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‎docs/_modules/index.html‎

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<!DOCTYPE html>
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<html lang="en" data-content_root="../">
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Overview: module code &#8212; pymatgen-diffusion 2023.8.15 documentation</title>
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<title>Overview: module code &#8212; pymatgen-diffusion 2024.6.10 documentation</title>
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<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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<link rel="stylesheet" type="text/css" href="../_static/flasky.css?v=8156beb0" />
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<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=7d1ab505"></script>
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<script src="../_static/doctools.js?v=888ff710"></script>
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<script src="../_static/sphinx_highlight.js?v=4825356b"></script>
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<script src="../_static/documentation_options.js?v=608d49bb"></script>
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<script src="../_static/doctools.js?v=9a2dae69"></script>
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<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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<link rel="index" title="Index" href="../genindex.html" />
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<link rel="search" title="Search" href="../search.html" />
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@@ -34,7 +34,7 @@ <h3>Navigation</h3>
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<li class="right" >
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<a href="../py-modindex.html" title="Python Module Index"
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>modules</a> |</li>
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<li class="nav-item nav-item-0"><a href="../index.html">pymatgen-diffusion 2023.8.15 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="../index.html">pymatgen-diffusion 2024.6.10 documentation</a> &#187;</li>
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<li class="nav-item nav-item-this"><a href="">Overview: module code</a></li>
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</ul>
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</div>
@@ -68,7 +68,6 @@ <h1>All modules for which code is available</h1>
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<li><a href="pymatgen/analysis/diffusion/utils/parse_entries.html">pymatgen.analysis.diffusion.utils.parse_entries</a></li>
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<li><a href="pymatgen/analysis/diffusion/utils/supercells.html">pymatgen.analysis.diffusion.utils.supercells</a></li>
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<li><a href="pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.html">pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc</a></li>
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<li><a href="pymatgen/analysis/diffusion/utils/tests/test_maggma.html">pymatgen.analysis.diffusion.utils.tests.test_maggma</a></li>
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<li><a href="pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html">pymatgen.analysis.diffusion.utils.tests.test_parse_entries</a></li>
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</ul>
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@@ -82,15 +81,15 @@ <h1>All modules for which code is available</h1>
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<li><a href="../index.html">Documentation overview</a><ul>
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</ul></li>
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</ul>
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<div id="searchbox" style="display: none" role="search">
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<search id="searchbox" style="display: none" role="search">
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<input type="submit" value="Go" />
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</search>
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<script>document.getElementById('searchbox').style.display = "block"</script>
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‎docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html‎

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‎docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html‎

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‎docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html‎

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‎docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html‎

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<!DOCTYPE html>
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<html lang="en" data-content_root="../../../../../../">
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2023.8.15 documentation</title>
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<title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2024.6.10 documentation</title>
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<link rel="stylesheet" type="text/css" href="../../../../../../_static/pygments.css?v=fa44fd50" />
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<link rel="stylesheet" type="text/css" href="../../../../../../_static/flasky.css?v=8156beb0" />
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<script data-url_root="../../../../../../" id="documentation_options" src="../../../../../../_static/documentation_options.js?v=7d1ab505"></script>
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<script src="../../../../../../_static/doctools.js?v=888ff710"></script>
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<script src="../../../../../../_static/sphinx_highlight.js?v=4825356b"></script>
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<script src="../../../../../../_static/documentation_options.js?v=608d49bb"></script>
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<script src="../../../../../../_static/doctools.js?v=9a2dae69"></script>
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<script src="../../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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<link rel="index" title="Index" href="../../../../../../genindex.html" />
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<link rel="search" title="Search" href="../../../../../../search.html" />
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<li class="right" >
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<a href="../../../../../../py-modindex.html" title="Python Module Index"
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>modules</a> |</li>
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<li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2023.8.15 documentation</a> &#187;</li>
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<li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2024.6.10 documentation</a> &#187;</li>
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<li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
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<span class="kn">from</span> <span class="nn">pymatgen.util.coord</span> <span class="kn">import</span> <span class="n">pbc_diff</span>
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<div class="viewcode-block" id="KmeansTest"><a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansTest">[docs]</a><span class="k">class</span> <span class="nc">KmeansTest</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansTest.test_cluster"><a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansTest.test_cluster">[docs]</a> <span class="k">def</span> <span class="nf">test_cluster</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansTest">
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<a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansTest">[docs]</a>
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<span class="k">class</span> <span class="nc">KmeansTest</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansTest.test_cluster">
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<a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansTest.test_cluster">[docs]</a>
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<span class="k">def</span> <span class="nf">test_cluster</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">uniform</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
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<span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
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<span class="n">d2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">uniform</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span> <span class="o">+</span> <span class="p">([</span><span class="mi">5</span><span class="p">]</span> <span class="o">*</span> <span class="mi">5</span><span class="p">)</span>
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<span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">a</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansPBCTest"><a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansPBCTest">[docs]</a><span class="k">class</span> <span class="nc">KmeansPBCTest</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansPBCTest.test_cluster"><a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansPBCTest.test_cluster">[docs]</a> <span class="k">def</span> <span class="nf">test_cluster</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansPBCTest">
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<a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansPBCTest">[docs]</a>
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<span class="k">class</span> <span class="nc">KmeansPBCTest</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
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<div class="viewcode-block" id="KmeansPBCTest.test_cluster">
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<a class="viewcode-back" href="../../../../../../pymatgen.analysis.diffusion.aimd.tests.test_clustering.html#pymatgen.analysis.diffusion.aimd.tests.test_clustering.KmeansPBCTest.test_cluster">[docs]</a>
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<span class="k">def</span> <span class="nf">test_cluster</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
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<span class="n">lattice</span> <span class="o">=</span> <span class="n">Lattice</span><span class="o">.</span><span class="n">cubic</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
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<span class="n">pts</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">pbc_diff</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">),</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">atol</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
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<div id="searchbox" style="display: none" role="search">
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<search id="searchbox" style="display: none" role="search">
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