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<div class="section" id="function-intercalls">
<span id="sec-intercalls"></span><h1>Function Intercalls<a class="headerlink" href="#function-intercalls" title="Permalink to this headline"></a></h1>
<p>For many of the <span class="sc">Psi4</span> Python functions described above, it makes scientific
sense that they could be called in combination. For instance, one could
optimize all the reagents in a database or compute a
counterpoise-corrected interaction energy with an extrapolated method. The
table below outlines permitted intercalls between functions, showing that
db(opt(cbs(energy()))) is allowed, while db(cp(energy())) is not. This
table is not yet validated for calls with cp().</p>
<table border="1" class="docutils" id="id1">
<span id="table-intercalls"></span><caption><span class="caption-text">Permitted nesting of Psithon functions</span><a class="headerlink" href="#id1" title="Permalink to this table"></a></caption>
<colgroup>
<col width="47%" />
<col width="9%" />
<col width="9%" />
<col width="9%" />
<col width="9%" />
<col width="15%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Caller</th>
<th class="head" colspan="5">Callee</th>
</tr>
<tr class="row-even"><th class="head">&nbsp;</th>
<th class="head">cp</th>
<th class="head">db</th>
<th class="head">opt</th>
<th class="head">cbs</th>
<th class="head">energy</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="cp.html#sec-cp"><span>Counterpoise Correct</span></a></td>
<td>&nbsp;</td>
<td>&#8212;</td>
<td>Y</td>
<td>Y</td>
<td>Y</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="db.html#sec-db"><span>Database</span></a></td>
<td>&#8212;</td>
<td>&nbsp;</td>
<td>Y</td>
<td>Y</td>
<td>Y</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="opt.html#sec-opt"><span>Optimize</span></a></td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&nbsp;</td>
<td>Y</td>
<td>Y</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="cbs.html#sec-cbs"><span>Complete Basis Set</span></a></td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&nbsp;</td>
<td>Y</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="energy.html#sec-energy"><span>Energy</span></a></td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&#8212;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
<ul class="simple">
<li>The command db(opt(cbs(energy()))) is actually expressed as <code class="docutils literal"><span class="pre">db(...,</span>
<span class="pre">db_func=opt,</span> <span class="pre">opt_func=cbs)</span></code>. The perhaps expected final argument of
<code class="docutils literal"><span class="pre">cbs_func=energy</span></code> is not necessary since energy() is always the function
called by default. Also, the outermost internal function call (<code class="docutils literal"><span class="pre">db_func</span></code>
above can be called as just <code class="docutils literal"><span class="pre">func</span></code>. Several examples of intercalls
between Python functions can be found in sample input <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/pywrap_all/input.dat">pywrap_all</a>.</li>
<li>All keyword arguments are passed along to each function traversed in the
Python driver, so there should be no concern for separating them, grouping
them, or designating them for a particular function when undertaking a
nested calculation. Where the same keyword is used by multiple functions,
prefixes are added, e.g., <strong>db_mode</strong> and <strong>opt_mode</strong>.</li>
<li>Function intercalls should not be used in sow/reap mode.</li>
</ul>
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