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<div class="section" id="generation-of-cube-files">
<span id="sec-cubeprop"></span><span id="index-0"></span><h1>Generation of cube files<a class="headerlink" href="#generation-of-cube-files" title="Permalink to this headline">¶</a></h1>
<p><em>Code author: Robert M. Parrish and Francesco A. Evangelista</em></p>
<p><em>Section author: Francesco A. Evangelista</em></p>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p><span class="sc">Psi4</span> has the ability to export cube files that store information about
basis functions, molecular orbitals, the electron density, and
the electrostatic potential (ESP). Cube files store the value of a scalar
quantity on a regular Cartesian grid, and can be visualized with several
visualization programs, some of which are free, like VMD
(<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/">http://www.ks.uiuc.edu/Research/vmd/</a>).</p>
<p>An example utilization of the code is:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule h2o {
0 1
O
H 1 1.0
H 1 1.0 2 104.5
}
set basis cc-pvdz
set scf_type df
set freeze_core True
set cubeprop_tasks ['orbitals']
set cubeprop_orbitals [5,6,-5,-6]
energy('scf')
cubeprop()
</pre></div>
</div>
<p>In this example, the <code class="docutils literal"><span class="pre">cubeprop()</span></code> call after the <code class="docutils literal"><span class="pre">energy('scf')</span></code> command
executes the cubeprop code. The array <code class="docutils literal"><span class="pre">CUBEPROP_TASKS</span></code> specifies which
tasks should be executed. In this case the task <code class="docutils literal"><span class="pre">'orbitals'</span></code> generates cube
files for orbitals. The <code class="docutils literal"><span class="pre">CUBEPROP_ORBITALS</span></code> option specifies that cube files
should be generated only for alpha orbitals 5 (HOMO) and 6 (LUMO) and
beta orbitals 5 (indicated as -5) and 6.
If the option <code class="docutils literal"><span class="pre">CUBEPROP_ORBITALS</span></code> is not provided, then cube files are
generated for all orbitals.
After running, the above input will generate four files: <cite>Psi_a_5.cube</cite>,
<cite>Psi_a_6.cube</cite>, <cite>Psi_b_5.cube</cite>, and <cite>Psi_b_6.cube</cite>.</p>
<div class="admonition tip">
<p class="first admonition-title">Tip</p>
<p class="last">If your cube plots are too coarse, try to decrease the grid spacing via
the option <code class="docutils literal"><span class="pre">CUBIC_GRID_SPACING</span></code>. If the edges of your plot are cut then
increase the size of the grid via the option <code class="docutils literal"><span class="pre">CUBIC_GRID_OVERAGE</span></code>.</p>
</div>
</div>
<div class="section" id="cubeprop-tasks">
<h2>Cubeprop Tasks<a class="headerlink" href="#cubeprop-tasks" title="Permalink to this headline">¶</a></h2>
<p>The cubeprop utility can be probided a list of tasks to perform.
Tasks are specified by the <code class="docutils literal"><span class="pre">CUBEPROP_TASKS</span></code> option, which is a list of strings
that identify the tasks. Several tasks are available. These include:</p>
<dl class="docutils">
<dt>ORBITALS [Default if <code class="docutils literal"><span class="pre">CUBEPROP_TASKS</span></code> is not specified]</dt>
<dd>Produces cube representations of the molecular orbitals
<img class="math" src="_images/math/c0bf591fea1884e206e976c69ad1d1fb419a33b7.png" alt="\psi_q(\mathbf{r})" style="vertical-align: -6px"/>. Orbitals are sorted according to increasing
orbital energy ignoring symmetry.</dd>
<dt>DENSITY</dt>
<dd>This task can be used to obtain the alpha and beta electron densities,
<img class="math" src="_images/math/13de9c06afbde7dfe8b43047ababf4ce2282ac92.png" alt="\rho_\alpha(\mathbf{r})" style="vertical-align: -4px"/> and <img class="math" src="_images/math/0ad5bc2babc211ea005693f7c12585657311e67f.png" alt="\rho_\beta(\mathbf{r})" style="vertical-align: -6px"/>, together
with the total density
<img class="math" src="_images/math/4d913a98b3a032036eea4e5f74cfa9a1e1feabb8.png" alt="\rho(\mathbf{r}) = \rho_\alpha(\mathbf{r}) + \rho_\beta(\mathbf{r})" style="vertical-align: -6px"/>,
and the spin density
<img class="math" src="_images/math/04b44a2c99d400a7d17af462fee747887f200e11.png" alt="\rho(\mathbf{r}) = \rho_\alpha(\mathbf{r}) - \rho_\beta(\mathbf{r})" style="vertical-align: -6px"/>.</dd>
<dt>BASIS_FUNCTIONS</dt>
<dd>This task is useful to produce cube files of the atomic orbital basis
functions <img class="math" src="_images/math/b0d0018c0b6f176b7ee7ee2c6a97357c2e4ab6f1.png" alt="\chi_\mu(\mathbf{r})" style="vertical-align: -6px"/>.</dd>
<dt>ESP</dt>
<dd>Calculates the total (nuclear + electronic) electrostatic potential
<img class="math" src="_images/math/56ee3e249a0a512924030a3934bc5fc06e6e96c8.png" alt="V(\mathbf{r})" style="vertical-align: -4px"/>.</dd>
</dl>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <code class="docutils literal"><span class="pre">ESP</span></code> task requires the user to specify a density-fitting basis
via the <a class="reference internal" href="autodoc_glossary_options_c.html#term-df-basis-scf-scf"><span class="xref std std-term">DF_BASIS_SCF</span></a> keyword.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is important to specify the <code class="docutils literal"><span class="pre">CUBEPROP_ORBITALS</span></code> option when
dealing with large molecules to avoid running out of disk space.
For example, using the default grid spacing of
0.2 Ångstroms, the size of a single cube file for a molecule like water
is of the order of 1.4 MB. For a molecule with 200 basis functions, the cube
files for all the orbitals occupy more than half a GB.</p>
</div>
</div>
<div class="section" id="cubeprop-options">
<h2>Cubeprop Options<a class="headerlink" href="#cubeprop-options" title="Permalink to this headline">¶</a></h2>
<dl class="docutils">
<dt>CUBEPROP_FILEPATH</dt>
<dd>The directory in which to place the cube files. The default is the
directory that contains the input file.</dd>
<dt>CUBEPROP_ORBITALS</dt>
<dd>A list of the orbitals for which cube files are generated. Alpha orbitals
are specified by positive integers, where the lowest orbital is 1.
Beta orbitals are indicated by prefixing the number with a minus sign.
Orbitals are ordered according to their energy.
Notice that if the <code class="docutils literal"><span class="pre">CUBEPROP_ORBITALS</span></code> list is empty then
cubeprop will produce cube files for all alpha and beta orbitals.</dd>
<dt>CUBEPROP_BASIS_FUNCTIONS</dt>
<dd>A list of basis functions for which cube files are generated. Basis
functions are numbered starting from 1.</dd>
<dt>CUBIC_GRID_SPACING</dt>
<dd>A vector that specifies the grid spacing in the X, Y, and Z directions.
The default value is [0.2,0.2,0.2] Ångstroms.</dd>
<dt>CUBIC_GRID_OVERAGE</dt>
<dd>A vector that controls the spatial extent of the grid in the X, Y, and Z
directions.
The default value is [4.0,4.0,4.0] Ångstroms.</dd>
</dl>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Generation of cube files</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#cubeprop-tasks">Cubeprop Tasks</a></li>
<li><a class="reference internal" href="#cubeprop-options">Cubeprop Options</a></li>
</ul>
</li>
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