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<div class="section" id="interface-to-dynamics-codes">
<span id="dynamics"></span><h1>Interface to dynamics codes<a class="headerlink" href="#interface-to-dynamics-codes" title="Permalink to this headline">¶</a></h1>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>BAGEL can be used for performing QM/MM calculations and direct dynamics simulations, by interfacing it to external software.
The “electrostatic embedding” scheme is used in inserting the QM region in MM region. BAGEL exports the gradients of the energy with respect
to the displacements of the QM particles and MM particles in a form that can be directly read by the dynamics codes.</p>
<div class="section" id="how-it-works">
<h3>How It Works<a class="headerlink" href="#how-it-works" title="Permalink to this headline">¶</a></h3>
<p>The communications between the quantum chemistry codes and the molecular dynamics codes are based on the text files.
For example, in molecular dynamics (MD) jobs, after the trajectory initiates, the positions of the QM atoms and MM particles,
and the charges of MM particles are passed into BAGEL, in a form of text input.
The quantum chemical calculation is performed to calculate any needed quantities
(such as energies, its gradients, and NACMEs for nonadiabatic dynamics). This is passed (exported) to the form that can be
read by the dynamics program, and the dynamics program propagates the trajectory according to these gradients. After a
one time integration step, the positions of QM atoms and MM particles are again passed into BAGEL.
This continues until the trajectory integration ends.</p>
<p>In summary, to perform the dynamics simulations with external programs one needs:</p>
<ol class="arabic simple">
<li>quantum chemistry input writer in the dynamics program</li>
<li>quantum chemistry information output writer in the quantum chemistry program</li>
<li>quantum chemistry output parser in the dynamics program</li>
</ol>
<ol class="arabic simple" start="2">
<li>is included in BAGEL (with a keyword of <code class="docutils literal"><span class="pre">export</span></code> and <code class="docutils literal"><span class="pre">export_single</span></code>); the users should insert (1) and (3) in the dynamics code.</li>
</ol>
</div>
<div class="section" id="input-format">
<h3>Input Format<a class="headerlink" href="#input-format" title="Permalink to this headline">¶</a></h3>
<p>The BAGEL input for QM/MM jobs is same to that used in the quantum chemistry, except for the external charges.
The external MM charge can be added in BAGEL calculation, as</p>
<div class="highlight-javascript"><div class="highlight"><pre><span></span><span class="p">{</span> <span class="s2">"atom"</span> <span class="o">:</span> <span class="s2">"Q"</span><span class="p">,</span> <span class="s2">"xyz"</span> <span class="o">:</span> <span class="p">[</span> <span class="o">%</span><span class="nx">lf</span><span class="p">,</span> <span class="o">%</span><span class="nx">lf</span><span class="p">,</span> <span class="o">%</span><span class="nx">lf</span> <span class="p">],</span> <span class="s2">"charge"</span> <span class="o">:</span> <span class="o">%</span><span class="nx">lf</span> <span class="p">}</span>
</pre></div>
</div>
<p>where <code class="docutils literal"><span class="pre">xyz</span></code> has the positions, and <code class="docutils literal"><span class="pre">charge</span></code> has the charge on the MM particle (in the units of e).</p>
</div>
<div class="section" id="export-format">
<h3>Export Format<a class="headerlink" href="#export-format" title="Permalink to this headline">¶</a></h3>
<p>Some of dynamics software reads the informations in a fixed form. The gradient export format is as follows.
The name of the file exported is <code class="docutils literal"><span class="pre">ENERGY.txt</span></code> (energy), <code class="docutils literal"><span class="pre">FORCE_%d.txt</span></code> (gradient, %d is the number of the state)
and <code class="docutils literal"><span class="pre">NACME_%d_%d.txt</span></code> (derivative coupling). The gradient is written in <code class="docutils literal"><span class="pre">FORCE.txt</span></code> when <code class="docutils literal"><span class="pre">export_single</span></code> is <code class="docutils literal"><span class="pre">true</span></code>.</p>
<div class="highlight-cpp"><div class="highlight"><pre><span></span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">2</span>
<span class="o">%</span><span class="mi">6</span><span class="n">d</span> <span class="o">%</span><span class="mf">20.10</span><span class="n">lf</span> <span class="o">%</span><span class="mf">20.10</span><span class="n">lf</span> <span class="o">%</span><span class="mf">20.10</span><span class="n">lf</span>
<span class="c1">//(atomno) (X component) (Y component) (Z component)</span>
</pre></div>
</div>
<p>Note that the QM and MM atoms is not distinguished to each other in the exported output.
The exported gradients and nonadiabatic couplings are in the units of Hartrees/bohr and 1/bohr.
The energy is also exported, as</p>
<div class="highlight-cpp"><div class="highlight"><pre><span></span> <span class="o">%</span><span class="mf">20.10</span><span class="n">lf</span>
<span class="c1">// (statewise energy)</span>
</pre></div>
</div>
<p>The energies for the multiple states in ascending order are exported in the same file when one does multi-state
calculations, such as SA-CASSCF and XMS-CASPT2.</p>
</div>
<div class="section" id="files-to-be-modified-in-dynamics-software">
<h3>Files to be Modified in Dynamics Software<a class="headerlink" href="#files-to-be-modified-in-dynamics-software" title="Permalink to this headline">¶</a></h3>
<p>Some source codes in the dynamics software should be modified. Many of the dynamics software in fact have QM/MM
interfaces to the other quantum chemistry software, and by modifying the existent interface, one can perform the
QM/MM dynamics or gas phase dynamics simulations. For instance, to perform QM/MM calculations in <code class="docutils literal"><span class="pre">GROMACS</span></code>, one should modify</p>
<p><code class="docutils literal"><span class="pre">src/gromacs/mdlib/qmmm.c</span></code>,</p>
<p>add a BAGEL interface code to</p>
<p><code class="docutils literal"><span class="pre">src/gromacs/mdlib/qm_bagel.c</span></code>.</p>
<p>This should contain the code for writing appropriately formatted input for BAGEL.
Additionally, include BAGEL for QM package for QM/MM in the CMake installation option in</p>
<p><code class="docutils literal"><span class="pre">CMakeLists.txt</span></code></p>
<p>(as of version 5.1.4).</p>
</div>
</div>
<div class="section" id="keywords">
<h2>Keywords<a class="headerlink" href="#keywords" title="Permalink to this headline">¶</a></h2>
<div class="topic">
<p class="topic-title first"><code class="docutils literal"><span class="pre">export</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> This option will export the nuclear gradient to a text file.</div>
<div class="line"><strong>Datatype:</strong> bool</div>
<div class="line"><strong>Values:</strong></div>
<div class="line-block">
<div class="line"><code class="docutils literal"><span class="pre">true</span></code>: Export file</div>
<div class="line"><code class="docutils literal"><span class="pre">false</span></code>: Do not export file</div>
</div>
<div class="line"><strong>Default:</strong> false</div>
<div class="line"><strong>Recommendation:</strong> Use <code class="docutils literal"><span class="pre">true</span></code>.</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal"><span class="pre">export_single</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> This option will export the nuclear gradient to a text file for a single state.</div>
<div class="line"><strong>Datatype:</strong> bool</div>
<div class="line"><strong>Values:</strong></div>
<div class="line-block">
<div class="line"><code class="docutils literal"><span class="pre">true</span></code>: Export file</div>
<div class="line"><code class="docutils literal"><span class="pre">false</span></code>: Do not export file</div>
</div>
<div class="line"><strong>Default:</strong> false</div>
<div class="line"><strong>Recommendation:</strong> Use <code class="docutils literal"><span class="pre">true</span></code> with single state dynamics / optimizations.</div>
</div>
</div>
</div>
<div class="section" id="example">
<h2>Example<a class="headerlink" href="#example" title="Permalink to this headline">¶</a></h2>
<div class="section" id="sample-input">
<h3>Sample input<a class="headerlink" href="#sample-input" title="Permalink to this headline">¶</a></h3>
<p>A sample input for HF molecule using CASSCF.
This input computes the nuclear gradient for states 0 and 1 as well as the derivative coupling vector between these two states:</p>
<div class="highlight-javascript"><div class="highlight"><pre><span></span><span class="p">{</span> <span class="s2">"bagel"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"molecule"</span><span class="p">,</span>
<span class="s2">"basis"</span> <span class="o">:</span> <span class="s2">"svp"</span><span class="p">,</span>
<span class="s2">"df_basis"</span> <span class="o">:</span> <span class="s2">"svp-jkfit"</span><span class="p">,</span>
<span class="s2">"angstrom"</span> <span class="o">:</span> <span class="kc">false</span><span class="p">,</span>
<span class="s2">"geometry"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">{</span> <span class="s2">"atom"</span> <span class="o">:</span> <span class="s2">"H"</span><span class="p">,</span> <span class="s2">"xyz"</span> <span class="o">:</span> <span class="p">[</span> <span class="o">-</span><span class="mf">0.000000</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.000000</span><span class="p">,</span> <span class="mf">1.700000</span><span class="p">]</span> <span class="p">},</span>
<span class="p">{</span> <span class="s2">"atom"</span> <span class="o">:</span> <span class="s2">"F"</span><span class="p">,</span> <span class="s2">"xyz"</span> <span class="o">:</span> <span class="p">[</span> <span class="o">-</span><span class="mf">0.000000</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.000000</span><span class="p">,</span> <span class="mf">0.000000</span><span class="p">]</span> <span class="p">}</span>
<span class="p">]</span>
<span class="p">},</span>
<span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"forces"</span><span class="p">,</span>
<span class="s2">"grads"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">{</span> <span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"force"</span><span class="p">,</span> <span class="s2">"target"</span> <span class="o">:</span> <span class="mi">0</span> <span class="p">},</span>
<span class="p">{</span> <span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"force"</span><span class="p">,</span> <span class="s2">"target"</span> <span class="o">:</span> <span class="mi">1</span> <span class="p">},</span>
<span class="p">{</span> <span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"nacme"</span><span class="p">,</span> <span class="s2">"target"</span> <span class="o">:</span> <span class="mi">0</span><span class="p">,</span> <span class="s2">"target2"</span> <span class="o">:</span> <span class="mi">1</span> <span class="p">}</span>
<span class="p">],</span>
<span class="s2">"export"</span> <span class="o">:</span> <span class="kc">true</span><span class="p">,</span>
<span class="s2">"method"</span> <span class="o">:</span> <span class="p">[</span> <span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"casscf"</span><span class="p">,</span>
<span class="s2">"nopen"</span> <span class="o">:</span> <span class="mi">0</span><span class="p">,</span>
<span class="s2">"nact"</span> <span class="o">:</span> <span class="mi">2</span><span class="p">,</span>
<span class="s2">"nclosed"</span> <span class="o">:</span> <span class="mi">4</span><span class="p">,</span>
<span class="s2">"nstate"</span> <span class="o">:</span> <span class="mi">2</span>
<span class="p">}</span> <span class="p">]</span>
<span class="p">}</span>
<span class="p">]}</span>
</pre></div>
</div>
<p>Executing BAGEL with this input will generate the following text files:</p>
</div>
<div class="section" id="energy-out">
<h3>ENERGY.out<a class="headerlink" href="#energy-out" title="Permalink to this headline">¶</a></h3>
<div class="highlight-none"><div class="highlight"><pre><span></span>-99.9135619715
-99.5339025461
</pre></div>
</div>
</div>
<div class="section" id="force-0-out">
<h3>FORCE_0.out<a class="headerlink" href="#force-0-out" title="Permalink to this headline">¶</a></h3>
<div class="highlight-none"><div class="highlight"><pre><span></span> 0 1 2
0 -0.0000000000 -0.0000000000 -0.0019342533
1 0.0000000000 0.0000000000 0.0019342533
</pre></div>
</div>
</div>
<div class="section" id="force-1-out">
<h3>FORCE_1.out<a class="headerlink" href="#force-1-out" title="Permalink to this headline">¶</a></h3>
<div class="highlight-none"><div class="highlight"><pre><span></span> 0 1 2
0 0.0000000000 0.0000000000 -0.2535235791
1 -0.0000000000 -0.0000000000 0.2535235791
</pre></div>
</div>
</div>
<div class="section" id="nacme-0-1-out">
<h3>NACME_0_1.out<a class="headerlink" href="#nacme-0-1-out" title="Permalink to this headline">¶</a></h3>
<div class="highlight-none"><div class="highlight"><pre><span></span> 0 1 2
0 -0.0355272749 -0.0991581135 0.0000000000
1 -0.0285426596 -0.0796637587 -0.0000000000
</pre></div>
</div>
</div>
</div>
<div class="section" id="references">
<h2>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h2>
<div class="section" id="general-references">
<h3>General References<a class="headerlink" href="#general-references" title="Permalink to this headline">¶</a></h3>
<table border="1" class="docutils">
<colgroup>
<col width="37%" />
<col width="63%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Description of Reference</th>
<th class="head">Reference</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Nonadiabatic dynamics (Surface hopping)</td>
<td>M. Barbatti, WIREs Comput. Mol. Sci. <strong>1</strong>, 620 (2011).</td>
</tr>
<tr class="row-odd"><td>Excited state QM/MM in biomolecules</td>
<td>E. Brunk and U. Rothlisburger, Chem. Rev. <strong>115</strong>, 6217 (2015).</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
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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>
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<li class="toctree-l2"><a class="reference internal" href="../ci/ci_methods.html">Configuration interaction</a></li>
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<li class="toctree-l2"><a class="reference internal" href="../smith/smith.html">SMITH3-generated code</a></li>
<li class="toctree-l2 current"><a class="reference internal" href="grad.html">Nuclear gradients and related functionalities</a></li>
<li class="toctree-l2"><a class="reference internal" href="../asd/asd.html">Active space decomposition method</a></li>
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<li class="toctree-l2"><a class="reference internal" href="../supp_info/supp_info.html">Supplementary information</a></li>
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