deploy: 500013b

genindex.html

@@ -342,8 +342,6 @@ <h2 id="B">B</h2>
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="usage.html#atomaton.analyze.calculate_distance">calculate_distance() (in module atomaton.analyze)</a>
-</li>
       <li><a href="visualize.html#atomaton.visualize.convert_images_to_gif">convert_images_to_gif() (in module atomaton.visualize)</a>
 </li>
   </ul></td>

index.html

@@ -308,7 +308,6 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 <li class="toctree-l2"><a class="reference internal" href="usage.html#installation">Installation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="usage.html#module-atomaton.analyze">Analyzer: <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomaton.analyze</span></code></a><ul>
 <li class="toctree-l3"><a class="reference internal" href="usage.html#atomaton.analyze.bin_data"><code class="docutils literal notranslate"><span class="pre">bin_data()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="usage.html#atomaton.analyze.calculate_distance"><code class="docutils literal notranslate"><span class="pre">calculate_distance()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="usage.html#atomaton.analyze.create_extended_cell"><code class="docutils literal notranslate"><span class="pre">create_extended_cell()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="usage.html#atomaton.analyze.create_extended_cell_minimal"><code class="docutils literal notranslate"><span class="pre">create_extended_cell_minimal()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="usage.html#atomaton.analyze.get_angle_properties"><code class="docutils literal notranslate"><span class="pre">get_angle_properties()</span></code></a></li>

usage.html

@@ -336,19 +336,6 @@ <h1>Usage<a class="headerlink" href="#usage" title="Link to this heading">#</a><
 <span class="sig-prename descclassname"><span class="pre">atomaton.analyze.</span></span><span class="sig-name descname"><span class="pre">bin_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">std_dev_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_bins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.analyze.bin_data" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
-<dl class="py function">
-<dt class="sig sig-object py" id="atomaton.analyze.calculate_distance">
-<span class="sig-prename descclassname"><span class="pre">atomaton.analyze.</span></span><span class="sig-name descname"><span class="pre">calculate_distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.analyze.calculate_distance" title="Link to this definition">#</a></dt>
-<dd><p>Function which calculates the distance between two positions in N-dimensional space.</p>
-<dl class="simple">
-<dt>Args:</dt><dd><p>p1 (list[float…]): position in N-dimensional space
-p2 (list[float…]): position in N-dimensional space</p>
-</dd>
-<dt>Returns:</dt><dd><p>float: distance between two positions</p>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py function">
 <dt class="sig sig-object py" id="atomaton.analyze.create_extended_cell">
 <span class="sig-prename descclassname"><span class="pre">atomaton.analyze.</span></span><span class="sig-name descname"><span class="pre">create_extended_cell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.analyze.create_extended_cell" title="Link to this definition">#</a></dt>
@@ -507,7 +494,6 @@ <h1>Usage<a class="headerlink" href="#usage" title="Link to this heading">#</a><
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#installation">Installation</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#module-atomaton.analyze">Analyzer: <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomaton.analyze</span></code></a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#atomaton.analyze.bin_data"><code class="docutils literal notranslate"><span class="pre">bin_data()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#atomaton.analyze.calculate_distance"><code class="docutils literal notranslate"><span class="pre">calculate_distance()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#atomaton.analyze.create_extended_cell"><code class="docutils literal notranslate"><span class="pre">create_extended_cell()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#atomaton.analyze.create_extended_cell_minimal"><code class="docutils literal notranslate"><span class="pre">create_extended_cell_minimal()</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#atomaton.analyze.get_angle_properties"><code class="docutils literal notranslate"><span class="pre">get_angle_properties()</span></code></a></li>

visualize.html

@@ -335,12 +335,12 @@ <h1>View structures<a class="headerlink" href="#view-structures" title="Link to
 
 <dl class="py function">
 <dt class="sig sig-object py" id="atomaton.visualize.draw_atoms">
-<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">draw_atoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_config_new</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.125</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.draw_atoms" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">draw_atoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.125</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.draw_atoms" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="atomaton.visualize.draw_bonds">
-<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">draw_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_config_new</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_bonds_across_boundary</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0.4,</span> <span class="pre">0.4,</span> <span class="pre">0.4)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.draw_bonds" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">draw_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_bonds_across_boundary</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0.4,</span> <span class="pre">0.4,</span> <span class="pre">0.4)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.draw_bonds" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
@@ -350,7 +350,7 @@ <h1>View structures<a class="headerlink" href="#view-structures" title="Link to
 
 <dl class="py function">
 <dt class="sig sig-object py" id="atomaton.visualize.view_structure">
-<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">view_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds_across_boundary</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unit_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interactive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">figure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">objects</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">camera</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_energies</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_cmap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Reds'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_bins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.view_structure" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">atomaton.visualize.</span></span><span class="sig-name descname"><span class="pre">view_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds_across_boundary</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unit_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interactive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">figure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">objects</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">camera</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_energies</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_cmap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Reds'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_bins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opacity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#atomaton.visualize.view_structure" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </section>