forked from lijiext/lammps
156 lines
6.5 KiB
Plaintext
156 lines
6.5 KiB
Plaintext
"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 gld command :h3
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[Syntax:]
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fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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gld = style name of this fix command :l
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Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
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N_k = number of terms in the Prony series representation of the memory kernel :l
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seed = random number seed to use for white noise (positive integer) :l
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series = {pprony} is presently the only available option :l
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c_k = the weight of the kth term in the Prony series (mass per time units) :l
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tau_k = the time constant of the kth term in the Prony series (time units) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {frozen} or {zero}
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{frozen} value = {no} or {yes}
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{no} = initialize extended variables using values drawn from equilibrium distribution at Tstart
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{yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
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{zero} value = {no} or {yes}
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{no} = do not set total random force to zero
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{yes} = set total random force to zero :pre
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:ule
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[Examples:]
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fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes
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fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643 :pre
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[Description:]
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Applies Generalized Langevin Dynamics to a group of atoms, as
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described in "(Baczewski)"_#Baczewski. This is intended to model the
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effect of an implicit solvent with a temporally non-local dissipative
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force and a colored Gaussian random force, consistent with the
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Fluctuation-Dissipation Theorem. The functional form of the memory
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kernel associated with the temporally non-local force is constrained
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to be a Prony series.
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NOTE: While this fix bears many similarities to "fix
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langevin"_fix_langevin.html, it has one significant
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difference. Namely, "fix gld"_fix_gld.html performs time integration,
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whereas "fix langevin"_fix_langevin.html does NOT. To this end, the
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specification of another fix to perform time integration, such as "fix
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nve"_fix_nve.html, is NOT necessary.
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With this fix active, the force on the {j}th atom is given as
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:c,image(Eqs/fix_gld1.jpg)
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Here, the first term is representative of all conservative (pairwise,
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bonded, etc) forces external to this fix, the second is the temporally
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non-local dissipative force given as a Prony series, and the third is
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the colored Gaussian random force.
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The Prony series form of the memory kernel is chosen to enable an
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extended variable formalism, with a number of exemplary mathematical
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features discussed in "(Baczewski)"_#Baczewski. In particular, 3N_k
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extended variables are added to each atom, which effect the action of
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the memory kernel without having to explicitly evaluate the integral
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over time in the second term of the force. This also has the benefit
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of requiring the generation of uncorrelated random forces, rather than
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correlated random forces as specified in the third term of the force.
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Presently, the Prony series coefficients are limited to being greater
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than or equal to zero, and the time constants are limited to being
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greater than zero. To this end, the value of series MUST be set to
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{pprony}, for now. Future updates will allow for negative coefficients
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and other representations of the memory kernel. It is with these
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updates in mind that the series option was included.
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The units of the Prony series coefficients are chosen to be mass per
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time to ensure that the numerical integration scheme stably approaches
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the Newtonian and Langevin limits. Details of these limits, and the
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associated numerical concerns are discussed in
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"(Baczewski)"_#Baczewski.
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The desired temperature at each timestep is ramped from {Tstart} to
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{Tstop} over the course of the next run.
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The random # {seed} must be a positive integer. A Marsaglia random
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number generator is used. Each processor uses the input seed to
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generate its own unique seed and its own stream of random
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numbers. Thus the dynamics of the system will not be identical on two
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runs on different numbers of processors.
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:line
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The keyword/value option pairs are used in the following ways.
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The keyword {frozen} can be used to specify how the extended variables
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associated with the GLD memory kernel are initialized. Specifying no
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(the default), the initial values are drawn at random from an
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equilibrium distribution at {Tstart}, consistent with the
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Fluctuation-Dissipation Theorem. Specifying yes, initializes the
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extended variables to zero.
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The keyword {zero} can be used to eliminate drift due to the
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thermostat. Because the random forces on different atoms are
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independent, they do not sum exactly to zero. As a result, this fix
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applies a small random force to the entire system, and the
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center-of-mass of the system undergoes a slow random walk. If the
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keyword {zero} is set to {yes}, the total random force is set exactly
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to zero by subtracting off an equal part of it from each atom in the
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group. As a result, the center-of-mass of a system with zero initial
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momentum will not drift over time.
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:line
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[Restart, run start/stop, minimize info:]
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The instantaneous values of the extended variables are written to
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"binary restart files"_restart.html. Because the state of the random
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number generator is not saved in restart files, this means you cannot
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do "exact" restarts with this fix, where the simulation continues on
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the same as if no restart had taken place. However, in a statistical
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sense, a restarted simulation should produce the same behavior.
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None of the "fix_modify"_fix_modify.html options are relevant to this
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fix. No global or per-atom quantities are stored by this fix for
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access by various "output commands"_Section_howto.html#howto_15.
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This fix can ramp its target temperature over multiple runs, using the
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{start} and {stop} keywords of the "run"_run.html command. See the
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"run"_run.html command for details of how to do this.
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This fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:]
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This fix is part of the MISC package. It is only enabled if LAMMPS
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was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"fix langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html,
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"pair_style dpd/tstat"_pair_dpd.html
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[Default:]
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The option defaults are frozen = no, zero = no.
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:line
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:link(Baczewski)
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[(Baczewski)] A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013).
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