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< title > fix qbmsst command — LAMMPS documentation< / title >
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< span id = "index-0" > < / span > < h1 > fix qbmsst command< a class = "headerlink" href = "#fix-qbmsst-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID qbmsst dir shockvel keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / 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*or *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)
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< 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 < i> & gamma;< /i>
< 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)
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
< / pre > < / div >
< / div >
< 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
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
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for shocked alpha quartz.< / p >
< img alt = "_images/qbmsst_init.jpg" class = "align-center" src = "_images/qbmsst_init.jpg" / >
< p > Figure 1. Classical temperature < i> T< /i> < sup> cl< /sup> = & sum;
< 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
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
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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
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and after the restart.< / p >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This command performs the Quantum-Bath coupled Multi-Scale Shock
Technique (QBMSST) integration. See < a class = "reference internal" href = "#qi" > < span > (Qi)< / span > < / a > for a detailed
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description of this method. The QBMSST provides description of the
thermodynamics and kinetics of shock processes while incorporating
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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" > < em > (fix qtb)< / em > < / a > can be crucial
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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
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reported as much as 30% of the temperatures < a class = "reference internal" href = "#goldman" > < span > (Goldman)< / span > < / a > . A
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self-consistent method that couples the shock to a quantum thermal
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 > (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
Hugoniot that is 40% lower than observed with classical molecular
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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" > < em > fix qtb< / em > < / 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 >
< 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" > < em > fix msst< / em > < / 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" > < em > fix qtb< / em > < / a > .< / p >
< 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> .
Here < i> etot< /i> consists of both the system energy and a thermal
term, see < a class = "reference internal" href = "#qi" > < span > (Qi)< / span > < / a > , and < i> etot< /i> < sub> 0< /sub> = < em > e0< / em > is the
initial total energy.< / p >
< p > The < em > eta< / em > (< i> & eta;< /i> ) parameter is a unitless coupling constant
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 >
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
the same final thermodynamic state behind the shock, as expected.< / p >
< p > The quantum temperature is updated every < em > beta< / em > (< i> & beta;< /i> ) steps
with an integration time interval < em > beta< / em > times longer than the
simulation time step. In that case, < i> etot< /i> is taken as its
average over the past < em > beta< / em > steps. The temperature of the quantum
thermal bath < i> T< /i> < sup> qm< /sup> changes dynamically according to
the following equation where & Delta;< i> t< /i> is the MD time step and
< i> & gamma;< /i> is the friction constant which is equal to the inverse
of the < em > damp< / em > parameter.< / p >
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< center > < font size = "4" > < i > dT< / i > < sup > qm< / sup > /< i > dt =
γ η < / i > ∑ < i > < sup > β < / sup > < sub > l =
1< / sub > < / i > [< i > etot< / i > (< i > t-l< / i > Δ < i > t< / i > )-< i > etot< / i > < sub > 0< / sub > ]/< i > 3β Nk< / i > < sub > B< / sub >
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< / 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
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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 >
< / 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< a class = "headerlink" href = "#restart-fix-modify-output-run-start-stop-minimize-info" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Because the state of the random number generator is not written to
< a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > , this fix cannot be restarted
“ exactly” in an uninterrupted fashion. However, in a statistical
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sense, a restarted simulation should produce similar behaviors of the
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 > ,
< 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
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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 >
< 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 < i> T< /i> < sup> qm< /sup> .< / li >
< / ol >
< 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" > < em > fix_modify< / em > < / a > energy command is also enabled to allow
the thermo keyword < em > etotal< / em > to print the quantity < i> etot< /i> . See
also the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command.< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix fix_id all msst z
fix_modify fix_id energy yes
variable dhug equal f_fix_id[1]
variable dray equal f_fix_id[2]
variable lgr_vel equal f_fix_id[3]
variable lgr_pos equal f_fix_id[4]
variable T_qm equal f_fix_id[5]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
< / pre > < / div >
< / div >
< p > The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of < i> etot< /i> . 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 > output commands< / span > < / a > . It is worth noting that the
temp keyword under the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command print
the instantaneous classical temperature < i> T< /i> < sup> cl< /sup> as
described in the command < a class = "reference internal" href = "fix_qtb.html" > < em > fix qtb< / em > < / a > .< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / 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 < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< 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 >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "fix_qtb.html" > < em > fix qtb< / em > < / a > , < a class = "reference internal" href = "fix_msst.html" > < em > fix msst< / em > < / a > < / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed
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= 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 >
< / div >
< / div >
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< / div >
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< script type = "text/javascript" >
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
< / script >
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< / body >
< / html >
