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