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<section id="votca-internal-contributor-language-guide">
<h1>VOTCA Internal Contributor Language Guide<a class="headerlink" href="#votca-internal-contributor-language-guide" title="Link to this heading">¶</a></h1>
<p>This language guide has been created to establish rules to keep VOTCA’s
code consistent between repositories. In the past, there has been
difficulty in translating functionality between repositories and within
the same repositories because different properties have been used to
describe the same object attribute. For general programming guidelines
look at the <a class="reference internal" href="DEVELOPERS_GUIDE.html"><span class="doc">Developers Guide</span></a></p>
<section id="types-and-ids">
<h2>Types and Ids<a class="headerlink" href="#types-and-ids" title="Link to this heading">¶</a></h2>
<p>As an example, consider the csg bead object which had at one time
contained the name, type and id attribute. The name of a bead is ill
defined and could be unique but was not guaranteed to be so.</p>
<p>If a bead were named C5 it was not clear if this was an arbitrary bead
name, or if it was the 5th carbon atom in the system. In any case the
name attribute is not needed because if a unique id is needed the id of
the bead could be used whereas if the type of the bead was needed the
type attribute could be used. As such, the name method and attribute has
been removed from the object.</p>
<p>As a general rule, objects should not have a name method or attribute
rather, any attribute that is not unique to an object should be
indicated with a type method and attribute.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">std</span><span class="p">::</span><span class="n">string</span> <span class="n">getBeadType</span><span class="p">();</span>
<span class="n">std</span><span class="p">::</span><span class="n">string</span> <span class="n">getResidueType</span><span class="p">();</span>
</pre></div>
</div>
<p>To indicate a unique attribute an id should be used.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">getBeadId</span><span class="p">();</span>
<span class="nb">int</span> <span class="n">getMoleculeId</span><span class="p">();</span>
</pre></div>
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</section>
<section id="units-in-votca">
<h2>Units in VOTCA<a class="headerlink" href="#units-in-votca" title="Link to this heading">¶</a></h2>
<p>VOTCA tried as much as possible to standardize units across both CSG and
XTP. Externally, we parse in the units of the respective file format,
e.g. <code class="docutils literal notranslate"><span class="pre">.xyz</span></code> <code class="docutils literal notranslate"><span class="pre">Angstrom</span></code>, <code class="docutils literal notranslate"><span class="pre">.gro</span></code> <code class="docutils literal notranslate"><span class="pre">nm</span></code>. Internally, we convert all
parsed units to:</p>
<ul class="simple">
<li><p>CSG: length <code class="docutils literal notranslate"><span class="pre">nm</span></code>, energy <code class="docutils literal notranslate"><span class="pre">kJ/mol</span></code> and time <code class="docutils literal notranslate"><span class="pre">ps</span></code></p></li>
<li><p>XTP: length <code class="docutils literal notranslate"><span class="pre">bohr</span></code>, energy <code class="docutils literal notranslate"><span class="pre">Hartree</span></code> and time <code class="docutils literal notranslate"><span class="pre">ps</span></code></p></li>
</ul>
</section>
<section id="indexing-in-votca">
<h2>Indexing in VOTCA<a class="headerlink" href="#indexing-in-votca" title="Link to this heading">¶</a></h2>
<p>All indices in VOTCA start at <code class="docutils literal notranslate"><span class="pre">0</span></code>. This is useful, because C++ arrays
start at index 0.</p>
<p>Apart from special cases all indices and integers in VOTCA should be
<code class="docutils literal notranslate"><span class="pre">votca::Index</span></code> which is a typedef for <code class="docutils literal notranslate"><span class="pre">long</span> <span class="pre">int</span></code>. <code class="docutils literal notranslate"><span class="pre">.size()</span></code>
methods of std::containers return an <code class="docutils literal notranslate"><span class="pre">unsigned</span> <span class="pre">long</span> <span class="pre">int</span></code> and should be
cast to <code class="docutils literal notranslate"><span class="pre">votca::Index</span></code>. i.e: <code class="docutils literal notranslate"><span class="pre">votca::Index(vector.size())</span></code></p>
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