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@shyuep
shyuep committed Jun 25, 2024
1 parent 566cad1 commit 9ab5f04
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15 changes: 3 additions & 12 deletions docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html
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Expand Up @@ -97,11 +97,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
<span class="sd"> provide the index for each point, and ss in the final sum squared</span>
<span class="sd"> distances.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">centroids</span> <span class="o">=</span> <span class="p">(</span>
<span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">points</span><span class="p">),</span> <span class="n">k</span><span class="p">))</span>
<span class="k">if</span> <span class="n">initial_centroids</span> <span class="ow">is</span> <span class="kc">None</span>
<span class="k">else</span> <span class="n">initial_centroids</span>
<span class="p">)</span>
<span class="n">centroids</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="n">random</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">points</span><span class="p">),</span> <span class="n">k</span><span class="p">))</span> <span class="k">if</span> <span class="n">initial_centroids</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">initial_centroids</span>

<span class="c1"># Initialize book keeping vars.</span>
<span class="n">iterations</span> <span class="o">=</span> <span class="mi">0</span>
Expand Down Expand Up @@ -243,9 +239,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">n</span><span class="p">)</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">ind</span><span class="p">:</span>
<span class="n">dist</span><span class="p">,</span> <span class="n">image</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_distance_and_image</span><span class="p">(</span>
<span class="n">centroids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
<span class="p">)</span>
<span class="n">dist</span><span class="p">,</span> <span class="n">image</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_distance_and_image</span><span class="p">(</span><span class="n">centroids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">])</span>
<span class="n">c</span> <span class="o">+=</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o">+</span> <span class="n">image</span>
<span class="n">c</span> <span class="o">/=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mod</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
Expand All @@ -272,10 +266,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
<span class="k">return</span> <span class="kc">True</span>
<span class="k">if</span> <span class="n">old_centroids</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>
<span class="k">return</span> <span class="nb">all</span><span class="p">(</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="k">for</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">old_centroids</span><span class="p">,</span> <span class="n">centroids</span><span class="p">)</span>
<span class="p">)</span></div>
<span class="k">return</span> <span class="nb">all</span><span class="p">(</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="k">for</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">old_centroids</span><span class="p">,</span> <span class="n">centroids</span><span class="p">))</span></div>
</div>


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19 changes: 9 additions & 10 deletions docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
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Expand Up @@ -279,11 +279,11 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.rdf</h1><div class="highlig

<span class="n">label</span> <span class="o">=</span> <span class="n">symbol_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">symbol_list</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s2">&quot;-&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">symbol_list</span><span class="p">)</span>

<span class="n">plt</span> <span class="o">=</span> <span class="n">pretty_plot</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mi">8</span><span class="p">)</span>
<span class="n">plt</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">interval</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdf</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">4.0</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">pretty_plot</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mi">8</span><span class="p">)</span>
<span class="n">ax</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">interval</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdf</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">4.0</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>

<span class="k">if</span> <span class="n">loc_peak</span><span class="p">:</span>
<span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span>
<span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peak_r</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peak_rdf</span><span class="p">,</span>
<span class="n">marker</span><span class="o">=</span><span class="s2">&quot;P&quot;</span><span class="p">,</span>
Expand All @@ -295,14 +295,13 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.rdf</h1><div class="highlig
<span class="n">label</span><span class="o">=</span><span class="s2">&quot;Peaks&quot;</span><span class="p">,</span>
<span class="p">)</span>

<span class="n">plt</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;$r$ ($</span><span class="se">\\</span><span class="s2">rm</span><span class="se">\\</span><span class="s2">AA$)&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;$g(r)$&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper right&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="mi">36</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xlim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ylim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;$r$ ($</span><span class="se">\\</span><span class="s2">rm</span><span class="se">\\</span><span class="s2">AA$)&quot;</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;$g(r)$&quot;</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper right&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="mi">36</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xlim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ylim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>

<span class="k">return</span> <span class="n">plt</span></div>
<span class="k">return</span> <span class="n">ax</span></div>


<div class="viewcode-block" id="RadialDistributionFunction.export_rdf">
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4 changes: 1 addition & 3 deletions docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
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Expand Up @@ -103,9 +103,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.tests.test_clustering</h1><
<span class="n">initial</span> <span class="o">=</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="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.25</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.5</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="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">initial</span><span class="p">:</span>
<span class="k">for</span> <span class="n">_i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
<span class="n">pts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
<span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">c</span><span class="p">)</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">randn</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.01</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">randint</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
<span class="p">)</span>
<span class="n">pts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">c</span><span class="p">)</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">randn</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.01</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">randint</span><span class="p">(</span><span class="mi">3</span><span class="p">))</span>
<span class="n">pts</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="n">pts</span><span class="p">)</span>
<span class="n">k</span> <span class="o">=</span> <span class="n">KmeansPBC</span><span class="p">(</span><span class="n">lattice</span><span class="p">)</span>
<span class="n">centroids</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span> <span class="n">ss</span> <span class="o">=</span> <span class="n">k</span><span class="o">.</span><span class="n">cluster</span><span class="p">(</span><span class="n">pts</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
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