0da2e1782b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14039 f3b2605a-c512-4ea7-a41b-209d697bcdaa
202 lines
8.8 KiB
HTML
202 lines
8.8 KiB
HTML
<HTML>
|
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>fix atom/swap command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>fix ID group-ID atom/swap N X seed T keyword values ...
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>atom/swap = style name of this fix command
|
|
|
|
<LI>N = invoke this fix every N steps
|
|
|
|
<LI>X = number of swaps to attempt every N steps
|
|
|
|
<LI>seed = random # seed (positive integer)
|
|
|
|
<LI>T = scaling temperature of the MC swaps (temperature units)
|
|
|
|
<LI>one or more keyword/value pairs may be appended to args
|
|
|
|
<LI>keyword = <I>types</I> or <I>mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
|
|
|
|
<PRE> <I>types</I> values = two or more atom types
|
|
<I>mu</I> values = chemical potential of swap types (energy units)
|
|
<I>ke</I> value = <I>no</I> or <I>yes</I>
|
|
<I>no</I> = no conservation of kinetic energy after atom swaps
|
|
<I>yes</I> = kinetic energy is conserved after atom swaps
|
|
<I>semi-grand</I> value = <I>no</I> or <I>yes</I>
|
|
<I>no</I> = particle type counts and fractions conserved
|
|
<I>yes</I> = semi-grand canonical ensemble, particle fractions not conserved
|
|
<I>region</I> value = region-ID
|
|
region-ID = ID of region to use as an exchange/move volume
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
|
|
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
|
|
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>This fix performs Monte Carlo swaps of atoms of one given atom type
|
|
with atoms of the other given atom types. The specified T is used in
|
|
the Metropolis criterion dictating swap probabilities.
|
|
</P>
|
|
<P>Perform X swaps of atoms of one type with atoms of another type
|
|
according to a Monte Carlo probability. Swap candidates must be in the
|
|
fix group, must be in the region (if specified), and must be of one of
|
|
the listed types. Swaps are attempted between candidates that are
|
|
chosen randomly with equal probability among the candidate
|
|
atoms. Swaps are not attempted between atoms of the same type since
|
|
nothing would happen.
|
|
</P>
|
|
<P>All atoms in the simulation domain can be moved using regular time
|
|
integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
|
|
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
|
|
be needed when running such a hybrid simulation, especially if the
|
|
swapped atoms are not well equilibrated.
|
|
</P>
|
|
<P>The <I>types</I> keyword is required. At least two atom types must be
|
|
specified.
|
|
</P>
|
|
<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
|
|
conservation for swaps. The default is <I>yes</I>, which means that swapped
|
|
atoms have their velocities scaled by the ratio of the masses of the
|
|
swapped atom types. This ensures that the kinetic energy of each atom
|
|
is the same after the swap as it was before the swap, even though the
|
|
atom masses have changed.
|
|
</P>
|
|
<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
|
|
semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
|
|
means that the total number of each particle type does not need to be
|
|
conserved. The default is <I>no</I>, which means that the only kind of swap
|
|
allowed exchanges an atom of one type with an atom of a different
|
|
given type. In other words, the relative mole fractions of the swapped
|
|
atoms remains constant. Whereas in the semi-grand canonical ensemble,
|
|
the composition of the system can change. Note that when using
|
|
<I>semi-grand</I>, atoms in the fix group whose type is not listed
|
|
in the <I>types</I> keyword are ineligible for attempted
|
|
conversion. An attempt is made to switch
|
|
the selected atom (if eligible) to one of the other listed types
|
|
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
|
|
</P>
|
|
<P>The <I>mu</I> keyword allows users to specify chemical
|
|
potentials. This is required and allowed only when using <I>semi-grand</I>.
|
|
All chemical potentials are absolute, so there is one for
|
|
each swap type listed following the <I>types</I> keyword.
|
|
In semi-grand canonical ensemble simulations the chemical composition
|
|
of the system is controlled by the difference in these values. So
|
|
shifting all values by a constant amount will have no effect
|
|
on the simulation.
|
|
</P>
|
|
<P>This command may optionally use the <I>region</I> keyword to define swap
|
|
volume. The specified region must have been previously defined with a
|
|
<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
|
|
Swap attempts occur only between atoms that are both within the
|
|
specified region. Swaps are not otherwise attempted.
|
|
</P>
|
|
<P>You should ensure you do not swap atoms belonging to a molecule, 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 swapping have a
|
|
non-zero molecule ID, but does not check for this at the time of
|
|
swapping.
|
|
</P>
|
|
<P>If not using <I>semi-grand</I> this fix checks to ensure all atoms of the
|
|
given types have the same atomic charge. LAMMPS doesn't enforce this
|
|
in general, but it is needed for this fix to simplify the
|
|
swapping procedure. Successful swaps will swap the atom type and charge
|
|
of the swapped atoms. Conversely, when using <I>semi-grand</I>, it is assumed that all the atom
|
|
types involved in switches have the same charge. Otherwise, charge
|
|
would not be conserved. As a consequence, no checks on atomic charges are
|
|
performed, and successful switches update the atom type but not the
|
|
atom charge. While it is possible to use <I>semi-grand</I> with groups of
|
|
atoms that have different charges, these charges will not be changed when the
|
|
atom types change.
|
|
</P>
|
|
<P>Since this fix computes total potential energies before and after
|
|
proposed swaps, so even complicated potential energy calculations are
|
|
OK, including the following:
|
|
</P>
|
|
<UL><LI> long-range electrostatics (kspace)
|
|
<LI> many body pair styles
|
|
<LI> hybrid pair styles
|
|
<LI> eam pair styles
|
|
<LI> triclinic systems
|
|
<LI> need to include potential energy contributions from other fixes
|
|
</UL>
|
|
<P>Some fixes have an associated potential energy. Examples of such fixes
|
|
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
|
|
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
|
|
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
|
|
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
|
|
For that energy to be included in the total potential energy of the
|
|
system (the quantity used when performing GCMC moves),
|
|
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
|
|
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
|
|
specify if this should be done.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
|
|
files</A>. This includes information about the random
|
|
number generator seed, the next timestep for MC exchanges, etc. See
|
|
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
|
|
re-specify a fix in an input script that reads a restart file, so that
|
|
the operation of the fix continues in an uninterrupted fashion.
|
|
</P>
|
|
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
|
fix.
|
|
</P>
|
|
<P>This fix computes a global vector of length 2, which can be accessed
|
|
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
|
|
values are the following global cumulative quantities:
|
|
</P>
|
|
<UL><LI>1 = swap attempts
|
|
<LI>2 = swap successes
|
|
</UL>
|
|
<P>The vector values calculated by this fix are "extensive".
|
|
</P>
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
|
minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
|
|
built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
|
|
<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
|
|
<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "fix_gcmc.html">fix_gcmc</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
|
|
all atom types.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Sadigh"></A>
|
|
|
|
<P><B>(Sadigh)</B> B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
|
|
L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
|
|
</P>
|
|
</HTML>
|