"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 gcmc command :h3

[Syntax:]

fix ID group-ID gcmc N X M type seed T mu displace keyword values ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
gcmc = style name of this fix command :l
N = invoke this fix every N steps :l
X = average number of GCMC exchanges to attempt every N steps :l
M = average number of MC moves to attempt every N steps :l
type = atom type for inserted atoms (must be 0 if mol keyword used) :l
seed = random # seed (positive integer) :l
T = temperature of the ideal gas reservoir (temperature units) :l
mu = chemical potential of the ideal gas reservoir (energy units) :l
displace = maximum Monte Carlo translation distance (length units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff}
  {mol} value = template-ID
    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
  {rigid} value = fix-ID
    fix-ID = ID of "fix rigid/small"_fix_rigid.html command
  {shake} value = fix-ID
    fix-ID = ID of "fix shake"_fix_shake.html command
  {region} value = region-ID
    region-ID = ID of region where MC moves are allowed
  {maxangle} value = maximum molecular rotation angle (degrees)
  {pressure} value = pressure of the gas reservoir (pressure units)
  {fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless)
  {full_energy} = compute the entire system energy when performing MC moves
  {charge} value = charge of inserted atoms (charge units)
  {group} value = group-ID
    group-ID = group-ID for inserted atoms (string)
  {grouptype} values = type group-ID
    type = atom type (int)
    group-ID = group-ID for inserted atoms (string)
  {intra_energy} value = intramolecular energy (energy units)
  {tfac_insert} value = scale up/down temperature of inserted atoms (unitless)
  {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units) :pre
:ule

[Examples:]

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

[Description:]

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 "(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html
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.

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.

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.

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 {group} and {grouptype} keywords.  If inserted
particles are individual atoms, they are assigned the atom type given
by the type argument.  If they are molecules, the type argument has no
effect and must be set to zero. Instead, the type of each atom in the
inserted molecule is specified in the file read by the
"molecule"_molecule.html command.

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 "fix nvt"_fix_nh.html,
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.

This command may optionally use the {region} keyword to define an
exchange and move volume.  The specified region must have been
previously defined with a "region"_region.html command.  It must be
defined with side = {in}.  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.

If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in fix nvt. Otherwise, the imaginary reservoir will not be in
thermal equilibrium with the simulation cell. Also, it is important
that the temperature used by fix nvt be dynamic/dof, which can be
achieved as follows:

compute mdtemp mdatoms temp
compute_modify mdtemp dynamic/dof yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
fix_modify mdnvt temp mdtemp :pre

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 "neighbor"_neighbor.html command for details.

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. The effective temperature for new atom
velocities can be increased or decreased using the optional keyword
{tfac_insert} (see below). Relative coordinates for atoms in a
molecule are taken from the template molecule provided by the
user. The center of mass of the molecule is placed at the insertion
point. The orientation of the molecule is chosen at random by rotating
about this point.

Individual atoms are inserted, unless the {mol} keyword is used.  It
specifies a {template-ID} previously defined using the
"molecule"_molecule.html 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 "molecule"_molecule.html
command for details.  The only settings required to be in this file
are the coordinates and types of atoms in the molecule.

When not using the {mol} 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.

If you wish to insert molecules via the {mol} keyword, that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html command
which also appears in your input script.

NOTE: If you wish the new rigid molecules (and other rigid molecules)
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
inform that fix that the molecule count will vary dynamically.

If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
shake"_fix_shake.html command which also appears in your input script.

Optionally, users may specify the maximum rotation angle for molecular
rotations using the {maxangle} 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 maximum angle is 360 degrees.

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.

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").

The chemical potential is a user-specified input parameter defined
as:

:c,image(Eqs/fix_gcmc1.jpg)

The second term mu_ex is the excess chemical potential due to
energetic interactions and is formally zero for the fictitious gas
reservoir but is non-zero for interacting systems. So, while the
chemical potential of the reservoir and the simulation cell are equal,
mu_ex is not, and as a result, the densities of the two are generally
quite different.  The first term mu_id is the ideal gas contribution
to the chemical potential.  mu_id can be related to the density or
pressure of the fictitious gas reservoir by:

:c,image(Eqs/fix_gcmc2.jpg)

where k is Boltzman's constant,
T is the user-specified temperature, rho is the number density,
P is the pressure, and phi is the fugacity coefficient.
The constant Lambda is required for dimensional consistency.
For all unit styles except {lj} it is defined as the thermal
de Broglie wavelength

:c,image(Eqs/fix_gcmc3.jpg)

where h is Planck's constant, and m is the mass of the exchanged atom
or molecule.  For unit style {lj}, Lambda is simply set to the
unity. Note that prior to March 2017, lambda for unit style {lj} was
calculated using the above formula with h set to the rather specific
value of 0.18292026.  Chemical potential under the old definition can
be converted to an equivalent value under the new definition by
subtracting 3kTln(Lambda_old).

As an alternative to specifying mu directly, the ideal gas reservoir
can be defined by its pressure P using the {pressure} keyword, in
which case the user-specified chemical potential is ignored. The user
may also specify the fugacity coefficient phi using the
{fugacity_coeff} keyword, which defaults to unity.

The {full_energy} 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.

The {full_energy} option is needed for systems with complicated
potential energy calculations, including the following:

  long-range electrostatics (kspace)
  many-body pair styles
  hybrid pair styles
  eam pair styles
  tail corrections
  need to include potential energy contributions from other fixes :ul

In these cases, LAMMPS will automatically apply the {full_energy}
keyword and issue a warning message.

When the {mol} keyword is used, the {full_energy} option also includes
the intramolecular energy of inserted and deleted molecules. If this
is not desired, the {intra_energy} 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
{full_energy} option is used.

Inserted atoms and molecules are assigned random velocities based on
the specified temperature T. Because the relative velocity of all
atoms in the molecule is zero, this may result in inserted molecules
that are systematically too cold. In addition, the intramolecular
potential energy of the inserted molecule may cause the kinetic energy
of the molecule to quickly increase or decrease after insertion.  The
{tfac_insert} keyword allows the user to counteract these effects by
changing the temperature used to assign velocities to inserted atoms
and molecules by a constant factor. For a particular application, some
experimentation may be required to find a value of {tfac_insert} that
results in inserted molecules that equilibrate quickly to the correct
temperature.

Some fixes have an associated potential energy. Examples of such fixes
include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
"restrain"_fix_restrain.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
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 "fix_modify"_fix_modify.html {energy} option for that fix.  The
doc pages for individual "fix"_fix.html commands specify if this
should be done.

Use the {charge} 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 "compute
group/group"_compute_group_group.html documentation for more details
about simulating non-neutral systems with kspace on.

Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
"compute_modify"_compute_modify.html 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:

NOTE: If the density of the cell is initially very small or zero, and
increases to a much larger density after a period of equilibration,
then certain quantities that are only calculated once at the start
(kspace parameters, tail corrections) may no longer be accurate.  The
solution is to start a new simulation after the equilibrium density
has been reached.

With some pair_styles, such as "Buckingham"_pair_buck.html,
"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reaxc.html, two
atoms placed close to each other may have an arbitrary large, negative
potential energy due to the functional form of the potential.  While
these unphysical configurations are inaccessible to typical dynamical
trajectories, they can be generated by Monte Carlo moves. The
{overlap_cutoff} keyword suppresses these moves by effectively
assigning an infinite positive energy to all new configurations that
place any pair of atoms closer than the specified overlap cutoff
distance.

compute_modify thermo_temp dynamic yes :pre

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.

The {group} keyword assigns all inserted atoms to the
"group"_group.html of the group-ID value. The {grouptype} keyword
assigns all inserted atoms of the specified type to the
"group"_group.html of the group-ID value.

[Restart, fix_modify, output, run start/stop, minimize info:]

This fix writes the state of the fix to "binary restart
files"_restart.html.  This includes information about the random
number generator seed, the next timestep for MC exchanges, etc.  See
the "read_restart"_read_restart.html 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.

None of the "fix_modify"_fix_modify.html options are relevant to this
fix.

This fix computes a global vector of length 8, which can be accessed
by various "output commands"_Section_howto.html#howto_15.  The vector
values are the following global cumulative quantities:

1 = translation attempts
2 = translation successes
3 = insertion attempts
4 = insertion successes
5 = deletion attempts
6 = deletion successes
7 = rotation attempts
8 = rotation successes :ul

The vector values calculated by this fix are "extensive".

No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.  This fix is not invoked during "energy
minimization"_minimize.html.

[Restrictions:]

This fix is part of the MC package.  It is only enabled if LAMMPS was
built with that package.  See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

Do not set "neigh_modify once yes" or else this fix will never be
called.  Reneighboring is required.

Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.

When using fix gcmc in combination with fix shake or fix rigid,
only gcmc exchange moves are supported.

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.

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.

[Related commands:]

"fix atom/swap"_fix_atom_swap.html,
"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html,
"delete_atoms"_delete_atoms.html

[Default:]

The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
fugacity_coeff = 1, and full_energy = no,
except for the situations where full_energy is required, as
listed above.

:line

:link(Frenkel)
[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
