forked from lijiext/lammps
241 lines
11 KiB
Plaintext
241 lines
11 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix gcmc command :h3
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[Syntax:]
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fix ID group-ID gcmc N X M type seed T mu displace keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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gcmc = style name of this fix command :l
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N = invoke this fix every N steps :l
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X = number of exchanges to attempt every N steps :l
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M = number of MC displacements to attempt every N steps :l
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type = atom type or molecule ID of exchanged gas :l
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seed = random # seed (positive integer) :l
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T = temperature of the ideal gas reservoir (temperature units) :l
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mu = chemical potential of the ideal gas reservoir (energy units) :l
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displace = maximum Monte Carlo displacement distance (length units) :l
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zero or more keyword/value pairs may be appended to args :l
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keyword = {molecule}, {region}, {maxangle}, {pressure}, or {fugacity_coeff} :l
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{molecule} value = {no} or {yes}
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{region} value = region-ID
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region-ID = ID of region to use as an exchange/move volume
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{maxangle} value = maximum molecular rotation angle (degrees)
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{pressure} value = pressue of the gas reservoir (pressure units)
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{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless) :pre
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:ule
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[Examples:]
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fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 Kr gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes maxrot 180
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fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
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[Description:]
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This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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atoms or molecules of the given type with an imaginary ideal gas reservoir at
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the specified T and chemical potential (mu) as discussed in
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"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
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simulations in the grand canonical enemble (muVT, constant chemical
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potential, constant volume, and constant temperature) can be
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performed. Specific uses include computing isotherms in microporous
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materials, or computing vapor-liquid coexistence curves.
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Perform up to X exchanges of gas atoms or molecules of the given type
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between the simulation domain and the imaginary reservoir every N
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timesteps. Also perform M Monte Carlo displacements or rotations
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(for molecules) of gas of the given type within the simulation domain.
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M should typically be chosen to be approximately equal to the expected
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number of gas atoms or molecules of the given type within the domain,
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which will result in roughly one MC translation per atom or molecule
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per MC cycle.
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For MC moves of molecular gasses, rotations and translations are each
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attempted with 50% probability. For MC moves of atomic gasses,
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translations are attempted 100% of the time. For MC exchanges of either
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molecular or atomic gasses, deletions and insertions are each attempted
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with 50% probability.
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This fix cannot be used to perform MC insertions of gas atoms or
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molecules other than the exchanged type, but MC deletions, translations,
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and rotations can be performed on any atom/molecule in the fix group.
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All atoms in the simulation domain can be moved using regular time
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integration displacements, e.g. via "fix_nvt"_fix_nvt.html, resulting
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in a hybrid GCMC+MD simulation. A smaller-than-usual timestep size
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may be needed when running such a hybrid simulation, especially if
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the inserted molecules are not well equilibrated.
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This command may optionally use the {region} keyword to define an
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exchange and move volume. The specified region must have been
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previously defined with a "region"_region.html command. It must be
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defined with side = {in}. Insertion attempts occur only within the
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specified region. Move and deletion attempt candidates are selected
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from gas atoms or molecules within the region. If no candidate can be
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found within the specified region after randomly selecting candidates
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1000 times, the move or deletion attempt is considered a failure. Moves
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must start within the specified region, but may move the atom or molecule
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slightly outside of the region.
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If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary
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reservoir, T, should be set to be equivalent to the target temperature
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used in "fix_nvt"_fix_nvt.html. Otherwise, the imaginary reservoir
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will not be in thermal equilibrium with the simulation domain.
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Note that neighbor lists are re-built every timestep that this fix is
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invoked, so you should not set N to be too small. However, periodic
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rebuilds are necessary in order to avoid dangerous rebuilds and missed
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interactions. Specifically, avoid performing so many MC displacements
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per timestep that atoms can move beyond the neighbor list skin
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distance. See the "neighbor"_neighbor.html command for details.
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When an atom or molecule is to be inserted, its center-of-mass
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coordinates are chosen as a random position within the current
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simulation domain, and new atom velocities are randomly chosen
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from the specified temperature distribution given by T. Relative
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coordinates for atoms in a molecule are taken from the template
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molecule provided by the user. A random initial rotation is used in the
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case of molecule insertions.
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If the setting for the {molecule} keyword is {no}, then only single
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atoms are exchanged. In this case, you should ensure you do not
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delete only a portion of a molecule (only some of its atoms), or
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LAMMPS will soon generate an error when it tries to find those atoms.
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LAMMPS will warn you if any of the atoms eligible for deletion have a
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non-zero molecule ID, but does not check for this at the time of
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deletion.
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If the setting for the {molecule} keyword is {yes}, entire molecules
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are exchanged. The user must supply a model molecule in the data
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file to use as a template for exchanges, and that molecule's number
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must be given in the fix GCMC command as the "type" of the exchanged
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gas. Note that the model molecule must be present whenever the fix
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is initialized. This is a limitation that will likely be remedied
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in the not-to-distant future.
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Optionally, users may specify the maximum rotation angle for
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molecular rotations using the {maxangle} keyword and specifying
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the angle in degrees. The specified angle will apply to all three
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Euler angles used internally to define the rotation matrix for
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molecular rotations. The max angle can be set to zero, but rotations
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will be pointless. Note that the default is ten degrees for each
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Euler angle.
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For atomic gasses, inserted atoms have the specified atom type, but
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deleted atoms are any atoms that have been inserted or that belong
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to the user-specified fix group. For molecular gasses, exchanged
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molecules use the same atom types as in the template molecule
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supplied by the user. In both cases, exchanged
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atoms/molecules are assigned to two groups: the default group "all"
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and the group specified in the fix gcmc command (which can also be
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"all").
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The gas reservoir pressure can be specified using the {pressure}
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keyword, in which case the user-specified chemical potential is
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ignored. For non-ideal gas reservoirs, the user may also specify the
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fugacity coefficient using the {fugacity_coeff} keyword.
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Use of this fix typically will cause the number of atoms to fluctuate,
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therefore, you will want to use the
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"compute_modify"_compute_modify.html command to insure that the
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current number of atoms is used as a normalizing factor each time
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temperature is computed. Here is the necessary command:
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compute_modify thermo_temp dynamic yes :pre
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If LJ units are used, note that a value of 0.18292026 is used by this
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fix as the reduced value for Planck's constant. This value was
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derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
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epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
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mass = 39.948 amu.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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This fix writes the state of the deposition to "binary restart
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files"_restart.html. This includes information about the random
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number generator seed, the next timestep for MC exchanges, etc. See
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the "read_restart"_read_restart.html command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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None of the "fix_modify"_fix_modify.html options are relevant to this
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fix.
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This fix computes a global vector of length 6, which can be accessed
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by various "output commands"_Section_howto.html#howto_15. The vector
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values are the following global cummulative quantities:
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1 = displacement attempts
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2 = displacement successes
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3 = insertion attempts
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4 = insertion successes
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5 = deletion attempts
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6 = deletion successes
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7 = rotation attempts
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8 = rotation successes :ul
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The vector values calculated by this fix are "extensive".
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:]
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This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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Do not set "neigh_modify once yes" or else this fix will never be
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called. Reneighboring is required.
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Only pairwise interactions, as defined by the
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"pair_style"_pair_style.html command, are included in this
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calculation. Long-range interactions due to a
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"kspace_style"_kspace_style.html command are not included. Not all
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pair potentials can be evaluated in a pairwise mode as required by
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this fix. For example, 3-body potentials, such as
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"Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot
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be used. "EAM"_pair_eam.html potentials for metals only include the
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pair potential portion of the EAM interaction, not the embedding term.
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Can be run in parallel, but aspects of the GCMC part will not scale
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well in parallel. Only usable for 3D simulations with orthogonal
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simulation cells.
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Note that very lengthy simulations involving insertions/deletions of
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billions of gas molecules may run out of atom or molecule IDs and
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trigger an error, so it is better to run multiple shorter-duration
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simulations. Likewise, very large molecules have not been tested
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and may turn out to be problematic.
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Use of multiple fix gcmc commands in the same input script can be
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problematic if using a template molecule. The issue is that the
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user-referenced template molecule in the second fix gcmc command
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may no longer exist since it might have been deleted by the first
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fix gcmc command. An existing template molecule will need to be
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referenced by the user for each subsequent fix gcmc command.
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[Related commands:]
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"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html,
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"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html,
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"delete_atoms"_delete_atoms.html
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[Default:]
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The option defaults are molecule = no, maxangle = 10.
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:line
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:link(Frenkel)
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[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
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Academic Press, London, 2002.
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