forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6799 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
e4b59d189f
commit
19399847e3
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>fix gcmc command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>gcmc = style name of this fix command
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<LI>N = invoke this fix every N steps
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<LI>X = number of exchanges to attempt every N steps
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<LI>M = number of MC displacements to attempt every N steps
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<LI>type = atom type of exchanged particles
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<LI>seed = random # seed (positive integer)
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<LI>T = temperature of the ideal gas reservoir (temperature units)
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<LI>mu = chemical potential of the ideal gas reservoir (energy units)
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<LI>displace = maximum Monte Carlo displacement distance (length units)
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<LI>zero or more keyword/value pairs may be appended to args
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<PRE>keyword = <I>molecule</I>
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<I>molecule</I> value = <I>no</I> or <I>yes</I>
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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particles 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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<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> 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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</P>
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<P>Perform up to X exchanges of particles of the given type between the
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simulation domain and the imaginary reservoir every N timesteps. Also
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perform M Monte Carlo displacements of particles of the given type
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within the simulation domain. M should typically be chosen to be
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approximately equal to the expected number of particles of the given
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type within the domain, which will result in roughly one MC
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translation per particle per MC cycle.
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</P>
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<P>This fix cannot be used to perform MC displacements of particles other
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than the exchanged type. All particles in the simulation domain can be
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moved using regular time integration displacements, e.g. via
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<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation.
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</P>
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<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, 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 <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
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will not be in thermal equilibrium with the simulation domain.
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</P>
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<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
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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 a particle can move beyond the neighbor list skin
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distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
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</P>
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<P>When a particle is to be inserted, its coordinates are chosen as a
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random position within the current simulation domain, and its velocity
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is randomly chosen from the specified temperature distribution given
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by T.
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</P>
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<P>Exchanged particles have the specified atom type and are assigned to
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two groups: the default group "all" and the group specified in the fix
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gcmc command (which can also be "all").
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</P>
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<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, 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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</P>
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<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, entire molecules
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are exchanged. This feature is not yet supported.
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</P>
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<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 HREF = "compute_modify.html">compute_modify</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:
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</P>
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<PRE>compute_modify thermo_temp dynamic yes
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</PRE>
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<P>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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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
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files</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 HREF = "read_restart.html">read_restart</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.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
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fix.
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</P>
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<P>This fix computes a global vector of length 6, which can be accessed
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by various <A HREF = "Section_howto.html#4_15">output commands</A>. The vector
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values are the following global cummulative quantities:
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</P>
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<UL><LI>1 = displacement attempts
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<LI>2 = displacement successes
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<LI>3 = deletion attempts
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<LI>4 = deletion successes
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<LI>5 = insertion attempts
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<LI>6 = insertion successes
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</UL>
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<P>The vector values calculated by this fix are "extensive".
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
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was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>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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</P>
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<P>You cannot currently exchange charged particles or molecules with a
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net charge.
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</P>
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<P>Only pairwise interactions, as defined by the
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<A HREF = "pair_style.html">pair_style</A> command, are included in this
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calculation. Long-range interactions due to a
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<A HREF = "kspace_style.html">kspace_style</A> 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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<A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot
|
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be used. <A HREF = "pair_eam.html">EAM</A> 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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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
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<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are molecule = no.
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</P>
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<HR>
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<A NAME = "Frenkel"></A>
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<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
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Academic Press, London, 2002.
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</P>
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</HTML>
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@ -0,0 +1,169 @@
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"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 of exchanged particles :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}
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{molecule} value = {no} or {yes} :pre
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:ule
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|
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[Examples:]
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fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
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fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes :pre
|
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|
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[Description:]
|
||||
|
||||
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
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particles 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 enemble (muVT, constant chemical
|
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potential, constant volume, and constant temperature) can be
|
||||
performed. Specific uses include computing isotherms in microporous
|
||||
materials, or computing vapor-liquid coexistence curves.
|
||||
|
||||
Perform up to X exchanges of particles of the given type between the
|
||||
simulation domain and the imaginary reservoir every N timesteps. Also
|
||||
perform M Monte Carlo displacements of particles of the given type
|
||||
within the simulation domain. M should typically be chosen to be
|
||||
approximately equal to the expected number of particles of the given
|
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type within the domain, which will result in roughly one MC
|
||||
translation per particle per MC cycle.
|
||||
|
||||
This fix cannot be used to perform MC displacements of particles other
|
||||
than the exchanged type. All particles in the simulation domain can be
|
||||
moved using regular time integration displacements, e.g. via
|
||||
"fix_nvt"_fix_nvt.html, resulting in a hybrid GCMC+MD simulation.
|
||||
|
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If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
used in "fix_nvt"_fix_nvt.html. Otherwise, the imaginary reservoir
|
||||
will not be in thermal equilibrium with the simulation domain.
|
||||
|
||||
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 a particle can move beyond the neighbor list skin
|
||||
distance. See the "neighbor"_neighbor.html command for details.
|
||||
|
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When a particle is to be inserted, its coordinates are chosen as a
|
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random position within the current simulation domain, and its velocity
|
||||
is randomly chosen from the specified temperature distribution given
|
||||
by T.
|
||||
|
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Exchanged particles have the specified atom type and are assigned to
|
||||
two groups: the default group "all" and the group specified in the fix
|
||||
gcmc command (which can also be "all").
|
||||
|
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If the setting for the {molecule} keyword is {no}, 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.
|
||||
|
||||
If the setting for the {molecule} keyword is {yes}, entire molecules
|
||||
are exchanged. This feature is not yet supported.
|
||||
|
||||
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:
|
||||
|
||||
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 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.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the state of the deposition 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 6, which can be accessed
|
||||
by various "output commands"_Section_howto.html#4_15. The vector
|
||||
values are the following global cummulative quantities:
|
||||
|
||||
1 = displacement attempts
|
||||
2 = displacement successes
|
||||
3 = deletion attempts
|
||||
4 = deletion successes
|
||||
5 = insertion attempts
|
||||
6 = insertion 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#2_3 section for more info.
|
||||
|
||||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
|
||||
You cannot currently exchange charged particles or molecules with a
|
||||
net charge.
|
||||
|
||||
Only pairwise interactions, as defined by the
|
||||
"pair_style"_pair_style.html command, are included in this
|
||||
calculation. Long-range interactions due to a
|
||||
"kspace_style"_kspace_style.html 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
|
||||
"Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot
|
||||
be used. "EAM"_pair_eam.html potentials for metals only include the
|
||||
pair potential portion of the EAM interaction, not the embedding term.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html,
|
||||
"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html
|
||||
|
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[Default:]
|
||||
|
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The option defaults are molecule = no.
|
||||
|
||||
:line
|
||||
|
||||
:link(Frenkel)
|
||||
[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
|
||||
Academic Press, London, 2002.
|
||||
Loading…
Reference in New Issue