Documentation for 0785c90d402cac6bae12045acb679ed4bf588abb

espressomd · May 24, 2024 · e83fab1 · e83fab1
1 parent 4fa92b5
commit e83fab1
Show file tree

Hide file tree

Showing 11,596 changed files with 5,204,465 additions and 0 deletions.
diff --git a/doc/_images/ccmake-example.png b/doc/_images/ccmake-example.png
diff --git a/doc/_images/conical_frustum.png b/doc/_images/conical_frustum.png
diff --git a/doc/_images/constraint-distance.png b/doc/_images/constraint-distance.png
diff --git a/doc/_images/constraint-force.png b/doc/_images/constraint-force.png
diff --git a/doc/_images/constraint-force_only_positive.png b/doc/_images/constraint-force_only_positive.png
diff --git a/doc/_images/correlator_scheme.png b/doc/_images/correlator_scheme.png
diff --git a/doc/_images/diamond.png b/doc/_images/diamond.png
diff --git a/doc/_images/dihedral-angle.pdf b/doc/_images/dihedral-angle.pdf
diff --git a/doc/_images/elc-errordist.pdf b/doc/_images/elc-errordist.pdf
diff --git a/doc/_images/inter_angle.png b/doc/_images/inter_angle.png
diff --git a/doc/_images/oif-arealocal.png b/doc/_images/oif-arealocal.png
diff --git a/doc/_images/oif-bending.png b/doc/_images/oif-bending.png
diff --git a/doc/_images/oif-stretching.png b/doc/_images/oif-stretching.png
diff --git a/doc/_images/oif-volcons.png b/doc/_images/oif-volcons.png
diff --git a/doc/_images/oif.png b/doc/_images/oif.png
diff --git a/doc/_images/oif1.png b/doc/_images/oif1.png
diff --git a/doc/_images/oif2.png b/doc/_images/oif2.png
diff --git a/doc/_images/oif3.png b/doc/_images/oif3.png
diff --git a/doc/_images/oifchannel.png b/doc/_images/oifchannel.png
diff --git a/doc/_images/oifcolored-triangles.png b/doc/_images/oifcolored-triangles.png
diff --git a/doc/_images/oifcylinder.png b/doc/_images/oifcylinder.png
diff --git a/doc/_images/oifrhomboid.png b/doc/_images/oifrhomboid.png
diff --git a/doc/_images/oifstretched-sphere.png b/doc/_images/oifstretched-sphere.png
diff --git a/doc/_images/oifvectordata.png b/doc/_images/oifvectordata.png
diff --git a/doc/_images/shape-conical_frustum.png b/doc/_images/shape-conical_frustum.png
diff --git a/doc/_images/shape-cylinder.png b/doc/_images/shape-cylinder.png
diff --git a/doc/_images/shape-ellipsoid.png b/doc/_images/shape-ellipsoid.png
diff --git a/doc/_images/shape-hollowconicalfrustum_central_angle.png b/doc/_images/shape-hollowconicalfrustum_central_angle.png
diff --git a/doc/_images/shape-simplepore.png b/doc/_images/shape-simplepore.png
diff --git a/doc/_images/shape-slitpore.png b/doc/_images/shape-slitpore.png
diff --git a/doc/_images/shape-sphere.png b/doc/_images/shape-sphere.png
diff --git a/doc/_images/shape-spherocylinder.png b/doc/_images/shape-spherocylinder.png
diff --git a/doc/_images/shape-torus.png b/doc/_images/shape-torus.png
diff --git a/doc/_images/shape-wall.png b/doc/_images/shape-wall.png
diff --git a/doc/_images/slitpore.png b/doc/_images/slitpore.png
diff --git a/doc/_images/vs-code-settings.png b/doc/_images/vs-code-settings.png
diff --git a/doc/_modules/espressomd/accumulators.html b/doc/_modules/espressomd/accumulators.html
diff --git a/doc/_modules/espressomd/analyze.html b/doc/_modules/espressomd/analyze.html
diff --git a/doc/_modules/espressomd/bond_breakage.html b/doc/_modules/espressomd/bond_breakage.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>espressomd.bond_breakage &#8212; ESPResSo 4.3-dev documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=97504538" />
+    <link rel="stylesheet" type="text/css" href="../../_static/blockquotes.css?v=270de11a" />
+    <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=539bf778" />
+    <script src="../../_static/documentation_options.js?v=2fd21666"></script>
+    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../../_static/toggleprompt.js?v=5801b3bb"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" />
+
+  <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+
+
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <h1>Source code for espressomd.bond_breakage</h1><div class="highlight"><pre>
+<span></span><span class="c1">#</span>
+<span class="c1"># Copyright (C) 2022 The ESPResSo project</span>
+<span class="c1">#</span>
+<span class="c1"># This file is part of ESPResSo.</span>
+<span class="c1">#</span>
+<span class="c1"># ESPResSo is free software: you can redistribute it and/or modify</span>
+<span class="c1"># it under the terms of the GNU General Public License as published by</span>
+<span class="c1"># the Free Software Foundation, either version 3 of the License, or</span>
+<span class="c1"># (at your option) any later version.</span>
+<span class="c1">#</span>
+<span class="c1"># ESPResSo is distributed in the hope that it will be useful,</span>
+<span class="c1"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<span class="c1"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<span class="c1"># GNU General Public License for more details.</span>
+<span class="c1">#</span>
+<span class="c1"># You should have received a copy of the GNU General Public License</span>
+<span class="c1"># along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
+<span class="c1">#</span>
+<span class="kn">from</span> <span class="nn">.script_interface</span> <span class="kn">import</span> <span class="n">script_interface_register</span><span class="p">,</span> <span class="n">ScriptObjectMap</span><span class="p">,</span> <span class="n">ScriptInterfaceHelper</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">interactions</span>
+
+
+<div class="viewcode-block" id="BreakageSpec">
+<a class="viewcode-back" href="../../espressomd.html#espressomd.bond_breakage.BreakageSpec">[docs]</a>
+<span class="nd">@script_interface_register</span>
+<span class="k">class</span> <span class="nc">BreakageSpec</span><span class="p">(</span><span class="n">ScriptInterfaceHelper</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Specifications for bond breakage.</span>
+<span class="sd">    See :ref:`Deleting bonds when particles are pulled apart` for more details.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    breakage_length: :obj:`float`</span>
+<span class="sd">        Maximal bond extension until the bond breaks.</span>
+<span class="sd">    action_type: :obj:`str`, {&#39;delete_bond&#39;, &#39;revert_bind_at_point_of_collision&#39;, &#39;none&#39;}</span>
+<span class="sd">        Action triggered when the bond reaches its maximal extension.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">_so_name</span> <span class="o">=</span> <span class="s2">&quot;BondBreakage::BreakageSpec&quot;</span></div>
+
+
+
+<div class="viewcode-block" id="BreakageSpecs">
+<a class="viewcode-back" href="../../espressomd.html#espressomd.bond_breakage.BreakageSpecs">[docs]</a>
+<span class="nd">@script_interface_register</span>
+<span class="k">class</span> <span class="nc">BreakageSpecs</span><span class="p">(</span><span class="n">ScriptObjectMap</span><span class="p">):</span>
+    <span class="n">_so_name</span> <span class="o">=</span> <span class="s2">&quot;BondBreakage::BreakageSpecs&quot;</span>
+
+    <span class="k">def</span> <span class="nf">_get_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Convert a bond object to a bond id.&quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">interactions</span><span class="o">.</span><span class="n">BondedInteraction</span><span class="p">):</span>
+            <span class="n">key</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">_bond_id</span>
+            <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Bond needs to be added to the system first&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">key</span>
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_get_key</span><span class="p">(</span><span class="n">key</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="fm">__setitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__setitem__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_get_key</span><span class="p">(</span><span class="n">key</span><span class="p">),</span> <span class="n">value</span><span class="p">)</span></div>
+
+</pre></div>
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2018-2023, The ESPResSo project.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>