Add 4.2.2 user guide and tutorials

espressomd · May 22, 2024 · da14802 · da14802
1 parent e27dca2
commit da14802
Show file tree

Hide file tree

Showing 174 changed files with 188,455 additions and 0 deletions.
diff --git a/doc4.2.2/_images/ccmake-example.png b/doc4.2.2/_images/ccmake-example.png
diff --git a/doc4.2.2/_images/conical_frustum.png b/doc4.2.2/_images/conical_frustum.png
diff --git a/doc4.2.2/_images/constraint-distance.png b/doc4.2.2/_images/constraint-distance.png
diff --git a/doc4.2.2/_images/constraint-force.png b/doc4.2.2/_images/constraint-force.png
diff --git a/doc4.2.2/_images/constraint-force_only_positive.png b/doc4.2.2/_images/constraint-force_only_positive.png
diff --git a/doc4.2.2/_images/correlator_scheme.png b/doc4.2.2/_images/correlator_scheme.png
diff --git a/doc4.2.2/_images/diamond.png b/doc4.2.2/_images/diamond.png
diff --git a/doc4.2.2/_images/dihedral-angle.pdf b/doc4.2.2/_images/dihedral-angle.pdf
diff --git a/doc4.2.2/_images/elc-errordist.pdf b/doc4.2.2/_images/elc-errordist.pdf
diff --git a/doc4.2.2/_images/inter_angle.png b/doc4.2.2/_images/inter_angle.png
diff --git a/doc4.2.2/_images/oif-arealocal.png b/doc4.2.2/_images/oif-arealocal.png
diff --git a/doc4.2.2/_images/oif-bending.png b/doc4.2.2/_images/oif-bending.png
diff --git a/doc4.2.2/_images/oif-stretching.png b/doc4.2.2/_images/oif-stretching.png
diff --git a/doc4.2.2/_images/oif-volcons.png b/doc4.2.2/_images/oif-volcons.png
diff --git a/doc4.2.2/_images/oif.png b/doc4.2.2/_images/oif.png
diff --git a/doc4.2.2/_images/oif1.png b/doc4.2.2/_images/oif1.png
diff --git a/doc4.2.2/_images/oif2.png b/doc4.2.2/_images/oif2.png
diff --git a/doc4.2.2/_images/oif3.png b/doc4.2.2/_images/oif3.png
diff --git a/doc4.2.2/_images/oifchannel.png b/doc4.2.2/_images/oifchannel.png
diff --git a/doc4.2.2/_images/oifcolored-triangles.png b/doc4.2.2/_images/oifcolored-triangles.png
diff --git a/doc4.2.2/_images/oifcylinder.png b/doc4.2.2/_images/oifcylinder.png
diff --git a/doc4.2.2/_images/oifrhomboid.png b/doc4.2.2/_images/oifrhomboid.png
diff --git a/doc4.2.2/_images/oifstretched-sphere.png b/doc4.2.2/_images/oifstretched-sphere.png
diff --git a/doc4.2.2/_images/oifvectordata.png b/doc4.2.2/_images/oifvectordata.png
diff --git a/doc4.2.2/_images/shape-conical_frustum.png b/doc4.2.2/_images/shape-conical_frustum.png
diff --git a/doc4.2.2/_images/shape-cylinder.png b/doc4.2.2/_images/shape-cylinder.png
diff --git a/doc4.2.2/_images/shape-ellipsoid.png b/doc4.2.2/_images/shape-ellipsoid.png
diff --git a/doc4.2.2/_images/shape-hollowconicalfrustum_central_angle.png b/doc4.2.2/_images/shape-hollowconicalfrustum_central_angle.png
diff --git a/doc4.2.2/_images/shape-simplepore.png b/doc4.2.2/_images/shape-simplepore.png
diff --git a/doc4.2.2/_images/shape-slitpore.png b/doc4.2.2/_images/shape-slitpore.png
diff --git a/doc4.2.2/_images/shape-sphere.png b/doc4.2.2/_images/shape-sphere.png
diff --git a/doc4.2.2/_images/shape-spherocylinder.png b/doc4.2.2/_images/shape-spherocylinder.png
diff --git a/doc4.2.2/_images/shape-torus.png b/doc4.2.2/_images/shape-torus.png
diff --git a/doc4.2.2/_images/shape-wall.png b/doc4.2.2/_images/shape-wall.png
diff --git a/doc4.2.2/_images/slitpore.png b/doc4.2.2/_images/slitpore.png
diff --git a/doc4.2.2/_images/vs-code-settings.png b/doc4.2.2/_images/vs-code-settings.png
diff --git a/doc4.2.2/_modules/espressomd.html b/doc4.2.2/_modules/espressomd.html
@@ -0,0 +1,149 @@
+
+<!DOCTYPE html>
+
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>espressomd &#8212; ESPResSo 4.2.2 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/blockquotes.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <script src="../_static/toggleprompt.js"></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</h1><div class="highlight"><pre>
+<span></span><span class="c1"># Copyright (C) 2016-2022 The ESPResSo project</span>
+<span class="c1"># Copyright (C) 2014 Olaf Lenz</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="c1"># Initialize MPI, start the main loop on the worker nodes</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="k">import</span> <span class="n">_init</span>
+
+<span class="kn">from</span> <span class="nn">.system</span> <span class="k">import</span> <span class="n">System</span>
+<span class="kn">from</span> <span class="nn">.code_info</span> <span class="k">import</span> <span class="n">features</span><span class="p">,</span> <span class="n">all_features</span>
+<span class="kn">from</span> <span class="nn">.cuda_init</span> <span class="k">import</span> <span class="n">gpu_available</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="k">import</span> <span class="n">code_info</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="k">import</span> <span class="n">utils</span>
+
+
+<div class="viewcode-block" id="FeaturesError"><a class="viewcode-back" href="../espressomd.html#espressomd.FeaturesError">[docs]</a><span class="k">class</span> <span class="nc">FeaturesError</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+
+    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">missing_features</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;Missing features {&#39;, &#39;.join(missing_features)}&quot;</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="has_features"><a class="viewcode-back" href="../espressomd.html#espressomd.has_features">[docs]</a><span class="k">def</span> <span class="nf">has_features</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Check whether a list of features is a subset of the compiled-in features.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">lvl</span> <span class="o">=</span> <span class="n">utils</span><span class="o">.</span><span class="n">nesting_level</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+    <span class="k">assert</span> <span class="n">lvl</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="s2">&quot;has_features() takes strings as argument&quot;</span>
+    <span class="k">if</span> <span class="n">lvl</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+        <span class="n">check_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">check_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">check_set</span> <span class="o">&lt;=</span> <span class="n">code_info</span><span class="o">.</span><span class="n">all_features</span><span class="p">():</span>
+        <span class="n">unknown_features</span> <span class="o">=</span> <span class="n">check_set</span> <span class="o">-</span> <span class="n">code_info</span><span class="o">.</span><span class="n">all_features</span><span class="p">()</span>
+        <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;unknown features {&#39;,&#39;.join(unknown_features)}&quot;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">check_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">(</span><span class="n">code_info</span><span class="o">.</span><span class="n">features</span><span class="p">())</span></div>
+
+
+<div class="viewcode-block" id="missing_features"><a class="viewcode-back" href="../espressomd.html#espressomd.missing_features">[docs]</a><span class="k">def</span> <span class="nf">missing_features</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Return a list of the missing features in the arguments.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">lvl</span> <span class="o">=</span> <span class="n">utils</span><span class="o">.</span><span class="n">nesting_level</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+    <span class="k">assert</span> <span class="n">lvl</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="s2">&quot;missing_features() takes strings as argument&quot;</span>
+    <span class="k">if</span> <span class="n">lvl</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+        <span class="n">features</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">features</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">features</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">code_info</span><span class="o">.</span><span class="n">features</span><span class="p">()))</span></div>
+
+
+<div class="viewcode-block" id="assert_features"><a class="viewcode-back" href="../espressomd.html#espressomd.assert_features">[docs]</a><span class="k">def</span> <span class="nf">assert_features</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Raise an exception when a list of features is not a subset of the</span>
+<span class="sd">    compiled-in features.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">has_features</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+        <span class="k">raise</span> <span class="n">FeaturesError</span><span class="p">(</span><span class="n">missing_features</span><span class="p">(</span><span class="o">*</span><span class="n">args</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>$('#searchbox').show(0);</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 4.2.0</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>