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materialsvirtuallab · Mar 6, 2021 · bb5497a · bb5497a
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diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>Overview: module code &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
       </ul>
     </div>  
@@ -55,13 +55,15 @@ <h1>All modules for which code is available</h1>
 <li><a href="pymatgen/analysis/diffusion/aimd/tests/test_rdf.html">pymatgen.analysis.diffusion.aimd.tests.test_rdf</a></li>
 <li><a href="pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html">pymatgen.analysis.diffusion.aimd.tests.test_van_hove</a></li>
 <li><a href="pymatgen/analysis/diffusion/aimd/van_hove.html">pymatgen.analysis.diffusion.aimd.van_hove</a></li>
+<li><a href="pymatgen/analysis/diffusion/analyzer.html">pymatgen.analysis.diffusion.analyzer</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/full_path_mapper.html">pymatgen.analysis.diffusion.neb.full_path_mapper</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/io.html">pymatgen.analysis.diffusion.neb.io</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/pathfinder.html">pymatgen.analysis.diffusion.neb.pathfinder</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/periodic_dijkstra.html">pymatgen.analysis.diffusion.neb.periodic_dijkstra</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.html">pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/tests/test_io.html">pymatgen.analysis.diffusion.neb.tests.test_io</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html">pymatgen.analysis.diffusion.neb.tests.test_pathfinder</a></li>
+<li><a href="pymatgen/analysis/diffusion/tests/test_analyzer.html">pymatgen.analysis.diffusion.tests.test_analyzer</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/parse_entries.html">pymatgen.analysis.diffusion.utils.parse_entries</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/supercells.html">pymatgen.analysis.diffusion.utils.supercells</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html">pymatgen.analysis.diffusion.utils.tests.test_parse_entries</a></li>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.clustering &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.clustering &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../" src="../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.clustering</a></li> 
       </ul>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.pathway &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.pathway &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../" src="../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.pathway</a></li> 
       </ul>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.rdf &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.rdf &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../" src="../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.rdf</a></li> 
       </ul>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../../" src="../../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_clustering</a></li> 
       </ul>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_pathway &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_pathway &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../../" src="../../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_pathway</a></li> 
       </ul>
@@ -64,7 +64,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway</h1><div
     <span class="n">ProbabilityDensityAnalysis</span><span class="p">,</span>
     <span class="n">SiteOccupancyAnalyzer</span><span class="p">,</span>
 <span class="p">)</span>
-<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion_analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
+<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion.analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
 <span class="kn">from</span> <span class="nn">pymatgen.core</span> <span class="kn">import</span> <span class="n">Structure</span>
 
 <span class="n">tests_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>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_rdf &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_rdf &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../../" src="../../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_rdf</a></li> 
       </ul>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_van_hove &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_van_hove &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../../" src="../../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_van_hove</a></li> 
       </ul>
@@ -64,7 +64,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.tests.test_van_hove</h1><di
 <span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">deepcopy</span>
 
 <span class="kn">from</span> <span class="nn">monty.serialization</span> <span class="kn">import</span> <span class="n">loadfn</span>
-<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion_analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
+<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion.analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
 <span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion.aimd.van_hove</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">VanHoveAnalysis</span><span class="p">,</span>
     <span class="n">RadialDistributionFunction</span><span class="p">,</span>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.van_hove &#8212; pymatgen-diffusion 2021.3.5 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.van_hove &#8212; pymatgen-diffusion 2021.3.6 documentation</title>
     <link rel="stylesheet" href="../../../../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../../../../../_static/flasky.css" type="text/css" />
     <script id="documentation_options" data-url_root="../../../../../" src="../../../../../_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2021.3.6 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.van_hove</a></li> 
       </ul>
@@ -65,7 +65,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.van_hove</h1><div class="hi
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pds</span>
 <span class="kn">from</span> <span class="nn">scipy.stats</span> <span class="kn">import</span> <span class="n">norm</span>
 <span class="kn">from</span> <span class="nn">pymatgen.core</span> <span class="kn">import</span> <span class="n">Structure</span>
-<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion_analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
+<span class="kn">from</span> <span class="nn">pymatgen.analysis.diffusion.analyzer</span> <span class="kn">import</span> <span class="n">DiffusionAnalyzer</span>
 <span class="kn">from</span> <span class="nn">pymatgen.util.plotting</span> <span class="kn">import</span> <span class="n">pretty_plot</span>
 <span class="kn">from</span> <span class="nn">pymatgen.util.typing</span> <span class="kn">import</span> <span class="n">ArrayLike</span>