span> <span class="s1">'arithmetic'</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">aweight</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Average type is "</span><span class="si">{}</span><span class="s1">" while it should be '</span>
<span class="s1">'"geometric" or "arithmetic"'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">average_type</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">=</span> <span class="n">aa</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">=</span> <span class="n">bb</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">invdist</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Both exponents are 0.'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">invndist</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ang</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angn</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">anginvdist</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">anginvndist</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angninvdist</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fda</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angninvndist</span>
<span class="k">def</span> <span class="nf">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">average_type</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">average_type</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">aa</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">bb</span>
<span class="k">def</span> <span class="nf">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.as_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.as_dict">[docs]</a> <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">{</span><span class="s2">"@module"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
<span class="s2">"@class"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
<span class="s2">"average_type"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">average_type</span><span class="p">,</span>
<span class="s2">"aa"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa</span><span class="p">,</span>
<span class="s2">"bb"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">bb</span>
<span class="p">}</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.from_dict"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.from_dict">[docs]</a> <span class="nd">@classmethod</span>
<span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dd</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">average_type</span><span class="o">=</span><span class="n">dd</span><span class="p">[</span><span class="s1">'average_type'</span><span class="p">],</span> <span class="n">aa</span><span class="o">=</span><span class="n">dd</span><span class="p">[</span><span class="s1">'aa'</span><span class="p">],</span> <span class="n">bb</span><span class="o">=</span><span class="n">dd</span><span class="p">[</span><span class="s1">'bb'</span><span class="p">])</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.invdist"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.invdist">[docs]</a> <span class="k">def</span> <span class="nf">invdist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span> <span class="o">/</span> <span class="n">dist</span> <span class="k">for</span> <span class="n">dist</span> <span class="ow">in</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_distances</span><span class="p">]</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.invndist"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.invndist">[docs]</a> <span class="k">def</span> <span class="nf">invndist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span> <span class="o">/</span> <span class="n">dist</span><span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="k">for</span> <span class="n">dist</span> <span class="ow">in</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_distances</span><span class="p">]</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.ang"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.ang">[docs]</a> <span class="k">def</span> <span class="nf">ang</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_angles</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.angn"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.angn">[docs]</a> <span class="k">def</span> <span class="nf">angn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="n">ang</span><span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">aa</span> <span class="k">for</span> <span class="n">ang</span> <span class="ow">in</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_angles</span><span class="p">]</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.anginvdist"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.anginvdist">[docs]</a> <span class="k">def</span> <span class="nf">anginvdist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="n">nangles</span> <span class="o">=</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_angles</span>
<span class="k">return</span> <span class="p">[</span><span class="n">nangles</span><span class="p">[</span><span class="n">ii</span><span class="p">]</span> <span class="o">/</span> <span class="n">dist</span> <span class="k">for</span> <span class="n">ii</span><span class="p">,</span> <span class="n">dist</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_distances</span><span class="p">)]</span></div>
<div class="viewcode-block" id="NormalizedAngleDistanceNbSetWeight.anginvndist"><a class="viewcode-back" href="../../../../../pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.NormalizedAngleDistanceNbSetWeight.anginvndist">[docs]</a> <span class="k">def</span> <span class="nf">anginvndist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_set</span><span class="p">):</span>
<span class="n">nangles</span> <span class="o">=</span> <span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_angles</span>
<span class="k">return</span> <span class="p">[</span><span class="n">nangles</span><span class="p">[</span><span class="n">ii</span><span class="p">]</span> <span class="o">/</span> <span class="n">dist</span><span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">bb</span> <span class="k">for</span> <span class="n">ii</span><span class="p">,</span> <span class="n">dist</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nb_set</span><span class="o">.</span><span class="n">normalized_distances</span><span class="p">)]</span></div>