2011-08-25 23:34:50 +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 gcmc command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
|
|
|
|
|
|
<LI>gcmc = style name of this fix command
|
|
|
|
|
|
|
|
|
|
<LI>N = invoke this fix every N steps
|
|
|
|
|
|
|
|
|
|
<LI>X = number of exchanges to attempt every N steps
|
|
|
|
|
|
|
|
|
|
<LI>M = number of MC displacements to attempt every N steps
|
|
|
|
|
|
|
|
|
|
<LI>type = atom type of exchanged particles
|
|
|
|
|
|
|
|
|
|
<LI>seed = random # seed (positive integer)
|
|
|
|
|
|
|
|
|
|
<LI>T = temperature of the ideal gas reservoir (temperature units)
|
|
|
|
|
|
|
|
|
|
<LI>mu = chemical potential of the ideal gas reservoir (energy units)
|
|
|
|
|
|
|
|
|
|
<LI>displace = maximum Monte Carlo displacement distance (length units)
|
|
|
|
|
|
|
|
|
|
<LI>zero or more keyword/value pairs may be appended to args
|
|
|
|
|
|
2012-08-08 22:16:01 +08:00
|
|
|
<LI>keyword = <I>molecule</I> or <I>region</I>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>molecule</I> value = <I>no</I> or <I>yes</I>
|
|
|
|
|
<I>region</I> value = region-ID
|
|
|
|
|
region-ID = ID of region to use as an exchange/move volume
|
2011-08-25 23:34:50 +08:00
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
|
2012-08-08 22:16:01 +08:00
|
|
|
fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes
|
|
|
|
|
fix 4 all gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
|
2011-08-25 23:34:50 +08:00
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
|
|
|
|
particles of the given type with an imaginary ideal gas reservoir at
|
2012-08-08 22:16:01 +08:00
|
|
|
the specified T and chemical potential (mu ) as discussed in
|
2011-08-25 23:34:50 +08:00
|
|
|
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
|
|
|
|
|
simulations in the grand canonical enemble (muVT, constant chemical
|
|
|
|
|
potential, constant volume, and constant temperature) can be
|
|
|
|
|
performed. Specific uses include computing isotherms in microporous
|
|
|
|
|
materials, or computing vapor-liquid coexistence curves.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Perform up to X exchanges of particles of the given type between the
|
|
|
|
|
simulation domain and the imaginary reservoir every N timesteps. Also
|
|
|
|
|
perform M Monte Carlo displacements of particles of the given type
|
|
|
|
|
within the simulation domain. M should typically be chosen to be
|
|
|
|
|
approximately equal to the expected number of particles of the given
|
|
|
|
|
type within the domain, which will result in roughly one MC
|
|
|
|
|
translation per particle per MC cycle.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This fix cannot be used to perform MC displacements of particles other
|
|
|
|
|
than the exchanged type. All particles in the simulation domain can be
|
|
|
|
|
moved using regular time integration displacements, e.g. via
|
|
|
|
|
<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation.
|
|
|
|
|
</P>
|
2012-08-08 22:16:01 +08:00
|
|
|
<P>This command may optionally use the <I>region</I> keyword to define an
|
|
|
|
|
exchange and move volume. The specified region must have been
|
|
|
|
|
previously defined with a <A HREF = "region.html">region</A> command. It must be
|
|
|
|
|
defined with side = <I>in</I>. Insertion attempts occur only within the
|
|
|
|
|
specified region. Move and deletion attempt candidates are selected
|
|
|
|
|
from particles within the region. If no candidate can be found within
|
|
|
|
|
the specified region after randomly selecting candidates 1000 times,
|
|
|
|
|
the move or deletion attempt is considered a failure. Moves must start
|
|
|
|
|
within the specified region, but may move the particle slightly
|
|
|
|
|
outside of the region.
|
|
|
|
|
</P>
|
2011-08-25 23:34:50 +08:00
|
|
|
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
|
|
|
|
|
reservoir, T, should be set to be equivalent to the target temperature
|
|
|
|
|
used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
|
|
|
|
|
will not be in thermal equilibrium with the simulation domain.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Note that neighbor lists are re-built every timestep that this fix is
|
|
|
|
|
invoked, so you should not set N to be too small. However, periodic
|
|
|
|
|
rebuilds are necessary in order to avoid dangerous rebuilds and missed
|
|
|
|
|
interactions. Specifically, avoid performing so many MC displacements
|
|
|
|
|
per timestep that a particle can move beyond the neighbor list skin
|
|
|
|
|
distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
|
|
|
|
|
</P>
|
|
|
|
|
<P>When a particle is to be inserted, its coordinates are chosen as a
|
|
|
|
|
random position within the current simulation domain, and its velocity
|
|
|
|
|
is randomly chosen from the specified temperature distribution given
|
|
|
|
|
by T.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Exchanged particles have the specified atom type and are assigned to
|
|
|
|
|
two groups: the default group "all" and the group specified in the fix
|
|
|
|
|
gcmc command (which can also be "all").
|
|
|
|
|
</P>
|
|
|
|
|
<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
|
|
|
|
|
atoms are exchanged. In this case, you should ensure you do not
|
|
|
|
|
delete only a portion of a molecule (only some of its atoms), or
|
|
|
|
|
LAMMPS will soon generate an error when it tries to find those atoms.
|
|
|
|
|
LAMMPS will warn you if any of the atoms eligible for deletion have a
|
|
|
|
|
non-zero molecule ID, but does not check for this at the time of
|
|
|
|
|
deletion.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, entire molecules
|
|
|
|
|
are exchanged. This feature is not yet supported.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Use of this fix typically will cause the number of atoms to fluctuate,
|
|
|
|
|
therefore, you will want to use the
|
|
|
|
|
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
|
|
|
|
|
current number of atoms is used as a normalizing factor each time
|
|
|
|
|
temperature is computed. Here is the necessary command:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute_modify thermo_temp dynamic yes
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>If LJ units are used, note that a value of 0.18292026 is used by this
|
|
|
|
|
fix as the reduced value for Planck's constant. This value was
|
|
|
|
|
derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
|
|
|
|
|
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
|
|
|
|
|
mass = 39.948 amu.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
|
|
|
|
|
files</A>. This includes information about the random
|
|
|
|
|
number generator seed, the next timestep for MC exchanges, etc. See
|
|
|
|
|
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
|
|
|
|
|
re-specify a fix in an input script that reads a restart file, so that
|
|
|
|
|
the operation of the fix continues in an uninterrupted fashion.
|
|
|
|
|
</P>
|
|
|
|
|
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
|
|
|
|
fix.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This fix computes a global vector of length 6, which can be accessed
|
2011-08-26 01:01:01 +08:00
|
|
|
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
|
2011-08-25 23:34:50 +08:00
|
|
|
values are the following global cummulative quantities:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>1 = displacement attempts
|
|
|
|
|
<LI>2 = displacement successes
|
|
|
|
|
<LI>3 = deletion attempts
|
|
|
|
|
<LI>4 = deletion successes
|
|
|
|
|
<LI>5 = insertion attempts
|
|
|
|
|
<LI>6 = insertion successes
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The vector values calculated by this fix are "extensive".
|
|
|
|
|
</P>
|
|
|
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
|
|
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
|
|
|
|
minimization</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2011-08-27 02:53:00 +08:00
|
|
|
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
|
|
|
|
|
built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
2011-08-25 23:34:50 +08:00
|
|
|
LAMMPS</A> section for more info.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Do not set "neigh_modify once yes" or else this fix will never be
|
|
|
|
|
called. Reneighboring is required.
|
|
|
|
|
</P>
|
|
|
|
|
<P>You cannot currently exchange charged particles or molecules with a
|
|
|
|
|
net charge.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Only pairwise interactions, as defined by the
|
|
|
|
|
<A HREF = "pair_style.html">pair_style</A> command, are included in this
|
|
|
|
|
calculation. Long-range interactions due to a
|
|
|
|
|
<A HREF = "kspace_style.html">kspace_style</A> command are not included. Not all
|
|
|
|
|
pair potentials can be evaluated in a pairwise mode as required by
|
|
|
|
|
this fix. For example, 3-body potentials, such as
|
|
|
|
|
<A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot
|
|
|
|
|
be used. <A HREF = "pair_eam.html">EAM</A> potentials for metals only include the
|
|
|
|
|
pair potential portion of the EAM interaction, not the embedding term.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
|
|
|
|
|
<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The option defaults are molecule = no.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Frenkel"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
|
|
|
|
|
Academic Press, London, 2002.
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
