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lammps/doc/src/fix_nve_dotc_langevin.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nve/dotc/langevin command :h3
[Syntax:]
fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
nve/dotc/langevin = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random number seed to use for white noise (positive integer) :l
keyword = {angmom} :l
{angmom} value = factor
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
:ule
[Examples:]
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
[Description:]
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
as described in "(Davidchack)"_#Davidchack2
to a group of atoms, which models an interaction with an implicit background
solvent. This command performs Brownian dynamics (BD)
via a technique that splits the integration into a deterministic Hamiltonian
part and the Ornstein-Uhlenbeck process for noise and damping.
The quaternion degrees of freedom are updated though an evolution
operator which performs a rotation in quaternion space, preserves
the quaternion norm and is akin to "(Miller)"_#Miller2.
In terms of syntax this command has been closely modelled on the
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
one single command. The main feature is improved stability
over the standard integrator, permitting slightly larger timestep sizes.
NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
also time integration of the translational and quaternion degrees of freedom.
The total force on each atom will have the form:
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html,
"bond_style"_bond_style.html, etc).
The Ff and Fr terms are implicitly taken into account by this fix
on a per-particle basis.
Ff is a frictional drag or viscous damping term proportional to the
particle's velocity. The proportionality constant for each atom is
computed as m/damp, where m is the mass of the particle and damp is
the damping factor specified by the user.
Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
a Gaussian random number) for speed.
:line
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
be variables. If used together with the oxDNA force field for
coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
corresponds to T = 300 K.
The {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 0.03
means to relax the temperature in a timespan of (roughly) 0.03 time
units tau (see the "units"_units.html command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent, i.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the "fix
viscous"_fix_viscous.html command for more details.
Note that the value 78.9375 in the second example above corresponds
to a diffusion constant, which is about an order of magnitude larger
than realistic ones. This has been used to sample configurations faster
in Brownian dynamics simulations.
The random # {seed} must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
The keyword/value option has to be used in the following way:
This fix has to be used together with the {angmom} keyword. The
particles are always considered to have a finite size.
The keyword {angmom} enables thermostatting of the rotational degrees of
freedom in addition to the usual translational degrees of freedom.
The scale factor after the {angmom} keyword gives the ratio of the rotational to
the translational friction coefficient.
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
A technical report with more information on this integrator can be found
"here"_PDF/USER-CGDNA-overview.pdf.
:line
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
[Default:] none
:line
:link(Davidchack2)
[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
:link(Miller2)
[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
:link(Dunweg3)
[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
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