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<div class="section" id="database">
<span id="sec-db"></span><span id="index-0"></span><h1>Database<a class="headerlink" href="#database" title="Permalink to this headline">¶</a></h1>
<p><em>Code author: Lori A. Burns</em></p>
<p><em>Section author: Lori A. Burns</em></p>
<dl class="function">
<dt id="wrappers.database">
<code class="descname">database</code><span class="sig-paren">(</span><em>name</em>, <em>db_name</em><span class="optional">[</span>, <em>func</em>, <em>mode</em>, <em>cp</em>, <em>rlxd</em>, <em>symm</em>, <em>zpe</em>, <em>benchmark</em>, <em>tabulate</em>, <em>subset</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/wrappers.html#database"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#wrappers.database" title="Permalink to this definition">¶</a></dt>
<dd><p>Function to access the molecule objects and reference energies of
popular chemical databases.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Aliases:</th><td class="field-body">db()</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(<em>float</em>) Mean absolute deviation of the database in kcal/mol</td>
</tr>
<tr class="field-odd field"><th class="field-name">PSI variables:</th><td class="field-body"></td>
</tr>
</tbody>
</table>
<table class="hlist"><tr><td><ul class="simple">
<li><a class="reference internal" href="glossary_psivariables.html#psivar-db_nameDATABASEMEANSIGNEDDEVIATION"><code class="xref std std-psivar docutils literal"><span class="pre">db_name</span> <span class="pre">DATABASE</span> <span class="pre">MEAN</span> <span class="pre">SIGNED</span> <span class="pre">DEVIATION</span></code></a></li>
<li><a class="reference internal" href="glossary_psivariables.html#psivar-db_nameDATABASEMEANABSOLUTEDEVIATION"><code class="xref std std-psivar docutils literal"><span class="pre">db_name</span> <span class="pre">DATABASE</span> <span class="pre">MEAN</span> <span class="pre">ABSOLUTE</span> <span class="pre">DEVIATION</span></code></a></li>
<li><a class="reference internal" href="glossary_psivariables.html#psivar-db_nameDATABASEROOT-MEAN-SQUARESIGNEDDEVIATION"><code class="xref std std-psivar docutils literal"><span class="pre">db_name</span> <span class="pre">DATABASE</span> <span class="pre">ROOT-MEAN-SQUARE</span> <span class="pre">DEVIATION</span></code></a></li>
<li>Python dictionaries of results accessible as <code class="docutils literal"><span class="pre">DB_RGT</span></code> and <code class="docutils literal"><span class="pre">DB_RXN</span></code>.</li>
</ul>
</td></tr></table>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is very easy to make a database from a collection of xyz files
using the script <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/scripts/ixyz2database.pl">psi4/lib/scripts/ixyz2database.pl</a>.
See <a class="reference internal" href="quickadddatabase.html#sec-createdatabase"><span>Creating a Database</span></a> for details.</p>
</div>
<div class="admonition caution">
<p class="first admonition-title">Caution</p>
<p>Some features are not yet implemented. Buy a developer some coffee.</p>
<ul class="last simple">
<li>In sow/reap mode, use only global options (e.g., the local option set by <code class="docutils literal"><span class="pre">set</span> <span class="pre">scf</span> <span class="pre">scf_type</span> <span class="pre">df</span></code> will not be respected).</li>
</ul>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">To access a database that is not embedded in a <span class="sc">Psi4</span>
distribution, add the path to the directory containing the database
to the environment variable <span class="target" id="index-1"></span><a class="reference internal" href="external.html#envvar-PYTHONPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></code></a>.</p>
</div>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>name</strong> (<em>string</em>) – <p><code class="docutils literal"><span class="pre">'scf'</span></code> || <code class="docutils literal"><span class="pre">'sapt0'</span></code> || <code class="docutils literal"><span class="pre">'ccsd(t)'</span></code> || etc.</p>
<p>First argument, usually unlabeled. Indicates the computational method
to be applied to the database. May be any valid argument to
<a class="reference internal" href="energy.html#driver.energy" title="driver.energy"><code class="xref py py-func docutils literal"><span class="pre">energy()</span></code></a>.</p>
</li>
<li><strong>db_name</strong> (<em>string</em>) – <p><code class="docutils literal"><span class="pre">'BASIC'</span></code> || <code class="docutils literal"><span class="pre">'S22'</span></code> || <code class="docutils literal"><span class="pre">'HTBH'</span></code> || etc.</p>
<p>Second argument, usually unlabeled. Indicates the requested database
name, matching (case insensitive) the name of a python file in
<code class="docutils literal"><span class="pre">psi4/lib/databases</span></code> or <span class="target" id="index-2"></span><a class="reference internal" href="external.html#envvar-PYTHONPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></code></a>. Consult that
directory for available databases and literature citations.</p>
</li>
<li><strong>func</strong> (<a class="reference internal" href="notes_py.html#op-py-function"><span>function</span></a>) – <p><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">energy</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> || <code class="docutils literal"><span class="pre">optimize</span></code> || <code class="docutils literal"><span class="pre">cbs</span></code></p>
<p>Indicates the type of calculation to be performed on each database
member. The default performs a single-point <code class="docutils literal"><span class="pre">energy('name')</span></code>, while
<code class="docutils literal"><span class="pre">optimize</span></code> perfoms a geometry optimization on each reagent, and
<code class="docutils literal"><span class="pre">cbs</span></code> performs a compound single-point energy. If a nested series
of python functions is intended (see <a class="reference internal" href="intercalls.html#sec-intercalls"><span>Function Intercalls</span></a>), use
keyword <code class="docutils literal"><span class="pre">db_func</span></code> instead of <code class="docutils literal"><span class="pre">func</span></code>.</p>
</li>
<li><strong>mode</strong> (<em>string</em>) – <p><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'continuous'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> || <code class="docutils literal"><span class="pre">'sow'</span></code> || <code class="docutils literal"><span class="pre">'reap'</span></code></p>
<p>Indicates whether the calculations required to complete the
database are to be run in one file (<code class="docutils literal"><span class="pre">'continuous'</span></code>) or are to be
farmed out in an embarrassingly parallel fashion
(<code class="docutils literal"><span class="pre">'sow'</span></code>/<code class="docutils literal"><span class="pre">'reap'</span></code>). For the latter, run an initial job with
<code class="docutils literal"><span class="pre">'sow'</span></code> and follow instructions in its output file.</p>
</li>
<li><strong>cp</strong> (<a class="reference internal" href="notes_py.html#op-py-boolean"><span>boolean</span></a>) – <p><code class="docutils literal"><span class="pre">'on'</span></code> || <img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'off'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/></p>
<p>Indicates whether counterpoise correction is employed in computing
interaction energies. Use this option and NOT the <a class="reference internal" href="cp.html#wrappers.cp" title="wrappers.cp"><code class="xref py py-func docutils literal"><span class="pre">cp()</span></code></a>
function for BSSE correction in database(). Option available
(See <a class="reference internal" href="#sec-availabledatabases"><span>Available Databases</span></a>) only for databases of bimolecular complexes.</p>
</li>
<li><strong>rlxd</strong> (<a class="reference internal" href="notes_py.html#op-py-boolean"><span>boolean</span></a>) – <p><code class="docutils literal"><span class="pre">'on'</span></code> || <img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'off'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/></p>
<p>Indicates whether correction for deformation energy is
employed in computing interaction energies. Option available
(See <a class="reference internal" href="#sec-availabledatabases"><span>Available Databases</span></a>) only for databases of bimolecular complexes
with non-frozen monomers, e.g., HBC6.</p>
</li>
<li><strong>symm</strong> (<a class="reference internal" href="notes_py.html#op-py-boolean"><span>boolean</span></a>) – <p><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'on'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> || <code class="docutils literal"><span class="pre">'off'</span></code></p>
<p>Indicates whether the native symmetry of the database reagents is
employed (<code class="docutils literal"><span class="pre">'on'</span></code>) or whether it is forced to <img class="math" src="_images/math/a7223a037dfd9076deee6e5754c08434bebef462.png" alt="C_1" style="vertical-align: -4px"/> symmetry
(<code class="docutils literal"><span class="pre">'off'</span></code>). Some computational methods (e.g., SAPT) require no
symmetry, and this will be set by database().</p>
</li>
<li><strong>zpe</strong> (<a class="reference internal" href="notes_py.html#op-py-boolean"><span>boolean</span></a>) – <p><code class="docutils literal"><span class="pre">'on'</span></code> || <img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'off'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/></p>
<p>Indicates whether zero-point-energy corrections are appended to
single-point energy values. Option valid only for certain
thermochemical databases. Disabled until Hessians ready.</p>
</li>
<li><strong>benchmark</strong> (<em>string</em>) – <p><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'default'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> || <code class="docutils literal"><span class="pre">'S22A'</span></code> || etc.</p>
<p>Indicates whether a non-default set of reference energies, if
available (See <a class="reference internal" href="#sec-availabledatabases"><span>Available Databases</span></a>), are employed for the
calculation of error statistics.</p>
</li>
<li><strong>tabulate</strong> (<em>array of strings</em>) – <p><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">[]</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> || <code class="docutils literal"><span class="pre">['scf</span> <span class="pre">total</span> <span class="pre">energy',</span> <span class="pre">'natom']</span></code> || etc.</p>
<p>Indicates whether to form tables of variables other than the
primary requested energy. Available for any PSI variable.</p>
</li>
<li><strong>subset</strong> (<em>string or array of strings</em>) – <p>Indicates a subset of the full database to run. This is a very
flexible option and can be used in three distinct ways, outlined
below. Note that two take a string and the last takes an array.
See <a class="reference internal" href="#available-databases">Available Databases</a> for available values.</p>
<ul>
<li><dl class="first docutils">
<dt><code class="docutils literal"><span class="pre">'small'</span></code> || <code class="docutils literal"><span class="pre">'large'</span></code> || <code class="docutils literal"><span class="pre">'equilibrium'</span></code></dt>
<dd>Calls predefined subsets of the requested database, either
<code class="docutils literal"><span class="pre">'small'</span></code>, a few of the smallest database members,
<code class="docutils literal"><span class="pre">'large'</span></code>, the largest of the database members, or
<code class="docutils literal"><span class="pre">'equilibrium'</span></code>, the equilibrium geometries for a database
composed of dissociation curves.</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt><code class="docutils literal"><span class="pre">'BzBz_S'</span></code> || <code class="docutils literal"><span class="pre">'FaOOFaON'</span></code> || <code class="docutils literal"><span class="pre">'ArNe'</span></code> || <code class="docutils literal"><span class="pre">'HB'</span></code> || etc.</dt>
<dd>For databases composed of dissociation curves, or otherwise
divided into subsets, individual curves and subsets can be
called by name. Consult the database python files for available
molecular systems (case insensitive).</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt><code class="docutils literal"><span class="pre">[1,2,5]</span></code> || <code class="docutils literal"><span class="pre">['1','2','5']</span></code> || <code class="docutils literal"><span class="pre">['BzMe-3.5',</span> <span class="pre">'MeMe-5.0']</span></code> || etc.</dt>
<dd>Specify a list of database members to run. Consult the
database python files for available molecular systems. This
is the only portion of database input that is case sensitive;
choices for this keyword must match the database python file.</dd>
</dl>
</li>
</ul>
</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Examples:</th><td class="field-body"></td>
</tr>
</tbody>
</table>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="c"># [1] Two-stage SCF calculation on short, equilibrium, and long helium dimer</span>
<span class="gp">>>> </span><span class="n">db</span><span class="p">(</span><span class="s">'scf'</span><span class="p">,</span><span class="s">'RGC10'</span><span class="p">,</span><span class="n">cast_up</span><span class="o">=</span><span class="s">'sto-3g'</span><span class="p">,</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s">'HeHe-0.85'</span><span class="p">,</span><span class="s">'HeHe-1.0'</span><span class="p">,</span><span class="s">'HeHe-1.5'</span><span class="p">],</span> <span class="n">tabulate</span><span class="o">=</span><span class="p">[</span><span class="s">'scf total energy'</span><span class="p">,</span><span class="s">'natom'</span><span class="p">])</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="c"># [2] Counterpoise-corrected interaction energies for three complexes in S22</span>
<span class="gp">>>> </span><span class="c"># Error statistics computed wrt an old benchmark, S22A</span>
<span class="gp">>>> </span><span class="n">database</span><span class="p">(</span><span class="s">'df-mp2'</span><span class="p">,</span><span class="s">'S22'</span><span class="p">,</span><span class="n">cp</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="mi">16</span><span class="p">,</span><span class="mi">17</span><span class="p">,</span><span class="mi">8</span><span class="p">],</span><span class="n">benchmark</span><span class="o">=</span><span class="s">'S22A'</span><span class="p">)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="c"># [3] SAPT0 on the neon dimer dissociation curve</span>
<span class="gp">>>> </span><span class="n">db</span><span class="p">(</span><span class="s">'sapt0'</span><span class="p">,</span><span class="n">subset</span><span class="o">=</span><span class="s">'NeNe'</span><span class="p">,</span><span class="n">cp</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span><span class="n">symm</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span><span class="n">db_name</span><span class="o">=</span><span class="s">'RGC10'</span><span class="p">)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="c"># [4] Optimize system 1 in database S22, producing tables of scf and mp2 energy</span>
<span class="gp">>>> </span><span class="n">db</span><span class="p">(</span><span class="s">'mp2'</span><span class="p">,</span><span class="s">'S22'</span><span class="p">,</span><span class="n">db_func</span><span class="o">=</span><span class="n">optimize</span><span class="p">,</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">tabulate</span><span class="o">=</span><span class="p">[</span><span class="s">'mp2 total energy'</span><span class="p">,</span><span class="s">'current energy'</span><span class="p">])</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="c"># [5] CCSD on the smallest systems of HTBH, a hydrogen-transfer database</span>
<span class="gp">>>> </span><span class="n">database</span><span class="p">(</span><span class="s">'ccsd'</span><span class="p">,</span><span class="s">'HTBH'</span><span class="p">,</span><span class="n">subset</span><span class="o">=</span><span class="s">'small'</span><span class="p">,</span> <span class="n">tabulate</span><span class="o">=</span><span class="p">[</span><span class="s">'ccsd total energy'</span><span class="p">,</span> <span class="s">'mp2 total energy'</span><span class="p">])</span>
</pre></div>
</div>
</dd></dl>
<div class="section" id="output">
<span id="index-3"></span><h2>Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h2>
<p>At the beginning of a database job is printed a listing of the individual system
calculations which will be performed. The output snippet below is from the example job [1]
above. It shows each reagent required for the subset of database reactions requested.
Note that this is an un-counterpoise-corrected example, and the wrapper is smart enough
to compute only once the monomer whose energy will be subtracted from each of the three dimers.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">RGC1</span><span class="o">-</span><span class="n">HeHe</span><span class="o">-</span><span class="mf">0.85</span><span class="o">-</span><span class="n">dimer</span>
<span class="n">RGC1</span><span class="o">-</span><span class="n">He</span><span class="o">-</span><span class="n">mono</span><span class="o">-</span><span class="n">unCP</span>
<span class="n">RGC1</span><span class="o">-</span><span class="n">HeHe</span><span class="o">-</span><span class="mf">1.0</span><span class="o">-</span><span class="n">dimer</span>
<span class="n">RGC1</span><span class="o">-</span><span class="n">HeHe</span><span class="o">-</span><span class="mf">1.5</span><span class="o">-</span><span class="n">dimer</span>
</pre></div>
</div>
<p>At the end of the job, the Requested Energy table is printed that gives the total
energies for the requested model chemistry for each reagent and each reaction, as
well as the stoichoimetric weights by which the reagent energies are transfromed
into the reaction energy. In this case, the dimer is +1 and the monomer is -2,
indicating the the interaction energy is computed from dimer less first monomer
less second (identical) monomer. Error statistics are computed with respect to the reference
energies stored in the database. One of these, the mean absolute deviation, is
returned by the wrapper as an ordinary Python variable. (For databases
without a stored reference energy, e.g., BASIC, large and meaningless numbers are
printed for error.) The other two tables tabulate the PSI variables requested
through keyword <code class="docutils literal"><span class="pre">tabulate</span></code>, in this case the total SCF energy and the number
of atoms in each reagent.</p>
<div class="highlight-python"><div class="highlight"><pre>==> Scf Total Energy <==
-----------------------------------------------------------------------------------
Reaction Reaction Value Reagent 1 Reagent 2
Value Wt Value Wt
-----------------------------------------------------------------------------------
RGC1-HeHe-0.85 0.00011520 -5.71020576 1 -2.85516048 -2
RGC1-HeHe-1.0 0.00000153 -5.71031943 1 -2.85516048 -2
RGC1-HeHe-1.5 -0.00000000 -5.71032096 1 -2.85516048 -2
-----------------------------------------------------------------------------------
==> Natom <==
-----------------------------------------------------------------------------------
Reaction Reaction Value Reagent 1 Reagent 2
Value Wt Value Wt
-----------------------------------------------------------------------------------
RGC1-HeHe-0.85 0.00000000 2.00000000 1 1.00000000 -2
RGC1-HeHe-1.0 0.00000000 2.00000000 1 1.00000000 -2
RGC1-HeHe-1.5 0.00000000 2.00000000 1 1.00000000 -2
-----------------------------------------------------------------------------------
==> Requested Energy <==
-----------------------------------------------------------------------------------
Reaction Reaction Energy Error Reagent 1 Reagent 2
Ref Calc [kcal/mol] [H] Wt [H] Wt
-----------------------------------------------------------------------------------
RGC1-HeHe-0.85 0.0376 0.0723 0.0347 -5.71020576 1 -2.85516048 -2
RGC1-HeHe-1.0 -0.0219 0.0010 0.0228 -5.71031943 1 -2.85516048 -2
RGC1-HeHe-1.5 -0.0029 -0.0000 0.0029 -5.71032096 1 -2.85516048 -2
-----------------------------------------------------------------------------------
Minimal Dev 0.0029
Maximal Dev 0.0347
Mean Signed Dev 0.0201
Mean Absolute Dev 0.0201
RMS Dev 0.0240
-----------------------------------------------------------------------------------
</pre></div>
</div>
<p>As well as being printed in the output file, database results from the
<code class="docutils literal"><span class="pre">tabulate</span></code> option are available in the input file as ordinary Python
dictionaries <code class="docutils literal"><span class="pre">DB_RGT</span></code> and <code class="docutils literal"><span class="pre">DB_RXN</span></code>, indexed firstly by reagent or reaction
name and secondly by the requested PSI variable name. See the first
paragraph of <a class="reference internal" href="quickadddatabase.html#sec-createdatabase"><span>Creating a Database</span></a> for the distinction between
reagents and reactions. For example, an input file like the following
requests a couple variables through <code class="docutils literal"><span class="pre">tabulate</span></code> and then makes use of the
resulting data structures, here, only to print.</p>
<div class="highlight-python"><div class="highlight"><pre>set basis 6-31g*
db('dfmp2','s22',subset='small',tabulate=['CURRENT ENERGY','DF-MP2 CORRELATION ENERGY'])
from pprint import pprint
print_stdout('\nDB_RGT')
pprint(DB_RGT)
print_stdout('\nDB_RXN')
pprint(DB_RXN)
print_stdout('\ndf-mp2 interaction energy of water dimer (S22-2)')
print_stdout(DB_RXN['S22-2']['CURRENT ENERGY'])
</pre></div>
</div>
<p>The output to the screen is as follows.</p>
<div class="highlight-python"><div class="highlight"><pre>DB_RGT
{'S22-16-dimer': {'CURRENT ENERGY': -155.37373581838636,
'DF-MP2 CORRELATION ENERGY': -0.523870772178089},
'S22-16-monoA-unCP': {'CURRENT ENERGY': -78.29412053242164,
'DF-MP2 CORRELATION ENERGY': -0.2629759351596186},
'S22-16-monoB-unCP': {'CURRENT ENERGY': -77.07606823017188,
'DF-MP2 CORRELATION ENERGY': -0.2594122526144091},
'S22-2-dimer': {'CURRENT ENERGY': -152.40958884746667,
'DF-MP2 CORRELATION ENERGY': -0.3797598812113561},
'S22-2-monoA-unCP': {'CURRENT ENERGY': -76.19905879745446,
'DF-MP2 CORRELATION ENERGY': -0.1887118848315123},
'S22-2-monoB-unCP': {'CURRENT ENERGY': -76.19902978067739,
'DF-MP2 CORRELATION ENERGY': -0.18857384937354635},
'S22-8-dimer': {'CURRENT ENERGY': -80.67416758080654,
'DF-MP2 CORRELATION ENERGY': -0.2844102558783027},
'S22-8-monoA-unCP': {'CURRENT ENERGY': -40.336952636980364,
'DF-MP2 CORRELATION ENERGY': -0.14185962536715307},
'S22-8-monoB-unCP': {'CURRENT ENERGY': -40.336952636980506,
'DF-MP2 CORRELATION ENERGY': -0.14185962536715097}}
DB_RXN
{'S22-16': {'CURRENT ENERGY': -0.0035470557928363178,
'DF-MP2 CORRELATION ENERGY': -0.0014825844040612934},
'S22-2': {'CURRENT ENERGY': -0.011500269334817403,
'DF-MP2 CORRELATION ENERGY': -0.0024741470062974724},
'S22-8': {'CURRENT ENERGY': -0.0002623068456699684,
'DF-MP2 CORRELATION ENERGY': -0.0006910051439986686}}
df-mp2 interaction energy of water dimer (S22-2)
-0.0115002693348
</pre></div>
</div>
</div>
<div class="section" id="available-databases">
<span id="sec-availabledatabases"></span><span id="index-4"></span><h2>Available Databases<a class="headerlink" href="#available-databases" title="Permalink to this headline">¶</a></h2>
<p>Below are documented for particular databases the availibility of the generic
database function options <strong>cp</strong>, <strong>rlxd</strong>, <strong>benchmark</strong>, and the string
options for <strong>subset</strong>. The full reagent member list, which can also be used
in conjunction with <strong>subset</strong>, is not included here for consideration of space
and may be found in the database file. The database Python files are very
readable and should be consulted for more particular questions.</p>
<hr class="docutils" />
<div class="toctree-wrapper compound">
</div>
<div class="section" id="module-JSCH">
<span id="jsch"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/JSCH.py">JSCH</a><a class="headerlink" href="#module-JSCH" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for nucelobase pairs.</div>
<div class="line">Geometries and reference interaction energies from Jurecka et al. PCCP 8 1985 (2006).</div>
<div class="line">Corrections implemented from footnote 92 of Burns et al., JCP 134 084107 (2011).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'HB'</span></code> hydrogen-bonded systems (coplanar base-pairs)</li>
<li><code class="docutils literal"><span class="pre">'MX'</span></code> interstrand systems (adjacent base-pairs on different strands)</li>
<li><code class="docutils literal"><span class="pre">'DD'</span></code> stacked systems (adjacent base-pairs on same strand)</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-S22by5">
<span id="s22by5"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/S22by5.py">S22by5</a><a class="headerlink" href="#module-S22by5" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for dissociation curves of bimolecular complexes.</div>
<div class="line">Geometries and reference interaction energies from Grafova et al. JCTC 6 2365 (2010).</div>
<div class="line">Note that the S22by5-N-1.0 members are essentially the same geometries as S22-N (there’s trivial round-off error) but the reference interaction energies for S22by5 are of lower quality than those of S22.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'equilibrium'</span></code></li>
<li><code class="docutils literal"><span class="pre">'mol1'</span></code> five-point (0.9, 1.0, 1.2, 1.5, 2.0) <img class="math" src="_images/math/6552511765201bf87c768c179194812e8b11552c.png" alt="\times R_{eq}" style="vertical-align: -6px"/> dissociation curve for molecule 1</li>
<li>...</li>
<li><code class="docutils literal"><span class="pre">'mol22'</span></code> five-point (0.9, 1.0, 1.2, 1.5, 2.0) <img class="math" src="_images/math/6552511765201bf87c768c179194812e8b11552c.png" alt="\times R_{eq}" style="vertical-align: -6px"/> dissociation curve for molecule 22</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-RSE42">
<span id="rse42"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/RSE42.py">RSE42</a><a class="headerlink" href="#module-RSE42" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of radical stabilization energies.</div>
<div class="line">Geometries from [E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)].</div>
<div class="line">Reference radical stabilization energies from [E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)] at CCSD(T)/cc-pCVTZ level.</div>
</div>
<ul class="simple">
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'RSE42'</span></code> [E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)].</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'RSE42'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> [E. Soydas and U. Bozkaya, JCTC, 9, 1452-1460 (2013)].</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'RSE30'</span></code> smaller systems in RSE42</li>
<li><code class="docutils literal"><span class="pre">'<subset>'</span></code> <members_description></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-HSG">
<span id="hsg"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/HSG.py">HSG</a><a class="headerlink" href="#module-HSG" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Merz) of interaction energies for bimolecular complexes from protein-indinavir reaction site.</div>
<div class="line">Geometries from and original reference energies from Faver et al. JCTC 7 790 (2011).</div>
<div class="line">Revised reference interaction energies (HSGA) from Marshall et al. JCP 135 194102 (2011).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'HSG0'</span></code> Faver et al. JCTC 7 790 (2011).</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'HSGA'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> Marshall et al. JCP 135 194102 (2011).</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-ACENES">
<span id="acenes"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/ACENES.py">ACENES</a><a class="headerlink" href="#module-ACENES" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of Ed and Rob’s favorite linear acene dimers.</div>
<div class="line">Geometries from nowhere special, and reference energies undefined.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'FIRST3'</span></code> benzene, napthalene, and anthracene dimers</li>
<li><code class="docutils literal"><span class="pre">'FIRST5'</span></code> benzene - pentacene dimers</li>
<li><code class="docutils literal"><span class="pre">'FIRST10'</span></code> benzene - decacene dimers</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-S66">
<span id="s66"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/S66.py">S66</a><a class="headerlink" href="#module-S66" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for bimolecular complexes.</div>
<div class="line">Geometries and reference energies from Rezac et al. JCTC 7 2427 (2011).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'HB'</span></code> hydrogen-bonded systems</li>
<li><code class="docutils literal"><span class="pre">'MX'</span></code> mixed-influence systems</li>
<li><code class="docutils literal"><span class="pre">'DD'</span></code> dispersion-dominated systems</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-S66by8">
<span id="s66by8"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/S66by8.py">S66by8</a><a class="headerlink" href="#module-S66by8" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for bimolecular complexes.</div>
<div class="line">Geometries and reference interaction energies from Rezac et al. JCTC 7 2427 (2011).</div>
<div class="line">Note that the S66by8-N-1.0 members are not quite the same geometries as S66-N.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'equilibrium'</span></code></li>
<li><code class="docutils literal"><span class="pre">'HB'</span></code> eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0) <img class="math" src="_images/math/6552511765201bf87c768c179194812e8b11552c.png" alt="\times R_{eq}" style="vertical-align: -6px"/> dissociation curve hydrogen-bonded systems</li>
<li><code class="docutils literal"><span class="pre">'MX'</span></code> eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0) <img class="math" src="_images/math/6552511765201bf87c768c179194812e8b11552c.png" alt="\times R_{eq}" style="vertical-align: -6px"/> dissociation curve mixed-influence systems</li>
<li><code class="docutils literal"><span class="pre">'DD'</span></code> eight-point (0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0) <img class="math" src="_images/math/6552511765201bf87c768c179194812e8b11552c.png" alt="\times R_{eq}" style="vertical-align: -6px"/> dissociation curve dispersion-dominated systems</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-HBC6">
<span id="hbc6"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/HBC6.py">HBC6</a><a class="headerlink" href="#module-HBC6" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Sherrill) of interaction energies for dissociation curves of doubly hydrogen-bonded bimolecular complexes.</div>
<div class="line">Geometries from and original reference interaction energies from Thanthiriwatte et al. JCTC 7 88 (2011).</div>
<div class="line">Revised reference interaction energies from Marshall et al. JCP 135 194102 (2011).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'HBC60'</span></code> Thanthiriwatte et al. JCTC 7 88 (2011).</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'HBC6A'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> Marshall et al. JCP 135 194102 (2011).</li>
<li><code class="docutils literal"><span class="pre">'HBC6ARLX'</span></code> Sherrill group, unpublished.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'equilibrium'</span></code> equilibrium points for the six systems</li>
<li><code class="docutils literal"><span class="pre">'FaOOFaOO'</span></code> dissociation curve for formic acid dimer</li>
<li><code class="docutils literal"><span class="pre">'FaONFaON'</span></code> dissociation curve for formamide dimer</li>
<li><code class="docutils literal"><span class="pre">'FaNNFaNN'</span></code> dissociation curve for formamidine dimer</li>
<li><code class="docutils literal"><span class="pre">'FaOOFaON'</span></code> dissociation curve for formic acid- formamide complex</li>
<li><code class="docutils literal"><span class="pre">'FaONFaNN'</span></code> dissociation curve for formamide- formamidine complex</li>
<li><code class="docutils literal"><span class="pre">'FaOOFaNN'</span></code> dissociation curve for formic acid- formamidine complex</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-CORE">
<span id="core"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/CORE.py">CORE</a><a class="headerlink" href="#module-CORE" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of Pulay corannulene structures. Subsumed into CFLOW.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-NBC10">
<span id="nbc10"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/NBC10.py">NBC10</a><a class="headerlink" href="#module-NBC10" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Sherrill) of interaction energies for dissociation curves of dispersion-bound bimolecular complexes.</div>
<div class="line">Geometries and Reference interaction energies from the following articles:</div>
<div class="line-block">
<div class="line">Benzene Dimers from Sherrill et al. JPCA 113 10146 (2009).</div>
<div class="line">Benzene-Hydrogen Sulfide from Sherrill et al. JPCA 113 10146 (2009).</div>
<div class="line">Benzene-Methane from Sherrill et al. JPCA 113 10146 (2009).</div>
<div class="line">Methane Dimer from Takatani et al. PCCP 9 6106 (2007).</div>
<div class="line">Pyridine Dimers from Hohenstein et al. JPCA 113 878 (2009).</div>
<div class="line">Collection into NBC10 from Burns et al. JCP 134 084107 (2011).</div>
<div class="line">Revised reference interaction energies (NBC10A) from Marshall et al. JCP 135 194102 (2011).</div>
</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'NBC100'</span></code> Burns et al. JCP 134 084107 (2011).</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'NBC10A'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> Marshall et al. JCP 135 194102 (2011).</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'equilibrium'</span></code></li>
<li><code class="docutils literal"><span class="pre">'BzBz_S'</span></code> dissociation curve for benzene dimer, sandwich</li>
<li><code class="docutils literal"><span class="pre">'BzBz_T'</span></code> dissociation curve for benzene dimer, t-shaped</li>
<li><code class="docutils literal"><span class="pre">'BzBz_PD34'</span></code> dissociation curve for benzene dimer, parallel displaced by 3.4A</li>
<li><code class="docutils literal"><span class="pre">'BzH2S'</span></code> dissociation curve for benzene-H2S</li>
<li><code class="docutils literal"><span class="pre">'BzMe'</span></code> dissociation curve for benzene-methane</li>
<li><code class="docutils literal"><span class="pre">'MeMe'</span></code> dissociation curve for methane dimer</li>
<li><code class="docutils literal"><span class="pre">'PyPy_S2'</span></code> dissociation curve for pyridine dimer, sandwich</li>
<li><code class="docutils literal"><span class="pre">'PyPy_T3'</span></code> dissociation curve for pyridine dimer, t-shaped</li>
<li><code class="docutils literal"><span class="pre">'BzBz_PD32'</span></code> dissociation curve for benzene dimer, parallel displaced by 3.2A</li>
<li><code class="docutils literal"><span class="pre">'BzBz_PD36'</span></code> dissociation curve for benzene dimer, parallel displaced by 3.6A</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-A24">
<span id="a24"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/A24.py">A24</a><a class="headerlink" href="#module-A24" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for bimolecular complexes.</div>
<div class="line">Geometries from <Reference>.</div>
<div class="line">Reference interaction energies from Rezac and Hobza, JCTC (in press).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> <erase this comment and after unless on is a valid option> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code> <erase this comment and after unless on is valid option> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'<benchmark_name>'</span></code> <Reference>.</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'<default_benchmark_name>'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> <Reference>.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'<subset>'</span></code> <members_description></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-BASIC">
<span id="basic"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/BASIC.py">BASIC</a><a class="headerlink" href="#module-BASIC" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of simple molecules, mostly for testing.</div>
<div class="line">Geometries from nowhere special, and no reference energies defined.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong> [<code class="docutils literal"><span class="pre">'h2o'</span></code>, <code class="docutils literal"><span class="pre">'nh3'</span></code>, <code class="docutils literal"><span class="pre">'ch4'</span></code>]</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-BAKERJCC96">
<span id="bakerjcc96"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/BAKERJCC96.py">BAKERJCC96</a><a class="headerlink" href="#module-BAKERJCC96" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Geometries from Baker and Chan J. Comput. Chem. 17 888 (1996),</div>
<div class="line-block">
<div class="line">as reported in Bakken and Helgaker, J. Chem. Phys. 117, 9160 (2002).</div>
</div>
<div class="line">No reference energies defined.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-BENCH12">
<span id="bench12"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/BENCH12.py">BENCH12</a><a class="headerlink" href="#module-BENCH12" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of <description of members and reference energy type>.</div>
<div class="line">Geometries from <Reference>.</div>
<div class="line">Reference interaction energies from <Reference>.</div>
</div>
<ul class="simple">
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'<benchmark_name>'</span></code> <Reference>.</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'<default_benchmark_name>'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> <Reference>.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'alkenes'</span></code></li>
<li><code class="docutils literal"><span class="pre">'alkanes'</span></code></li>
<li><code class="docutils literal"><span class="pre">'acenes'</span></code></li>
<li><code class="docutils literal"><span class="pre">'thiophenes'</span></code></li>
<li><code class="docutils literal"><span class="pre">'h2o_size'</span></code></li>
<li><code class="docutils literal"><span class="pre">'h2o_shape'</span></code></li>
<li><code class="docutils literal"><span class="pre">'atoms'</span></code></li>
<li><code class="docutils literal"><span class="pre">'S22_HB'</span></code></li>
<li><code class="docutils literal"><span class="pre">'S22_MX'</span></code></li>
<li><code class="docutils literal"><span class="pre">'S22_DD'</span></code></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-NCB31">
<span id="ncb31"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/NCB31.py">NCB31</a><a class="headerlink" href="#module-NCB31" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Truhlar) of several classes of noncovalent interactions.</div>
<div class="line">Geometries from Truhlar and coworkers at site <a class="reference external" href="http://comp.chem.umn.edu/database_noncov/noncovalent.htm">http://comp.chem.umn.edu/database_noncov/noncovalent.htm</a></div>
<div class="line">Reference energies from Truhlar and coworkers at site <a class="reference external" href="http://comp.chem.umn.edu/database_noncov/noncovalent.htm">http://comp.chem.umn.edu/database_noncov/noncovalent.htm</a></div>
<div class="line">First comprehensive citation JPCA 109 5656 (2005). </div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'<benchmark_name>'</span></code> <Reference>.</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'<default_benchmark_name>'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> <Reference>.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> 3: HF-HF, He-Ne, HCCH-HCCH</li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> 1: BzBz_PD</li>
<li><code class="docutils literal"><span class="pre">'HB6'</span></code> hydrogen-bonded</li>
<li><code class="docutils literal"><span class="pre">'CT7'</span></code> charge-transfer</li>
<li><code class="docutils literal"><span class="pre">'DI6'</span></code> dipole-interacting</li>
<li><code class="docutils literal"><span class="pre">'WI7'</span></code> weakly interacting</li>
<li><code class="docutils literal"><span class="pre">'PPS5'</span></code> pi-pi stacking</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-RGC10">
<span id="rgc10"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/RGC10.py">RGC10</a><a class="headerlink" href="#module-RGC10" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Sherrill) of interaction energies for dissociation curves of rare-gas biatomic complexes.</div>
<div class="line">Geometries and reference interaction energies from Tang et al. JCP 118 4976 (2003).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
<li><code class="docutils literal"><span class="pre">'equilibrium'</span></code></li>
<li><code class="docutils literal"><span class="pre">'HeHe'</span></code> 18-point dissociation curve for helium dimer</li>
<li><code class="docutils literal"><span class="pre">'HeNe'</span></code> 18-point dissociation curve for helium-neon complex</li>
<li><code class="docutils literal"><span class="pre">'HeAr'</span></code> 18-point dissociation curve for helium-argon complex</li>
<li><code class="docutils literal"><span class="pre">'HeKr'</span></code> 18-point dissociation curve for helium-krypton complex</li>
<li><code class="docutils literal"><span class="pre">'NeNe'</span></code> 18-point dissociation curve for neon dimer</li>
<li><code class="docutils literal"><span class="pre">'NeAr'</span></code> 18-point dissociation curve for neon-argon complex</li>
<li><code class="docutils literal"><span class="pre">'NeKr'</span></code> 18-point dissociation curve for neon-krypton complex</li>
<li><code class="docutils literal"><span class="pre">'ArAr'</span></code> 18-point dissociation curve for argon dimer</li>
<li><code class="docutils literal"><span class="pre">'ArKr'</span></code> 18-point dissociation curve for argon-krypton complex</li>
<li><code class="docutils literal"><span class="pre">'KrKr'</span></code> 18-point dissociation curve for krypton dimer</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-S22">
<span id="s22"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/S22.py">S22</a><a class="headerlink" href="#module-S22" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for bimolecular complexes.</div>
<div class="line">Geometries from Jurecka et al. PCCP 8 1985 (2006).</div>
<div class="line">First revision to interaction energies (S22A) from Takatani et al. JCP 132 144104 (2010).</div>
<div class="line">Second revision to interaction energies (S22B) from Marshall et al. JCP 135 194102 (2011).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'S220'</span></code> Jurecka et al. PCCP 8 1985 (2006).</li>
<li><code class="docutils literal"><span class="pre">'S22A'</span></code> Takatani et al. JCP 132 144104 (2010).</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'S22B'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> Marshall et al. JCP 135 194102 (2011).</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> water dimer, methane dimer, ethene-ethine</li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> adenine-thymine</li>
<li><code class="docutils literal"><span class="pre">'HB'</span></code> hydrogen-bonded systems</li>
<li><code class="docutils literal"><span class="pre">'MX'</span></code> mixed-influence systems</li>
<li><code class="docutils literal"><span class="pre">'DD'</span></code> dispersion-dominated systems</li>
<li><code class="docutils literal"><span class="pre">'S11'</span></code> smaller systems in S22</li>
<li><code class="docutils literal"><span class="pre">'WATER'</span></code> water dimer</li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-NHTBH">
<span id="nhtbh"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/NHTBH.py">NHTBH</a><a class="headerlink" href="#module-NHTBH" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Truhlar) of non-hydrogen-transfer barrier height reactions.</div>
<div class="line">Geometries and Reaction energies from Truhlar and coworkers at site <a class="reference external" href="http://t1.chem.umn.edu/misc/database_group/database_therm_bh/non_H.htm">http://t1.chem.umn.edu/misc/database_group/database_therm_bh/non_H.htm</a>.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-A24alt">
<span id="a24alt"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/A24alt.py">A24alt</a><a class="headerlink" href="#module-A24alt" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Hobza) of interaction energies for bimolecular complexes.</div>
<div class="line">Geometries from <Reference>.</div>
<div class="line">Reference interaction energies from Rezac and Hobza, JCTC (in press).</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code> <erase this comment and after unless on is a valid option> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code> <erase this comment and after unless on is valid option> || <code class="docutils literal"><span class="pre">'on'</span></code></li>
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'<benchmark_name>'</span></code> <Reference>.</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'<default_benchmark_name>'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> <Reference>.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'<subset>'</span></code> <members_description></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-HTBH">
<span id="htbh"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/HTBH.py">HTBH</a><a class="headerlink" href="#module-HTBH" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database (Truhlar) of hydrogen-transfer barrier height reactions.</div>
<div class="line">Geometries from Truhlar and coworkers at site <a class="reference external" href="http://t1.chem.umn.edu/misc/database_group/database_therm_bh/raw_geom.cgi">http://t1.chem.umn.edu/misc/database_group/database_therm_bh/raw_geom.cgi</a> .</div>
<div class="line">Reference energies from Zhao et al. JPCA, 109 2012-2018 (2005) doi: 10.1021/jp045141s [in supporting information].</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-BAKERJCC93">
<span id="bakerjcc93"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/BAKERJCC93.py">BAKERJCC93</a><a class="headerlink" href="#module-BAKERJCC93" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of molecules that are challenging to optimize.</div>
<div class="line">Geometries from Baker J. Comput. Chem. 14 1085 (1993), as reported
in Bakken and Helgaker, J. Chem. Phys. 117, 9160 (2002), with a few
further corrections.</div>
<div class="line">No reference energies defined.</div>
</div>
<ul class="simple">
<li><strong>cp</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>rlxd</strong> <code class="docutils literal"><span class="pre">'off'</span></code></li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code></li>
</ul>
</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="module-HTR40">
<span id="htr40"></span><h3><a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases/HTR40.py">HTR40</a><a class="headerlink" href="#module-HTR40" title="Permalink to this headline">¶</a></h3>
<div class="line-block">
<div class="line">Database of Hydrogen transfer reactions.</div>
<div class="line">Geometries from Bozkaya and Sherrill.</div>
<div class="line">Reference energies from Bozkaya and Sherrill.</div>
</div>
<ul class="simple">
<li><strong>benchmark</strong><ul>
<li><code class="docutils literal"><span class="pre">'<benchmark_name>'</span></code> <Reference>.</li>
<li><img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/> <code class="docutils literal"><span class="pre">'<default_benchmark_name>'</span></code> <img class="math" src="_images/math/589f0defd3f7d56ed5fb2872215af7ebba9db67a.png" alt="\Leftarrow" style="vertical-align: -1px"/> <Reference>.</li>
</ul>
</li>
<li><strong>subset</strong><ul>
<li><code class="docutils literal"><span class="pre">'small'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'large'</span></code> <members_description></li>
<li><code class="docutils literal"><span class="pre">'<subset>'</span></code> <members_description></li>
</ul>
</li>
</ul>
<hr class="docutils" />
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Database</a><ul>
<li><a class="reference internal" href="#output">Output</a></li>
<li><a class="reference internal" href="#available-databases">Available Databases</a><ul>
<li><a class="reference internal" href="#module-JSCH">JSCH</a></li>
<li><a class="reference internal" href="#module-S22by5">S22by5</a></li>
<li><a class="reference internal" href="#module-RSE42">RSE42</a></li>
<li><a class="reference internal" href="#module-HSG">HSG</a></li>
<li><a class="reference internal" href="#module-ACENES">ACENES</a></li>
<li><a class="reference internal" href="#module-S66">S66</a></li>
<li><a class="reference internal" href="#module-S66by8">S66by8</a></li>
<li><a class="reference internal" href="#module-HBC6">HBC6</a></li>
<li><a class="reference internal" href="#module-CORE">CORE</a></li>
<li><a class="reference internal" href="#module-NBC10">NBC10</a></li>
<li><a class="reference internal" href="#module-A24">A24</a></li>
<li><a class="reference internal" href="#module-BASIC">BASIC</a></li>
<li><a class="reference internal" href="#module-BAKERJCC96">BAKERJCC96</a></li>
<li><a class="reference internal" href="#module-BENCH12">BENCH12</a></li>
<li><a class="reference internal" href="#module-NCB31">NCB31</a></li>
<li><a class="reference internal" href="#module-RGC10">RGC10</a></li>
<li><a class="reference internal" href="#module-S22">S22</a></li>
<li><a class="reference internal" href="#module-NHTBH">NHTBH</a></li>
<li><a class="reference internal" href="#module-A24alt">A24alt</a></li>
<li><a class="reference internal" href="#module-HTBH">HTBH</a></li>
<li><a class="reference internal" href="#module-BAKERJCC93">BAKERJCC93</a></li>
<li><a class="reference internal" href="#module-HTR40">HTR40</a></li>
</ul>
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