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rLAMMPS lammps
fix_gcmc.html
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<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 or molecule ID of exchanged gas
<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
<LI>
keyword =
<I>
molecule
</I>
,
<I>
region
</I>
,
<I>
maxangle
</I>
,
<I>
pressure
</I>
, or
<I>
fugacity_coeff
</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
<I>
maxangle
</I>
value = maximum molecular rotation angle (degrees)
<I>
pressure
</I>
value = pressue of the gas reservoir (pressure units)
<I>
fugacity_coeff
</I>
value = fugacity coefficient of the gas reservoir (unitless)
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxangle 180
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</PRE>
<P><B>
Description:
</B>
</P>
<P>
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
<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 gas atoms or molecules of the given type
between the simulation domain and the imaginary reservoir every N
timesteps. Also perform M Monte Carlo displacements or rotations
(for molecules) of gas of the given type within the simulation domain.
M should typically be chosen to be approximately equal to the expected
number of gas atoms or molecules of the given type within the domain,
which will result in roughly one MC translation per atom or molecule
per MC cycle.
</P>
<P>
For MC moves of molecular gasses, rotations and translations are each
attempted with 50% probability. For MC moves of atomic gasses,
translations are attempted 100% of the time. For MC exchanges of either
molecular or atomic gasses, deletions and insertions are each attempted
with 50% probability.
</P>
<P>
This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions, translations,
and rotations can be performed on any atom/molecule in the fix group.
All atoms 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. A smaller-than-usual timestep size
may be needed when running such a hybrid simulation, especially if
the inserted molecules are not well equilibrated.
</P>
<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 gas atoms or molecules 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 atom or molecule
slightly outside of the region.
</P>
<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 atoms can move beyond the neighbor list skin
distance. See the
<A
HREF =
"neighbor.html"
>
neighbor
</A>
command for details.
</P>
<P>
When an atom or molecule is to be inserted, its center-of-mass
coordinates are chosen as a random position within the current
simulation domain, and new atom velocities are randomly chosen
from the specified temperature distribution given by T. Relative
coordinates for atoms in a molecule are taken from the template
molecule provided by the user. A random initial rotation is used in the
case of molecule insertions.
</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. The user must supply a model molecule in the data
file to use as a template for exchanges, and that molecule's number
must be given in the fix GCMC command as the "type" of the exchanged
gas. Note that the model molecule must be present whenever the fix
is initialized. This is a limitation that will likely be remedied
in the not-to-distant future.
</P>
<P>
Optionally, users may specify the maximum rotation angle for
molecular rotations using the
<I>
maxangle
</I>
keyword and specifying
the angle in degrees. The specified angle will apply to all three
Euler angles used internally to define the rotation matrix for
molecular rotations. The max angle can be set to zero, but rotations
will be pointless. Note that the default is ten degrees for each
Euler angle.
</P>
<P>
For atomic gasses, inserted atoms have the specified atom type, but
deleted atoms are any atoms that have been inserted or that belong
to the user-specified fix group. For molecular gasses, exchanged
molecules use the same atom types as in the template molecule
supplied by the user. In both cases, exchanged
atoms/molecules 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>
The gas reservoir pressure can be specified using the
<I>
pressure
</I>
keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the
<I>
fugacity_coeff
</I>
keyword.
</P>
<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>
IMPORTANT NOTE: If you are monitoring the temperature of a system
where the particle count is changing due to adding/deleting particles,
you typically should use the
<A
HREF =
"compute_modify.html"
>
compute_modify dynamic
yes
</A>
command for the temperature compute you are
using.
</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
by various
<A
HREF =
"Section_howto.html#howto_15"
>
output commands
</A>
. The vector
values are the following global cummulative quantities:
</P>
<UL><LI>
1 = displacement attempts
<LI>
2 = displacement successes
<LI>
3 = insertion attempts
<LI>
4 = insertion successes
<LI>
5 = deletion attempts
<LI>
6 = deletion successes
<LI>
7 = rotation attempts
<LI>
8 = rotation 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>
<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
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>
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>
Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations with orthogonal
simulation cells.
</P>
<P>
Note that very lengthy simulations involving insertions/deletions of
billions of gas molecules may run out of atom or molecule IDs and
trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
and may turn out to be problematic.
</P>
<P>
Use of multiple fix gcmc commands in the same input using a template
molecule are not supported. There are multiple issues where the
current implmentation makes assumptions that are no longer valid
in this case. Resolving all of them require significant changes to
the implementation.
</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>
,
<A
HREF =
"delete_atoms.html"
>
delete_atoms
</A>
</P>
<P><B>
Default:
</B>
</P>
<P>
The option defaults are molecule = no, maxangle = 10.
</P>
<HR>
<A
NAME =
"Frenkel"
></A>
<P><B>
(Frenkel)
</B>
Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
</P>
</HTML>
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