forked from lijiext/lammps
273 lines
12 KiB
Plaintext
273 lines
12 KiB
Plaintext
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix langevin/drude command :h3
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[Syntax:]
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fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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langevin/drude = style name of this fix command :l
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Tcom = desired temperature of the centers of mass (temperature units) :l
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damp_com = damping parameter for the thermostat on centers of mass (time units) :l
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seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) :l
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Tdrude = desired temperature of the Drude oscillators (temperature units) :l
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damp_drude = damping parameter for the thermostat on Drude oscillators (time units) :l
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seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {zero} :l
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{zero} value = {no} or {yes}
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{no} = do not set total random force on centers of mass to zero
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{yes} = set total random force on centers of mass to zero :pre
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:ule
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[Examples:]
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fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
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fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre
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[Description:]
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Apply two Langevin thermostats as described in "(Jiang)"_#Jiang for
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thermalizing the reduced degrees of freedom of Drude oscillators.
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This link describes how to use the "thermalized Drude oscillator
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model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
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are discussed in "this Section"_Section_howto.html#howto_25.
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Drude oscillators are a way to simulate polarizables atoms, by
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splitting them into a core and a Drude particle bound by a harmonic
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bond. The thermalization works by transforming the particles degrees
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of freedom by these equations. In these equations upper case denotes
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atomic or center of mass values and lower case denotes Drude particle
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or dipole values. Primes denote the transformed (reduced) values,
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while bare letters denote the original values.
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Velocities:
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\begin\{equation\} V' = \frac \{M\, V + m\, v\} \{M'\} \end\{equation\}
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\begin\{equation\} v' = v - V \end\{equation\}
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Masses:
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\begin\{equation\} M' = M + m \end\{equation\}
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\begin\{equation\} m' = \frac \{M\, m \} \{M'\} \end\{equation\}
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The Langevin forces are computed as
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\begin\{equation\} F' = - \frac \{M'\} \{\mathtt\{damp\_com\}\}\, V' + F_r' \end\{equation\}
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\begin\{equation\} f' = - \frac \{m'\} \{\mathtt\{damp\_drude\}\}\, v' + f_r' \end\{equation\}
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\(F_r'\) is a random force proportional to
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\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
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\{\mathrm dt\, \mathtt\{damp\_com\} \}
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\} \). :b
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\(f_r'\) is a random force proportional to
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\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
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\{\mathrm dt\, \mathtt\{damp\_drude\} \}
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\} \). :b
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Then the real forces acting on the particles are computed from the inverse
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transform:
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\begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}
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\begin\{equation\} f = \frac m \{M'\}\, F' + f' \end\{equation\}
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This fix also thermostates non-polarizable atoms in the group at
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temperature {Tcom}, as if they had a massless Drude partner. The
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Drude particles themselves need not be in the group. The center of
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mass and the dipole are thermostated iff the core atom is in the
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group.
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Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom of the particles, which is an
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important consideration if finite-size particles, which have
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rotational degrees of freedom, are being thermostated. The
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translational degrees of freedom can also have a bias velocity removed
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from them before thermostating takes place; see the description below.
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NOTE: Like the "fix langevin"_fix_langevin.html command, this fix does
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NOT perform time integration. It only modifies forces to effect
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thermostating. Thus you must use a separate time integration fix, like
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"fix nve"_fix_nve.html or "fix nph"_fix_nh.html to actually update the
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velocities and positions of atoms using the modified forces.
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Likewise, this fix should not normally be used on atoms that also have
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their temperature controlled by another fix - e.g. by "fix
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nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands.
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See "this howto section"_Section_howto.html#howto_16 of the manual for
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a discussion of different ways to compute temperature and perform
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thermostating.
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:line
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This fix requires each atom know whether it is a Drude particle or
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not. You must therefore use the "fix drude"_fix_drude.html command to
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specify the Drude status of each atom type.
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NOTE: only the Drude core atoms need to be in the group specified for
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this fix. A Drude electron will be transformed together with its cores
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even if it is not itself in the group. It is safe to include Drude
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electrons or non-polarizable atoms in the group. The non-polarizable
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atoms will simply be thermostatted as if they had a massless Drude
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partner (electron).
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NOTE: Ghost atoms need to know their velocity for this fix to act
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correctly. You must use the "comm_modify"_comm_modify.html command to
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enable this, e.g.
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comm_modify vel yes :pre
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:line
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{Tcom} is the target temperature of the centers of mass, which would
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be used to thermostate the non-polarizable atoms. {Tdrude} is the
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(normally low) target temperature of the core-Drude particle pairs
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(dipoles). {Tcom} and {Tdrude} can be specified as an equal-style
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"variable"_variable.html. If the value is a variable, it should be
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specified as v_name, where name is the variable name. In this case,
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the variable will be evaluated each timestep, and its value used to
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determine the target temperature.
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Equal-style variables can specify formulas with various mathematical
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functions, and include "thermo_style"_thermo_style.html command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.
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Like other fixes that perform thermostating, this fix can be used with
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"compute commands"_compute.html that remove a "bias" from the atom
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velocities. E.g. removing the center-of-mass velocity from a group of
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atoms. This is not done by default, but only if the
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"fix_modify"_fix_modify.html command is used to assign a temperature
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compute to this fix that includes such a bias term. See the doc pages
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for individual "compute commands"_compute.html to determine which ones
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include a bias. In this case, the thermostat works in the following
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manner: bias is removed from each atom, thermostating is performed on
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the remaining thermal degrees of freedom, and the bias is added back
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in. NOTE: this feature has not been tested.
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Note: The temperature thermostating the core-Drude particle pairs
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should be chosen low enough, so as to mimic as closely as possible the
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self-consistent minimization. It must however be high enough, so that
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the dipoles can follow the local electric field exerted by the
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neighbouring atoms. The optimal value probably depends on the
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temperature of the centers of mass and on the mass of the Drude
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particles.
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{damp_com} is the characteristic time for reaching thermal equilibrium
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of the centers of mass. For example, a value of 100.0 means to relax
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the temperature of the centers of mass in a timespan of (roughly) 100
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time units (tau or fmsec or psec - see the "units"_units.html
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command). {damp_drude} is the characteristic time for reaching
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thermal equilibrium of the dipoles. It is typically a few timesteps.
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The number {seed_com} and {seed_drude} are positive integers. They set
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the seeds of the Marsaglia random number generators used for
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generating the random forces on centers of mass and on the
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dipoles. Each processor uses the input seed to generate its own unique
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seed and its own stream of random numbers. Thus the dynamics of the
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system will not be identical on two runs on different numbers of
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processors.
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The keyword {zero} can be used to eliminate drift due to the
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thermostat on centers of mass. Because the random forces on different
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centers of mass are independent, they do not sum exactly to zero. As
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a result, this fix applies a small random force to the entire system,
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and the momentum of the total center of mass of the system undergoes a
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slow random walk. If the keyword {zero} is set to {yes}, the total
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random force on the centers of mass is set exactly to zero by
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subtracting off an equal part of it from each center of mass in the
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group. As a result, the total center of mass of a system with zero
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initial momentum will not drift over time.
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The actual temperatures of cores and Drude particles, in
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center-of-mass and relative coordinates, respectively, can be
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calculated using the "compute temp/drude"_compute_temp_drude.html
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command.
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:line
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Usage example for rigid bodies in the NPT ensemble:
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comm_modify vel yes
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fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
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fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
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fix NVE DRUDES nve
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compute TDRUDE all temp/drude
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thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE\[1\] c_TDRUDE\[2\] :pre
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Comments:
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Drude particles should not be in the rigid group, otherwise the Drude
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oscillators will be frozen and the system will lose its
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polarizability. :ulb,l
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{zero yes} avoids a drift of the center of mass of
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the system, but is a bit slower. :l
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Use two different random seeds to avoid unphysical correlations. :l
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Temperature is controlled by the fix {langevin/drude}, so the
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time-integration fixes do not thermostate. Don't forget to
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time-integrate both cores and Drude particles. :l
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Pressure is time-integrated only once by using {nve} for Drude
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particles and {nph} for atoms/cores (or vice versa). Do not use {nph}
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for both. :l
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The temperatures of cores and Drude particles are calculated by
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"compute temp/drude"_compute_temp_drude.html :l
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Contrary to the alternative thermostating using Nose-Hoover thermostat
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fix {npt} and "fix drude/transform"_fix_drude_transform.html, the
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{fix_modify} command is not required here, because the fix {nph}
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computes the global pressure even if its group is {ATOMS}. This is
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what we want. If we thermostated {ATOMS} using {npt}, the pressure
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should be the global one, but the temperature should be only that of
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the cores. That's why the command {fix_modify} should be called in
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that case. :l,ule
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. Because the state of the random number generator
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is not saved in restart files, this means you cannot do "exact"
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restarts with this fix, where the simulation continues on the same as
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if no restart had taken place. However, in a statistical sense, a
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restarted simulation should produce the same behavior.
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The "fix_modify"_fix_modify.html {temp} option is supported by this
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fix. You can use it to assign a temperature "compute"_compute.html
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you have defined to this fix which will be used in its thermostating
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procedure, as described above. For consistency, the group used by the
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compute should include the group of this fix and the Drude particles.
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This fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:] none
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[Related commands:]
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"fix langevin"_fix_langevin.html,
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"fix drude"_fix_drude.html,
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"fix drude/transform"_fix_drude_transform.html,
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"compute temp/drude"_compute_temp_drude.html,
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"pair_style thole"_pair_thole.html
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[Default:]
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The option defaults are zero = no.
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:line
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:link(Jiang)
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[(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
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Phys Chem Lett, 2, 87-92 (2011).
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