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<li><a class="reference internal" href="#">fix qbmsst command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
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<div class="section" id="fix-qbmsst-command">
<span id="index-0"></span><h1>fix qbmsst command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">qbmsst</span> <span class="nb">dir</span> <span class="n">shockvel</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>qbmsst = style name of this fix</li>
<li>dir = <em>x</em> or <em>y</em> or <em>z</em></li>
<li>shockvel = shock velocity (strictly positive, velocity units)</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>q</em> or <em>mu</em> or <em>p0</em> or <em>v0</em> or <em>e0</em> or <em>tscale</em> or <em>damp</em> or <em>seed</em>or <em>f_max</em> or <em>N_f</em> or <em>eta</em> or <em>beta</em> or <em>T_init</em></li>
</ul>
<pre class="literal-block">
<em>q</em> value = cell mass-like parameter (mass^2/distance^4 units)
<em>mu</em> value = artificial viscosity (mass/distance/time units)
<em>p0</em> value = initial pressure in the shock equations (pressure units)
<em>v0</em> value = initial simulation cell volume in the shock equations (distance^3 units)
<em>e0</em> value = initial total energy (energy units)
<em>tscale</em> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
<em>damp</em> value = damping parameter (time units) inverse of friction &lt;i&gt;&amp;gamma;&lt;/i&gt;
<em>seed</em> value = random number seed (positive integer)
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
<em>N_f</em> value = number of frequency bins (positive integer)
<em>eta</em> value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
<em>beta</em> value = the quantum temperature is updated every beta time steps (positive integer)
<em>T_init</em> value = quantum temperature for the initial state (temperature units)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qbmsst</span> <span class="n">z</span> <span class="mf">0.122</span> <span class="n">q</span> <span class="mi">25</span> <span class="n">mu</span> <span class="mf">0.9</span> <span class="n">tscale</span> <span class="mf">0.01</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mi">1</span> <span class="n">beta</span> <span class="mi">400</span> <span class="n">T_init</span> <span class="mi">110</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qbmsst</span> <span class="n">z</span> <span class="mi">72</span> <span class="n">q</span> <span class="mi">40</span> <span class="n">tscale</span> <span class="mf">0.05</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mf">1.0</span> <span class="n">beta</span> <span class="mi">500</span> <span class="n">T_init</span> <span class="mi">300</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
</pre></div>
</div>
<p>Two example input scripts are given, including shocked alpha quartz
and shocked liquid methane. The input script first equilibrate an
initial state with the quantum thermal bath at the target temperature
and then apply the qbmsst to simulate shock compression with quantum
nuclear correction. The following two figures plot related quantities
for shocked alpha quartz.</p>
<img alt="_images/qbmsst_init.jpg" class="align-center" src="_images/qbmsst_init.jpg" />
<p>Figure 1. Classical temperature &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; = &amp;sum;
&lt;i&gt;m&lt;sub&gt;i&lt;/sub&gt;v&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;2&lt;/sup&gt;/3Nk&lt;/i&gt;&lt;sub&gt;B&lt;/sub&gt; vs. time
for coupling the alpha quartz initial state with the quantum thermal
bath at target quantum temperature &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;qm&lt;/sup&gt; = 300 K. The
NpH ensemble is used for time integration while QTB provides the
colored random force. &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; converges at the timescale
of <em>damp</em> which is set to be 1 ps.</p>
<img alt="_images/qbmsst_shock.jpg" class="align-center" src="_images/qbmsst_shock.jpg" />
<p>Figure 2. Quantum temperature and pressure vs. time for simulating
shocked alpha quartz with the QBMSST. The shock propagates along the z
direction. Restart of the QBMSST command is demonstrated in the
example input script. Thermodynamic quantities stay continuous before
and after the restart.</p>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This command performs the Quantum-Bath coupled Multi-Scale Shock
Technique (QBMSST) integration. See <a class="reference internal" href="#qi"><span class="std std-ref">(Qi)</span></a> for a detailed
description of this method. The QBMSST provides description of the
thermodynamics and kinetics of shock processes while incorporating
quantum nuclear effects. The <em>shockvel</em> setting determines the steady
shock velocity that will be simulated along direction <em>dir</em>.</p>
<p>Quantum nuclear effects <a class="reference internal" href="fix_qtb.html"><span class="doc">(fix qtb)</span></a> can be crucial
especially when the temperature of the initial state is below the
classical limit or there is a great change in the zero point energies
between the initial and final states. Theoretical post processing
quantum corrections of shock compressed water and methane have been
reported as much as 30% of the temperatures <a class="reference internal" href="#goldman"><span class="std std-ref">(Goldman)</span></a>. A
self-consistent method that couples the shock to a quantum thermal
bath described by a colored noise Langevin thermostat has been
developed by Qi et al <a class="reference internal" href="#qi"><span class="std std-ref">(Qi)</span></a> and applied to shocked methane. The
onset of chemistry is reported to be at a pressure on the shock
Hugoniot that is 40% lower than observed with classical molecular
dynamics.</p>
<p>It is highly recommended that the system be already in an equilibrium
state with a quantum thermal bath at temperature of <em>T_init</em>. The fix
command <a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a> at constant temperature <em>T_init</em> could
be used before applying this command to introduce self-consistent
quantum nuclear effects into the initial state.</p>
<p>The parameters <em>q</em>, <em>mu</em>, <em>e0</em>, <em>p0</em>, <em>v0</em> and <em>tscale</em> are described
in the command <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a>. The values of <em>e0</em>, <em>p0</em>, or
<em>v0</em> will be calculated on the first step if not specified. The
parameter of <em>damp</em>, <em>f_max</em>, and <em>N_f</em> are described in the command
<a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a>.</p>
<p>The fix qbmsst command couples the shock system to a quantum thermal
bath with a rate that is proportional to the change of the total
energy of the shock system, &lt;i&gt;etot&lt;/i&gt; - &lt;i&gt;etot&lt;/i&gt;&lt;sub&gt;0&lt;/sub&gt;.
Here &lt;i&gt;etot&lt;/i&gt; consists of both the system energy and a thermal
term, see <a class="reference internal" href="#qi"><span class="std std-ref">(Qi)</span></a>, and &lt;i&gt;etot&lt;/i&gt;&lt;sub&gt;0&lt;/sub&gt; = <em>e0</em> is the
initial total energy.</p>
<p>The <em>eta</em> (&lt;i&gt;&amp;eta;&lt;/i&gt;) parameter is a unitless coupling constant
between the shock system and the quantum thermal bath. A small <em>eta</em>
value cannot adjust the quantum temperature fast enough during the
temperature ramping period of shock compression while large <em>eta</em>
leads to big temperature oscillation. A value of <em>eta</em> between 0.3 and
1 is usually appropriate for simulating most systems under shock
compression. We observe that different values of <em>eta</em> lead to almost
the same final thermodynamic state behind the shock, as expected.</p>
<p>The quantum temperature is updated every <em>beta</em> (&lt;i&gt;&amp;beta;&lt;/i&gt;) steps
with an integration time interval <em>beta</em> times longer than the
simulation time step. In that case, &lt;i&gt;etot&lt;/i&gt; is taken as its
average over the past <em>beta</em> steps. The temperature of the quantum
thermal bath &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;qm&lt;/sup&gt; changes dynamically according to
the following equation where &amp;Delta;&lt;i&gt;t&lt;/i&gt; is the MD time step and
&lt;i&gt;&amp;gamma;&lt;/i&gt; is the friction constant which is equal to the inverse
of the <em>damp</em> parameter.</p>
<center><font size="4"> <i>dT</i><sup>qm</sup>/<i>dt =
&gamma;&eta;</i>&sum;<i><sup>&beta;</sup><sub>l =
1</sub></i>[<i>etot</i>(<i>t-l</i>&Delta;<i>t</i>)-<i>etot</i><sub>0</sub>]/<i>3&beta;Nk</i><sub>B</sub>
</font></center><p>The parameter <em>T_init</em> is the initial temperature of the quantum
thermal bath and the system before shock loading.</p>
<p>For all pressure styles, the simulation box stays orthorhombic in
shape. Parrinello-Rahman boundary conditions (tilted box) are
supported by LAMMPS, but are not implemented for QBMSST.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Because the state of the random number generator is not written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, this fix cannot be restarted
&#8220;exactly&#8221; in an uninterrupted fashion. However, in a statistical
sense, a restarted simulation should produce similar behaviors of the
system as if it is not interrupted. To achieve such a restart, one
should write explicitly the same value for <em>q</em>, <em>mu</em>, <em>damp</em>, <em>f_max</em>,
<em>N_f</em>, <em>eta</em>, and <em>beta</em> and set <em>tscale</em> = 0 if the system is
compressed during the first run.</p>
<p>The progress of the QBMSST can be monitored by printing the global
scalar and global vector quantities computed by the fix. The global
vector contains five values in this order:</p>
<p>[<em>dhugoniot</em>, <em>drayleigh</em>, <em>lagrangian_speed</em>, <em>lagrangian_position</em>,
<em>quantum_temperature</em>]</p>
<ol class="arabic simple">
<li><em>dhugoniot</em> is the departure from the Hugoniot (temperature units).</li>
<li><em>drayleigh</em> is the departure from the Rayleigh line (pressure units).</li>
<li><em>lagrangian_speed</em> is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).</li>
<li><em>lagrangian_position</em> is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front.</li>
<li><em>quantum_temperature</em> is the temperature of the quantum thermal bath &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;qm&lt;/sup&gt;.</li>
</ol>
<p>To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested. Here the
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> energy command is also enabled to allow
the thermo keyword <em>etotal</em> to print the quantity &lt;i&gt;etot&lt;/i&gt;. See
also the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fix_id</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
<span class="n">fix_modify</span> <span class="n">fix_id</span> <span class="n">energy</span> <span class="n">yes</span>
<span class="n">variable</span> <span class="n">dhug</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">dray</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">T_qm</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">v_T_qm</span> <span class="n">f_fix_id</span>
</pre></div>
</div>
<p>The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of &lt;i&gt;etot&lt;/i&gt;. This global scalar and the
vector of 5 quantities can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. It is worth noting that the
temp keyword under the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command print
the instantaneous classical temperature &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; as
described in the command <a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix style is part of the USER-QTB package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The QBMSST fix has been tested only for the group-ID
all.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_qtb.html"><span class="doc">fix qtb</span></a>, <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a></p>
</div>
<hr class="docutils" />
<div class="section" id="default">
<h2>Default</h2>
<p>The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed
= 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and
T_init=300.0. e0, p0, and v0 are calculated on the first step.</p>
<hr class="docutils" />
<p id="goldman"><strong>(Goldman)</strong> Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)</p>
<p id="qi"><strong>(Qi)</strong> Qi and Reed, J. Phys. Chem. A 116, 10451 (2012).</p>
</div>
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