forked from lijiext/lammps
355 lines
17 KiB
HTML
355 lines
17 KiB
HTML
<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 = average number of GCMC exchanges to attempt every N steps
|
|
|
|
<LI>M = average number of MC moves to attempt every N steps
|
|
|
|
<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
|
|
|
|
<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>translate = maximum Monte Carlo translation distance (length units)
|
|
|
|
<LI>zero or more keyword/value pairs may be appended to args
|
|
|
|
<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, or <I>intra_energy</I>
|
|
<I>mol</I> value = template-ID
|
|
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
|
<I>shake</I> value = fix-ID
|
|
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
|
|
<I>region</I> value = region-ID
|
|
region-ID = ID of region where MC moves are allowed
|
|
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
|
|
<I>pressure</I> value = pressure of the gas reservoir (pressure units)
|
|
<I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
|
|
<I>full_energy</I> = compute the entire system energy when performing MC moves
|
|
<I>charge</I> value = charge of inserted atoms (charge units)
|
|
<I>group</I> value = group-ID
|
|
group-ID = group-ID for inserted atoms (string)
|
|
<I>grouptype</I> values = type group-ID
|
|
type = atom type (int)
|
|
group-ID = group-ID for inserted atoms (string)
|
|
<I>intra_energy</I> value = intramolecular energy (energy units)
|
|
</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 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
|
|
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 ensemble (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>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
|
|
or deletions) of gas atoms or molecules of
|
|
the given type between the simulation cell and the imaginary
|
|
reservoir. It also attempts a number of Monte Carlo
|
|
moves (translations and molecule rotations) of gas of the given type
|
|
within the simulation cell or region. The average number of
|
|
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
|
|
M should typically be chosen to be
|
|
approximately equal to the expected number of gas atoms or molecules
|
|
of the given type within the simulation cell or region,
|
|
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>All inserted particles are always assigned to two groups: the default group
|
|
"all" and the group specified in the fix gcmc command (which can also
|
|
be "all"). In addition, particles are also added to any groups specified
|
|
by the <I>group</I> and <I>grouptype</I> keywords.
|
|
If inserted particles are individual atoms, they are
|
|
assigned the specified atom type. If they are molecules, the type of
|
|
each atom in the inserted molecule is specified in the file read by
|
|
the <A HREF = "molecule.html">molecule</A> command, and those values are added to
|
|
the specified atom type. E.g. if <I>type</I> = 2, and the file specifies
|
|
atom types 1,2,3, then the inserted molecule will have atom types
|
|
3,4,5.
|
|
</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 cell can be moved using
|
|
regular time integration translations, 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. For non-rectangular regions, random trial
|
|
points are generated within the rectangular bounding box until a point is found
|
|
that lies inside the region. If no valid point is generated after 1000 trials,
|
|
no insertion is performed, but it is counted as an attempted insertion.
|
|
Move and deletion attempt candidates are selected
|
|
from gas atoms or molecules within the region. If there are no candidates,
|
|
no move or deletion is performed, but it is counted as an attempt move
|
|
or deletion. If an attempted move places the atom or molecule center-of-mass outside
|
|
the specified region, a new attempted move is generated. This process is repeated
|
|
until the atom or molecule center-of-mass is inside the specified 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 cell.
|
|
</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 translations
|
|
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
|
|
coordinates are chosen at a random position within the current
|
|
simulation cell or region, 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, with the origin of the relative
|
|
coordinates coinciding with the chosen insertion point. This means
|
|
that if the origin of the template molecule coordinate system
|
|
lies far from the center of the template molecule,
|
|
the inserted molecule will lie far from the insertion point.
|
|
A random initial rotation is used in
|
|
the case of molecule insertions.
|
|
</P>
|
|
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
|
|
specifies a <I>template-ID</I> previously defined using the
|
|
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
|
|
molecule. The coordinates, atom types, charges, etc, as well as any
|
|
bond/angle/etc and special neighbor information for the molecule can
|
|
be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
|
|
command for details. The only settings required to be in this file
|
|
are the coordinates and types of atoms in the molecule.
|
|
</P>
|
|
<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
|
|
atoms that are bonded to other atoms, or LAMMPS will
|
|
soon generate an error when it tries to find bonded neighbors. 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 you wish to insert molecules via the <I>mol</I> keyword, that will have
|
|
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
|
|
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
|
|
shake</A> command which also appears in your input script.
|
|
</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. Rotations are performed by generating a random
|
|
point on the unit sphere and a random rotation angle on the
|
|
range [0,maxangle). The molecule is then rotated by that angle about an
|
|
axis passing through the molecule center of mass. The axis is parallel
|
|
to the unit vector defined by the point on the unit sphere. The
|
|
same procedure is used for randomly rotating molecules when they
|
|
are inserted, except that the rotation axis passes through whatever
|
|
origin is used for the molecule template, and the maximum angle is
|
|
360 degrees.
|
|
</P>
|
|
<P>Note that fix GCMC does not use configurational bias
|
|
MC or any other kind of sampling of intramolecular degrees of freedom.
|
|
Inserted molecules can have different orientations, but they will all
|
|
have the same intramolecular configuration,
|
|
which was specified in the molecule command input.
|
|
</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>The <I>full_energy</I> option means that fix GCMC will compute the total
|
|
potential energy of the entire simulated system. The total system
|
|
energy before and after the proposed GCMC move is then used in the
|
|
Metropolis criterion to determine whether or not to accept the
|
|
proposed GCMC move. By default, this option is off, in which case
|
|
only partial energies are computed to determine the difference in
|
|
energy that would be caused by the proposed GCMC move.
|
|
</P>
|
|
<P>The <I>full_energy</I> option is needed for systems with complicated
|
|
potential energy calculations, including the following:
|
|
</P>
|
|
<UL><LI> long-range electrostatics (kspace)
|
|
<LI> many-body pair styles
|
|
<LI> hybrid pair styles
|
|
<LI> eam pair styles
|
|
<LI> triclinic systems
|
|
<LI> need to include potential energy contributions from other fixes
|
|
</UL>
|
|
<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
|
|
keyword and issue a warning message.
|
|
</P>
|
|
<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
|
|
the intramolecular energy of inserted and deleted molecules. If this
|
|
is not desired, the <I>intra_energy</I> keyword can be used to define an
|
|
amount of energy that is subtracted from the final energy when a molecule
|
|
is inserted, and added to the initial energy when a molecule is
|
|
deleted. For molecules that have a non-zero intramolecular energy, this
|
|
will ensure roughly the same behavior whether or not the <I>full_energy</I>
|
|
option is used.
|
|
</P>
|
|
<P>Some fixes have an associated potential energy. Examples of such fixes
|
|
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
|
|
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
|
|
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
|
|
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
|
|
For that energy to be included in the total potential energy of the
|
|
system (the quantity used when performing GCMC moves),
|
|
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
|
|
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
|
|
specify if this should be done.
|
|
</P>
|
|
<P>Use the <I>charge</I> option to insert atoms with a user-specified point
|
|
charge. Note that doing so will cause the system to become non-neutral.
|
|
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
|
with non-neutral systems. See the
|
|
<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
|
|
details about simulating non-neutral systems with kspace on.
|
|
</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 parameters 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>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
|
|
of the group-ID value. The <I>grouptype</I> keyword assigns all
|
|
inserted atoms of the specified type to the <A HREF = "group.html">group</A>
|
|
of the group-ID value.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>This fix writes the state of the fix 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 8, which can be accessed
|
|
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
|
|
values are the following global cumulative quantities:
|
|
</P>
|
|
<UL><LI>1 = translation attempts
|
|
<LI>2 = translation 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>Can be run in parallel, but aspects of the GCMC part will not scale
|
|
well in parallel. Only usable for 3D simulations.
|
|
</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 script can be
|
|
problematic if using a template molecule. The issue is that the
|
|
user-referenced template molecule in the second fix gcmc command
|
|
may no longer exist since it might have been deleted by the first
|
|
fix gcmc command. An existing template molecule will need to be
|
|
referenced by the user for each subsequent fix gcmc command.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_atom_swap.html">fix_atom_swap</A>,
|
|
<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 mol = no, maxangle = 10, full_energy = no,
|
|
except for the situations where full_energy is required, as
|
|
listed above.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Frenkel"></A>
|
|
|
|
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
|
|
Academic Press, London, 2002.
|
|
</P>
|
|
</HTML>
|