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46 <section id="introduction">
47 <h1>Introduction<a class="headerlink" href="#introduction" title="Link to this heading">¶</a></h1>
48 <p><code class="docutils literal notranslate"><span class="pre">sphere</span></code> is used for three-dimensional DEM particle simulations with optional
49 two-way coupled fluid flow. Simulation setup and post-processing are usually
50 performed through the bundled Python API, while the compiled <code class="docutils literal notranslate"><span class="pre">sphere</span></code> binary
51 executes the time integration.</p>
52 <p>The source code can be built for either a CUDA GPU or an OpenMP CPU. See
53 <a class="reference internal" href="quickstart.html"><span class="doc">Quick start</span></a> for current build requirements and commands.</p>
54 <p>The ultimate aim of the <code class="docutils literal notranslate"><span class="pre">sphere</span></code> software is to simulate soft-bedded subglacial
55 conditions, while retaining the flexibility to perform simulations of granular
56 material in other environments.</p>
57 <p>The purpose of this documentation is to provide the user with a walk-through of
58 the workflow, data-analysis and visualization methods of <code class="docutils literal notranslate"><span class="pre">sphere</span></code>. In
59 addition, the <code class="docutils literal notranslate"><span class="pre">sphere</span></code> internals are exposed to provide a way to understand the
60 numerical routines used by the discrete element method implementation.</p>
61 <div class="admonition note">
62 <p class="admonition-title">Note</p>
63 <p>Command examples in this document starting with the symbol <code class="docutils literal notranslate"><span class="pre">$</span></code> are
64 meant to be executed in the shell of the operating system, and <code class="docutils literal notranslate"><span class="pre">>>></span></code> means
65 execution in Python. <a class="reference external" href="http://ipython.org">IPython</a> is an excellent,
66 interactive Python shell.</p>
67 </div>
68 <p>All numerical values in this document, the source code, and the configuration
69 files are typeset with strict respect to the SI unit system.</p>
70 <section id="workflow">
71 <h2>Workflow<a class="headerlink" href="#workflow" title="Link to this heading">¶</a></h2>
72 <p>A typical simulation workflow is:</p>
73 <ol class="arabic simple">
74 <li><p>Create a <code class="docutils literal notranslate"><span class="pre">sphere.sim</span></code> object in Python and write an input binary.</p></li>
75 <li><p>Run <code class="docutils literal notranslate"><span class="pre">./sphere</span></code> on the input file, optionally with <code class="docutils literal notranslate"><span class="pre">--fluid</span></code>.</p></li>
76 <li><p>Read output binaries in Python for analysis, visualization, or export.</p></li>
77 </ol>
78 </section>
79 <section id="updating-sphere">
80 <h2>Updating sphere<a class="headerlink" href="#updating-sphere" title="Link to this heading">¶</a></h2>
81 <p>To update your local version, type the following commands in the <code class="docutils literal notranslate"><span class="pre">sphere</span></code> root
82 directory:</p>
83 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">pull</span>
84 <span class="n">cmake</span> <span class="o">-</span><span class="n">DSPHERE_GPU</span><span class="o">=</span><span class="n">OFF</span> <span class="o">.</span>
85 <span class="n">make</span>
86 </pre></div>
87 </div>
88 <p>Use the CUDA default build by omitting <code class="docutils literal notranslate"><span class="pre">-DSPHERE_GPU=OFF</span></code> when CUDA is the
89 intended backend.</p>
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103 <li><a class="reference internal" href="#">Introduction</a><ul>
104 <li><a class="reference internal" href="#workflow">Workflow</a></li>
105 <li><a class="reference internal" href="#updating-sphere">Updating sphere</a></li>
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