2006-09-22 00:22:34 +08:00
|
|
|
<HTML>
|
|
|
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
<H3>fix langevin command
|
|
|
|
</H3>
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
</P>
|
|
|
|
<PRE>fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
|
|
|
|
</PRE>
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
|
|
|
|
<LI>langevin = style name of this fix command
|
|
|
|
|
|
|
|
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
|
|
|
|
|
|
|
|
<LI>damp = damping parameter (time units)
|
|
|
|
|
2007-10-10 07:40:45 +08:00
|
|
|
<LI>seed = random # seed to use for white noise (positive integer)
|
2006-09-22 00:22:34 +08:00
|
|
|
|
2007-07-03 04:04:44 +08:00
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
<PRE>keyword = <I>axes</I> or <I>scale</I> or <I>region</I>
|
|
|
|
<I>axes</I> values = xflag yflag zflag
|
|
|
|
xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
|
|
|
|
<I>scale</I> values = type ratio
|
|
|
|
type = atom type (1-N)
|
|
|
|
ratio = factor to scale the damping coefficient by
|
|
|
|
<I>region</I> values = region-ID
|
|
|
|
region-ID = ID of region to apply thermostat to
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
</P>
|
|
|
|
<PRE>fix 3 boundary langevin 1.0 1.0 1000.0 699483
|
|
|
|
fix 1 all langevin 1.0 1.1 100.0 48279 axes 0 1 1
|
|
|
|
fix 3 boundary langevin 1.0 1.0 1000.0 699483 region boundary
|
|
|
|
</PRE>
|
|
|
|
<P><B>Description:</B>
|
|
|
|
</P>
|
|
|
|
<P>Apply a Langevin thermostat to a group of atoms which models an
|
|
|
|
interaction with a background implicit solvent. Used with <A HREF = "fix_nve.html">fix
|
|
|
|
nve</A>, this command performs Brownian dynamics (BD), since
|
|
|
|
the total force on each atom will have the form:
|
|
|
|
</P>
|
|
|
|
<PRE>F = Fc + Ff + Fr
|
|
|
|
</PRE>
|
|
|
|
<P>Fc is the conservative force computed via the usual inter-particle
|
|
|
|
interactions (<A HREF = "pair_style.html">pair_style</A>,
|
|
|
|
<A HREF = "bond_style.html">bond_style</A>, etc).
|
|
|
|
</P>
|
|
|
|
<P>The Ff and Fr terms are added by this fix. Ff = - gamma v and is a
|
|
|
|
frictional drag or viscous damping term proportional to the particle's
|
|
|
|
velocity. Gamma 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.
|
|
|
|
</P>
|
|
|
|
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
|
|
|
|
into the particle. As derived from the fluctuation/dissipation
|
|
|
|
theorum, its magnitude is proportional to sqrt(T m / dt damp), where 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.
|
|
|
|
</P>
|
|
|
|
<P>The desired temperature at each timestep is a ramped value during the
|
2007-06-26 08:03:39 +08:00
|
|
|
run from <I>Tstart</I> to <I>Tstop</I>.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<P>The <I>damp</I> parameter is specified in time units and determines how
|
|
|
|
rapidly the temperature is relaxed. For example, a value of 100.0
|
|
|
|
means to relax the temperature in a timespan of (roughly) 100 time
|
|
|
|
units (tau or fmsec or psec - see the <A HREF = "units.html">units</A> 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 <A HREF = "fix_viscous.html">fix
|
|
|
|
viscous</A> command for more details.
|
|
|
|
</P>
|
|
|
|
<P>The random # <I>seed</I> should be a non-zero integer with 1 to 8 digits.
|
|
|
|
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
|
2007-06-26 08:03:39 +08:00
|
|
|
on two runs on different numbers of processors.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<P>The keyword <I>axes</I> can be used to specify which dimensions to add Ff
|
|
|
|
and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
|
|
|
|
include that dimension. The default is 1 for all 3 dimensions.
|
|
|
|
</P>
|
|
|
|
<P>The keyword <I>scale</I> allows the damp factor to be scaled up or down by
|
|
|
|
the specified factor for atoms of that type. It can be used multiple
|
|
|
|
times to adjust damp for several atom types. Note that specifying a
|
|
|
|
ratio of 2 increase the relaxation time which is equivalent to the the
|
|
|
|
solvent's viscosity acting on particles with 1/2 the diameter. This
|
|
|
|
is the opposite effect of scale factors used by the <A HREF = "fix_viscous.html">fix
|
|
|
|
viscous</A> command, since the damp factor in fix
|
|
|
|
<I>langevin</I> is inversely related to the gamma factor in fix <I>viscous</I>.
|
|
|
|
Also note that the damping factor in fix <I>langevin</I> includes the
|
|
|
|
particle mass in Ff, unlike fix <I>viscous</I>. Thus the mass and size of
|
|
|
|
different atom types should be accounted for in the choice of ratio
|
|
|
|
values.
|
|
|
|
</P>
|
|
|
|
<P>The keyword <I>region</I> applies the fix only to atoms that are in the
|
|
|
|
specified geometric region (and in the fix group). Since atoms can
|
|
|
|
enter/leave a region, this test is performed each timestep.
|
|
|
|
</P>
|
|
|
|
<P>As noted above, fix <I>langevin</I> does not update the coordinates or
|
|
|
|
velocities of its atoms, only the forces. It is normally used with a
|
|
|
|
<A HREF = "fix_nve.html">fix nve</A> that does the time integration. Fix <I>langevin</I>
|
|
|
|
should not normally be used on atoms that also have their temperature
|
|
|
|
controlled by another fix - e.g. a <A HREF = "fix_nvt.html">nvt</A> or
|
|
|
|
<A HREF = "fix_temp_rescale.html">temp/rescale</A> fix.
|
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
|
|
|
|
</P>
|
|
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
|
|
files</A>. Because the state of the random number generator
|
|
|
|
is not saved in restart files, this means you cannot do "exact"
|
|
|
|
restarts with this fix, where the simulation continues on the same as
|
|
|
|
if no restart had taken place. However, in a statistical sense, a
|
|
|
|
restarted simulation should produce the same behavior.
|
|
|
|
</P>
|
|
|
|
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|
|
|
are relevant to this fix. No quantities calculated by this fix can be
|
|
|
|
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
|
|
|
|
</P>
|
|
|
|
<P>This fix can ramp its target temperature over multiple runs, using the
|
|
|
|
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
|
|
|
|
<A HREF = "run.html">run</A> command for details of how to do this.
|
|
|
|
</P>
|
|
|
|
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Restrictions:</B> none
|
|
|
|
</P>
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
</P>
|
|
|
|
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
|
|
|
|
viscous</A>
|
|
|
|
</P>
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
</P>
|
|
|
|
</HTML>
|