Skip to content

Commit

Permalink
Documentation for 1f672a00e22a9bc5fec1f7070bd28ff7718a706e
Browse files Browse the repository at this point in the history
  • Loading branch information
espresso-ci committed Oct 29, 2024
1 parent 32d14aa commit 252e242
Show file tree
Hide file tree
Showing 11,932 changed files with 5,552,260 additions and 0 deletions.
The diff you're trying to view is too large. We only load the first 3000 changed files.
Binary file added doc/_images/ccmake-example.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/conical_frustum.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/constraint-distance.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/constraint-force.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/constraint-force_only_positive.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/correlator_scheme.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/diamond.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/dihedral-angle.pdf
Binary file not shown.
Binary file added doc/_images/elc-errordist.pdf
Binary file not shown.
Binary file added doc/_images/inter_angle.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif-arealocal.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif-bending.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif-stretching.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif-volcons.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oif3.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifchannel.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifcolored-triangles.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifcylinder.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifrhomboid.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifstretched-sphere.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/oifvectordata.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/shape-conical_frustum.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/shape-cylinder.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/shape-ellipsoid.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/_images/shape-simplepore.png
Binary file added doc/_images/shape-slitpore.png
Binary file added doc/_images/shape-sphere.png
Binary file added doc/_images/shape-spherocylinder.png
Binary file added doc/_images/shape-torus.png
Binary file added doc/_images/shape-wall.png
Binary file added doc/_images/slitpore.png
Binary file added doc/_images/vs-code-settings.png
452 changes: 452 additions & 0 deletions doc/_modules/espressomd/accumulators.html

Large diffs are not rendered by default.

740 changes: 740 additions & 0 deletions doc/_modules/espressomd/analyze.html

Large diffs are not rendered by default.

133 changes: 133 additions & 0 deletions doc/_modules/espressomd/bond_breakage.html
Original file line number Diff line number Diff line change
@@ -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>
Loading

0 comments on commit 252e242

Please sign in to comment.