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< title > fix gcmc command — LAMMPS documentation< / title >
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< span id = "index-0" > < / span > < h1 > fix gcmc command< a class = "headerlink" href = "#fix-gcmc-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > gcmc = style name of this fix command< / li >
< li > N = invoke this fix every N steps< / li >
< li > X = average number of GCMC exchanges to attempt every N steps< / li >
< li > M = average number of MC moves to attempt every N steps< / li >
< li > type = atom type for inserted atoms (must be 0 if mol keyword used)< / li >
< li > seed = random # seed (positive integer)< / li >
< li > T = temperature of the ideal gas reservoir (temperature units)< / li >
< li > mu = chemical potential of the ideal gas reservoir (energy units)< / li >
< li > translate = maximum Monte Carlo translation distance (length units)< / li >
< li > zero or more keyword/value pairs may be appended to args< / li >
< / ul >
< pre class = "literal-block" >
keyword = < em > mol< / em > , < em > region< / em > , < em > maxangle< / em > , < em > pressure< / em > , < em > fugacity_coeff< / em > , < em > full_energy< / em > , < em > charge< / em > , < em > group< / em > , < em > grouptype< / em > , < em > intra_energy< / em > , or < em > tfac_insert< / em >
< em > mol< / em > value = template-ID
template-ID = ID of molecule template specified in a separate < a class = "reference internal" href = "molecule.html" > < em > molecule< / em > < / a > command
< em > shake< / em > value = fix-ID
fix-ID = ID of < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > command
< em > region< / em > value = region-ID
region-ID = ID of region where MC moves are allowed
< em > maxangle< / em > value = maximum molecular rotation angle (degrees)
< em > pressure< / em > value = pressure of the gas reservoir (pressure units)
< em > fugacity_coeff< / em > value = fugacity coefficient of the gas reservoir (unitless)
< em > full_energy< / em > = compute the entire system energy when performing MC moves
< em > charge< / em > value = charge of inserted atoms (charge units)
< em > group< / em > value = group-ID
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group-ID = group-ID for inserted atoms (string)
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< em > grouptype< / em > values = type group-ID
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type = atom type (int)
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group-ID = group-ID for inserted atoms (string)
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< em > intra_energy< / em > value = intramolecular energy (energy units)
< em > tfac_insert< / em > value = scale up/down temperature of inserted atoms (unitless)
< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
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fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > 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
the specified T and chemical potential (mu) as discussed in
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< a class = "reference internal" href = "fix_ti_spring.html#frenkel" > < span > (Frenkel)< / span > < / a > . If used with the < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > command,
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simulations in the grand canonical ensemble (muVT, constant chemical
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.< / p >
< p > Every N timesteps the fix attempts a number of GCMC exchanges (insertions
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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
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within the simulation cell or region. The average number of
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attempted GCMC exchanges is X. The average number of attempted MC moves is M.
M should typically be chosen to be
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approximately equal to the expected number of gas atoms or molecules
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of the given type within the simulation cell or region,
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which will result in roughly one
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MC translation per atom or molecule per MC cycle.< / p >
< p > 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,
translations are attempted 100% of the time. For MC exchanges of
either molecular or atomic gasses, deletions and insertions are each
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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 < em > group< / em > and < em > grouptype< / em > keywords.
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If inserted particles are individual atoms, they are
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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 < a class = "reference internal" href = "molecule.html" > < em > molecule< / em > < / a > command.< / p >
< p > 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, and rotations can be performed on any atom/molecule in
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the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via
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< code class = "xref doc docutils literal" > < span class = "pre" > fix_nvt< / span > < / code > , resulting in a hybrid GCMC+MD simulation. A
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smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well
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equilibrated.< / p >
< p > This command may optionally use the < em > region< / em > keyword to define an
exchange and move volume. The specified region must have been
previously defined with a < a class = "reference internal" href = "region.html" > < em > region< / em > < / a > command. It must be
defined with side = < em > in< / em > . Insertion attempts occur only within the
specified region. For non-rectangular regions, random trial
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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.
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Move and deletion attempt candidates are selected
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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
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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 < code class = "xref doc docutils literal" > < span class = "pre" > fix_nvt< / span > < / code > , 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 < code class = "xref doc docutils literal" > < span class = "pre" > fix_nvt< / span > < / code > . Otherwise, the imaginary reservoir
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will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic,
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which can be achieved as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute mdtemp mdatoms temp
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compute_modify mdtemp dynamic yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
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fix_modify mdnvt temp mdtemp
< / pre > < / div >
< / div >
< p > 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
rebuilds are necessary in order to avoid dangerous rebuilds and missed
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interactions. Specifically, avoid performing so many MC translations
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per timestep that atoms can move beyond the neighbor list skin
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distance. See the < a class = "reference internal" href = "neighbor.html" > < em > neighbor< / em > < / a > command for details.< / p >
< p > When an atom or molecule is to be inserted, its
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coordinates are chosen at a random position within the current
simulation cell or region, and new atom velocities are randomly chosen from
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the specified temperature distribution given by T. The effective
temperature for new atom velocities can be increased or decreased
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using the optional keyword < em > tfac_insert< / em > (see below). 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. The center of mass of the molecule
is placed at the insertion point. The orientation of the molecule
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is chosen at random by rotating about this point.< / p >
< p > Individual atoms are inserted, unless the < em > mol< / em > keyword is used. It
specifies a < em > template-ID< / em > previously defined using the
< a class = "reference internal" href = "molecule.html" > < em > molecule< / em > < / a > command, which reads a file that defines the
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molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
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be specified in the molecule file. See the < a class = "reference internal" href = "molecule.html" > < em > molecule< / em > < / a >
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command for details. The only settings required to be in this file
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are the coordinates and types of atoms in the molecule.< / p >
< p > When not using the < em > mol< / em > keyword, you should ensure you do not delete
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atoms that are bonded to other atoms, or LAMMPS will
soon generate an error when it tries to find bonded neighbors. LAMMPS will
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warn you if any of the atoms eligible for deletion have a non-zero
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molecule ID, but does not check for this at the time of deletion.< / p >
< p > If you wish to insert molecules via the < em > mol< / em > keyword, that will have
their bonds or angles constrained via SHAKE, use the < em > shake< / em > keyword,
specifying as its value the ID of a separate < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > command which also appears in your input script.< / p >
< p > Optionally, users may specify the maximum rotation angle for
molecular rotations using the < em > maxangle< / em > keyword and specifying
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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
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axis passing through the molecule center of mass. The axis is parallel
to the unit vector defined by the point on the unit sphere.
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The same procedure is used for randomly rotating molecules when they
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are inserted, except that 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
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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”
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 < em > pressure< / em >
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 < em > fugacity_coeff< / em > keyword.< / p >
< p > The < em > full_energy< / em > option means that fix GCMC will compute the total
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potential energy of the entire simulated system. The total system
energy before and after the proposed GCMC move is then used in the
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Metropolis criterion to determine whether or not to accept the
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proposed GCMC move. By default, this option is off, in which case
only partial energies are computed to determine the difference in
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energy that would be caused by the proposed GCMC move.< / p >
< p > The < em > full_energy< / em > option is needed for systems with complicated
potential energy calculations, including the following:< / p >
< ul class = "simple" >
< li > long-range electrostatics (kspace)< / li >
< li > many-body pair styles< / li >
< li > hybrid pair styles< / li >
< li > eam pair styles< / li >
< li > triclinic systems< / li >
< li > need to include potential energy contributions from other fixes< / li >
< / ul >
< p > In these cases, LAMMPS will automatically apply the < em > full_energy< / em >
keyword and issue a warning message.< / p >
< p > When the < em > mol< / em > keyword is used, the < em > full_energy< / em > option also includes
the intramolecular energy of inserted and deleted molecules. If this
is not desired, the < em > intra_energy< / em > keyword can be used to define an
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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
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will ensure roughly the same behavior whether or not the < em > full_energy< / em >
option is used.< / p >
< p > Inserted atoms and molecules are assigned random velocities based on the
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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
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of the molecule to quickly increase or decrease after insertion.
The < em > tfac_insert< / em > keyword allows the user to counteract these effects
by changing the temperature used to assign velocities to
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inserted atoms and molecules by a constant factor. For a
particular application, some experimentation may be required
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to find a value of < em > tfac_insert< / em > that results in inserted molecules that
equilibrate quickly to the correct temperature.< / p >
< p > Some fixes have an associated potential energy. Examples of such fixes
include: < a class = "reference internal" href = "fix_efield.html" > < em > efield< / em > < / a > , < a class = "reference internal" href = "fix_gravity.html" > < em > gravity< / em > < / a > ,
< a class = "reference internal" href = "fix_addforce.html" > < em > addforce< / em > < / a > , < a class = "reference internal" href = "fix_langevin.html" > < em > langevin< / em > < / a > ,
< a class = "reference internal" href = "fix_restrain.html" > < em > restrain< / em > < / a > , < a class = "reference internal" href = "fix_temp_berendsen.html" > < em > temp/berendsen< / em > < / a > ,
< a class = "reference internal" href = "fix_temp_rescale.html" > < em > temp/rescale< / em > < / a > , and < a class = "reference internal" href = "fix_wall.html" > < em > wall fixes< / em > < / a > .
For that energy to be included in the total potential energy of the
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system (the quantity used when performing GCMC moves),
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you MUST enable the < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > < em > energy< / em > option for
that fix. The doc pages for individual < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > commands
specify if this should be done.< / p >
< p > Use the < em > charge< / em > 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 class = "reference internal" href = "compute_group_group.html" > < em > compute_group_group< / em > < / 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,
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therefore, you will want to use the
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< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > 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:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute_modify thermo_temp dynamic yes
< / pre > < / div >
< / div >
< 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
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derived from LJ parameters 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.< / p >
< p > The < em > group< / em > keyword assigns all inserted atoms to the < a class = "reference internal" href = "group.html" > < em > group< / em > < / a >
of the group-ID value. The < em > grouptype< / em > keyword assigns all
inserted atoms of the specified type to the < a class = "reference internal" href = "group.html" > < em > group< / em > < / a >
of the group-ID value.< / p >
< / div >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< a class = "headerlink" href = "#restart-fix-modify-output-run-start-stop-minimize-info" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This fix writes the state of the fix to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > . 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 < a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a > 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.< / p >
< p > None of the < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / 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 class = "reference internal" href = "Section_howto.html#howto-15" > < span > output commands< / span > < / a > . The vector
values are the following global cumulative quantities:< / p >
< ul class = "simple" >
< li > 1 = translation attempts< / li >
< li > 2 = translation successes< / li >
< li > 3 = insertion attempts< / li >
< li > 4 = insertion successes< / li >
< li > 5 = deletion attempts< / li >
< li > 6 = deletion successes< / li >
< li > 7 = rotation attempts< / li >
< li > 8 = rotation successes< / li >
< / ul >
< p > The vector values calculated by this fix are “ extensive” .< / p >
< p > No parameter of this fix can be used with the < em > start/stop< / em > keywords of
the < a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command. This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < em > energy minimization< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / 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
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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.< / 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
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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
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referenced by the user for each subsequent fix gcmc command.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "fix_atom_swap.html" > < em > fix atom/swap< / em > < / a > ,
< code class = "xref doc docutils literal" > < span class = "pre" > fix< / span > < span class = "pre" > nvt< / span > < / code > , < a class = "reference internal" href = "neighbor.html" > < em > neighbor< / em > < / a > ,
< a class = "reference internal" href = "fix_deposit.html" > < em > fix deposit< / em > < / a > , < a class = "reference internal" href = "fix_evaporate.html" > < em > fix evaporate< / em > < / a > ,
< a class = "reference internal" href = "delete_atoms.html" > < em > delete_atoms< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are mol = no, maxangle = 10, full_energy = no,
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except for the situations where full_energy is required, as
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listed above.< / p >
< hr class = "docutils" / >
< p id = "frenkel" > < strong > (Frenkel)< / strong > Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.< / p >
< / div >
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