Significant code clean up and documentation adding

arm61 · May 15, 2018 · d28ebd6 · d28ebd6
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diff --git a/README.md b/README.md
diff --git a/README.rst b/README.rst
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+pylj
+====
+
+what is pylj?
+-------------
+
+pylj is an open-source library to facilitate student interaction with classical simulation. It is designed to operate within the Jupyter notebook framework, making it easy to implement in the classroom, or computer lab. Additionally, due to the open-source, and documented, nature of the code it is easy for educators to add unique, custom extensions. 
+
+what does pylj offer?
+---------------------
+
+Currently pylj will perform the simulation of a 2D argon system by molecular dynamics, with both NVE and NVT ensembles available and making use of a Velocity-Verlet integrator. A series of sampling classes exist (found in the sample module), such as the Interactions and Scattering classes. However, it is straightforward to build a custom sampling class either from scratch or using the sampling class building tools. 
+
+example exercises
+-----------------
+
+We are currently in the process of developing example laboratory exercises that make use of pylj. These will include a study of ideal and non-ideal gas conditions and the effect of the phase transitions on the radial distribution function, scattering profiles and mean squared deviation. 
+
+how do i get pylj?
+------------------
+
+If you are interested in using pylj, in any sense, fork the code at http://www.github.com/arm61/pylj or email Andrew (arm61 'at' bath.ac.uk). We are currently investigating the feasibility of hosting a freely available test instance on Amazon Web Services.
+
+requirements
+------------
+To run pylj locally it is necessary to have:
+
+- python 3
+- numpy
+- matplotlib
+- cython
+- C++ complier
+
+todo
+----
+- unit testing 
+- complete example lesssons
+- add Monte-Carlo
+- add energy minimisation
diff --git a/docs/Makefile b/docs/Makefile
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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = pylj
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree
diff --git a/docs/build/doctrees/pylj.doctree b/docs/build/doctrees/pylj.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 3e24725cde270cd0e889a75e43e9746b
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -0,0 +1,104 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Overview: module code &#8212; pylj 0.0.6a documentation</title>
+    <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '0.0.6a',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true,
+        SOURCELINK_SUFFIX: '.txt'
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></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>All modules for which code is available</h1>
+<ul><li><a href="pylj/comp.html">pylj.comp</a></li>
+<li><a href="pylj/examples.html">pylj.examples</a></li>
+<li><a href="pylj/md.html">pylj.md</a></li>
+<li><a href="pylj/sample.html">pylj.sample</a></li>
+<li><a href="pylj/util.html">pylj.util</a></li>
+</ul>
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">pylj</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">pylj</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="../search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2018, Andrew R. McCluskey.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.6.3</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>