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materialsvirtuallab · May 29, 2022 · 8d6befa · 8d6befa
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diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html
@@ -130,7 +130,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">dists</span> <span class="o">=</span> <span class="n">all_distances</span><span class="p">(</span><span class="n">points</span><span class="p">,</span> <span class="n">centroids</span><span class="p">)</span>
         <span class="n">min_dists</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">dists</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o">==</span> <span class="n">min_dists</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">min_dists</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o">==</span> <span class="n">min_dists</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">min_dists</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="Kmeans.get_centroids"><a class="viewcode-back" href="../../../../../pymatgen.analysis.diffusion.aimd.clustering.html#pymatgen.analysis.diffusion.aimd.clustering.Kmeans.get_centroids">[docs]</a>    <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">get_centroids</span><span class="p">(</span><span class="n">points</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">centroids</span><span class="p">):</span>
@@ -199,7 +199,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">dists</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">get_all_distances</span><span class="p">(</span><span class="n">points</span><span class="p">,</span> <span class="n">centroids</span><span class="p">)</span>
         <span class="n">min_dists</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">dists</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o">==</span> <span class="n">min_dists</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">min_dists</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o">==</span> <span class="n">min_dists</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">])[</span><span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">min_dists</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="KmeansPBC.get_centroids"><a class="viewcode-back" href="../../../../../pymatgen.analysis.diffusion.aimd.clustering.html#pymatgen.analysis.diffusion.aimd.clustering.KmeansPBC.get_centroids">[docs]</a>    <span class="k">def</span> <span class="nf">get_centroids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">points</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">centroids</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
@@ -55,6 +55,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.pathway</h1><div class="hig
 <span class="sd"> Algorithms for diffusion pathway analysis</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="kn">import</span> <span class="nn">itertools</span>
 <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">Counter</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -276,8 +277,9 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.pathway</h1><div class="hig
 <span class="sd">        &quot;&quot;&quot;</span>
 
         <span class="n">count</span> <span class="o">=</span> <span class="mi">1</span>
-        <span class="n">VolinAu</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">volume</span> <span class="o">/</span> <span class="mf">0.5291772083</span> <span class="o">**</span> <span class="mi">3</span>
-        <span class="n">symbols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">symbol_set</span>
+        <span class="n">VolinAu</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">volume</span> <span class="o">/</span> <span class="mf">0.5291772083</span><span class="o">**</span><span class="mi">3</span>
+        <span class="n">syms</span> <span class="o">=</span> <span class="p">[</span><span class="n">site</span><span class="o">.</span><span class="n">specie</span><span class="o">.</span><span class="n">symbol</span> <span class="k">for</span> <span class="n">site</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">]</span>
+        <span class="n">symbols</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">syms</span><span class="p">)]</span>
         <span class="n">natoms</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</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">structure</span><span class="o">.</span><span class="n">composition</span><span class="p">[</span><span class="n">symbol</span><span class="p">]))</span> <span class="k">for</span> <span class="n">symbol</span> <span class="ow">in</span> <span class="n">symbols</span><span class="p">]</span>
         <span class="n">init_fcoords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">)</span>