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<title>Description — BAGEL Manual</title>
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<div class="section" id="description">
<span id="dimer"></span><h1>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h1>
<p>The constructor of dimer molecule. The dimer fragments can either be covalently linked or not. The active subspaces should be well separated.</p>
</div>
<div class="section" id="keywords">
<h1>Keywords<a class="headerlink" href="#keywords" title="Permalink to this headline">¶</a></h1>
<div class="section" id="common-keywords">
<h2>Common keywords<a class="headerlink" href="#common-keywords" title="Permalink to this headline">¶</a></h2>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">dimerize</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Set <code class="docutils literal notranslate"><span class="pre">title</span></code> to <code class="docutils literal notranslate"><span class="pre">dimerize</span></code> to start constructing dimer.</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">form</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Whether the dimer fragments are covalently linked.</div>
<div class="line"><strong>Datatype:</strong> string</div>
<div class="line"><strong>Value:</strong></div>
<div class="line-block">
<div class="line"><code class="docutils literal notranslate"><span class="pre">linked</span></code>: covalently linked dimer</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">displace</span></code>: separated fragments</div>
</div>
<div class="line"><strong>Default:</strong> displace</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">dimer_active</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong></div>
<div class="line-block">
<div class="line">for non-covalently linked dimer: specify monomer active orbitals,</div>
<div class="line">for covalently linked dimer: specify dimer active orbitals.</div>
</div>
<div class="line"><strong>Datatype:</strong> set<int></div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">hf</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Dimer restricted Hartree-Fock calculation options.</div>
<div class="line"><strong>Default:</strong> use the same options as monomer <a class="reference internal" href="../scf/hf.html#hf"><span class="std std-ref">Hartree–Fock</span></a> calculations</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">localization</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Localize dimer molecular orbitals.</div>
<div class="line"><strong>Default:</strong> use default <a class="reference internal" href="../miscellaneous/localization.html#localization"><span class="std std-ref">Orbital localization</span></a></div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">active_thresh</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Threshold overlap for obitals to be treated as active.</div>
<div class="line"><strong>Datatype:</strong> double</div>
<div class="line"><strong>Default:</strong> 0.5</div>
</div>
</div>
</div>
<div class="section" id="keywords-for-non-covalently-linked-dimer">
<h2>Keywords for non-covalently linked dimer<a class="headerlink" href="#keywords-for-non-covalently-linked-dimer" title="Permalink to this headline">¶</a></h2>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">translate</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Spatial distance in Cartesian coordinates, duplicate and translate one monomer to form the dimer.</div>
<div class="line"><strong>Datatype:</strong> array<double, 3></div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">angstrom</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Whether the translation is in a.u. or angstrom.</div>
<div class="line"><strong>Datatype:</strong> bool</div>
<div class="line"><strong>Default:</strong> false</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">scheme</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Options to assign dimer active orbitals.</div>
<div class="line"><strong>Datatype:</strong> string</div>
<div class="line"><strong>Values:</strong></div>
<div class="line-block">
<div class="line"><code class="docutils literal notranslate"><span class="pre">active_first</span></code>: pick active space from dimer orbitals first, then attempt to localize</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">localize_first</span></code>: localize dimer orbitals, then pick the active space within each fragment</div>
</div>
<div class="line"><strong>Default:</strong> active_first</div>
</div>
</div>
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<div class="section" id="keywords-for-covalently-linked-dimer">
<h2>Keywords for covalently linked dimer<a class="headerlink" href="#keywords-for-covalently-linked-dimer" title="Permalink to this headline">¶</a></h2>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">region_sizes</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Number of atoms in three regions [left, bridge, right].</div>
<div class="line"><strong>Datatype:</strong> vector<int></div>
</div>
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<div class="section" id="prerequisite">
<h1>Prerequisite<a class="headerlink" href="#prerequisite" title="Permalink to this headline">¶</a></h1>
<p><a class="reference internal" href="../scf/hf.html#hf"><span class="std std-ref">Hartree–Fock</span></a> calculations are needed to obtain fragment molecular orbitals.</p>
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<li class="toctree-l1 current"><a class="reference internal" href="../user-manual.html"><strong>BAGEL user manual</strong></a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../quickstart/quickstart.html">First steps with BAGEL</a></li>
<li class="toctree-l2"><a class="reference internal" href="../molecule/molecule-toc.html">Molecule specification</a></li>
<li class="toctree-l2"><a class="reference internal" href="../scf/scf.html">Self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../ci/ci_methods.html">Configuration interaction</a></li>
<li class="toctree-l2"><a class="reference internal" href="../multi/multi.html">Multiconfiguration self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../pt2/pt2.html">Perturbation theory</a></li>
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<li class="toctree-l2"><a class="reference internal" href="../grad/grad.html">Nuclear gradients and related functionalities</a></li>
<li class="toctree-l2 current"><a class="reference internal" href="asd.html">Active space decomposition method</a></li>
<li class="toctree-l2"><a class="reference internal" href="../miscellaneous/misc.html">Miscellaneous features</a></li>
<li class="toctree-l2"><a class="reference internal" href="../supp_info/supp_info.html">Supplementary information</a></li>
<li class="toctree-l2"><a class="reference internal" href="../author.html">Author contributions</a></li>
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