Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/fix_atom_swap.txt
b0c8caa669a0lammm-master

Last Change
Raw File

fix_atom_swap.txt
View Options

"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 atom/swap command :h3
[Syntax:]
fix ID group-ID atom/swap N X type_1 type_2 seed T keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
atom/swap = style name of this fix command :l
N = invoke this fix every N steps :l
X = number of swaps to attempt every N steps :l
type_1 = first atom type to swap :l
type_2 = second atom type to swap :l
seed = random # seed (positive integer) :l
T = scaling temperature of the MC swaps (temperature units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {ke} or {semi-grand} or {region} :l
{ke} value = {no} or {yes}
{no} = no conservation of kinetic energy after atom swaps
{yes} = kinetic energy is conserved after atom swaps
{semi-grand} value = {no} or {yes}
{no} = particle type counts and fractions conserved
{yes} = semi-grand canonical ensemble, particle fractions not conserved
{region} value = region-ID
region-ID = ID of region to use as a swap volume :pre
:ule
[Examples:]
fix 2 all atom/swap 1 1 1 2 29494 300.0 ke no
fix atom_swap_fix all atom/swap 100 1 5 6 12345 298.0 region my_swap_region :pre
[Description:]
This fix performs Monte Carlo swaps of atoms of one type with atoms of
a second type. The specified temperature {T} is used to scale the
energy in the criterion for accepting or rejecting each swap. The fix
is invoked once every {N} steps. Each time the fix is invoked {X}
swap attempts are made, one after the other, bewteen pairs of randomly
selected atoms. Two attributes of the atoms in the pair are swapped:
the atom type and the atom charge (if defined). Each attempted swap
is accepted or rejected based on the Metropolis criterion using the
Boltzmann factor exp(-Edelta / kT), where Edelta is the change in the
system potential energy due to the swap, k is the Boltzmann constant,
and {T} is the specified temperature.
In addition to the MC swaps, atoms in the simulation domain will move
via normal dynamic timestepping if a time integration fix is defined,
e.g. "fix_nvt"_fix_nvt.html, which will result in a hybrid MC+MD
simulation. If a swap produces a poorly equilibrated system, a
smaller-than-usual timestep size may be needed when running such a
simulation.
The {ke} keyword can be set to {no} to turn off kinetic energy
conservation for swaps. The default is {yes}, 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.
The {semi-grand} keyword can be set to {yes} to switch to the semi-grand
canonical ensemble, meaning that the total number of each particle type
does not need to be conserved. The default is {no}, which means that the
only kind of swap allowed exchanges an atom of type_1 with an atom of type_2.
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. Particles of type_1 can independently be converted
to type_2, and particles of type_2 can independently be converted to type_1.
Swaps in each direction are attempted half of the time.
If the {region} keyword is not used, all atoms of {type_1} and
{type_2} which are in the specified group are candidates for swapping.
If the {region} keyword is used, swappable atoms must also be in the
specified region. Each time a swap is performed one random atom is
chosen from the list of candidate {type_1} atoms, and one random atom
from the list of candidate {type_2} atoms. A pair of swapped atoms
can thus be far apart geometrically. If multiple swaps are attempted
in the same timestep, an individual atom may be swapped multiple
times.
An additional requirement for charged systems is that all swappable
atoms of {type_1} must have the same charge, and likewise for {type_2}.
Atoms of {type_1} need not have the same charge as atoms of {type_2}.
Note that this fix computes total potential energies before and after
attempted swaps, so even systems with complicated potential energy
calculations can be used, including the following:
long-range electrostatics (KSpace)
many-body pair styles
hybrid pair styles
EAM pair styles
triclinic systems :ul
Some fixes have an associated potential energy. Currently, the
potential energy contribution due to these fixes is not included in
the Metropolis criterion dictating atom swap probabilities. Examples
of such fixes include: "efield"_fix_efield.html,
"gravity"_fix_gravity.html, "addforce"_fix_addforce.html,
"restrain"_fix_restrain.html, and "wall fixes"_fix_wall.html.
IMPORTANT NOTE: During the swaps performed within a single timestep,
this fix performs minimal communication to update the state of the
system. If the cutoff distance for all type pairs, as defined by the
"pair_style"_pair_style.html is the same, the neighbor list does not
need to be rebuilt when a swap takes place. The CPU cost per swap
will then be equivalent to roughly a single MD timestep. If the
cutoff distances are not the same for all type pairs, then the
neighbor list will be rebuilt, and the CPU cost per swap will be
higher.
:line
IMPORTANT NOTE: If you only wish to use this fix to relax a system
without dynamics, e.g. to model surface segregation in an alloy, then
you do not need to define a time integration fix. In this scenario an
MC-only simulation can be run in a single timestep or multiple
timesteps as follows:
fix mc all atom/swap 1 100000 ...
run 1 :pre
or
fix mc all atom/swap 1 1000 ...
run 100 :pre
In the first case, 100000 swaps are attempted in the first (only)
timestep. A neighbor list will only be built once, which is
sufficient since atoms are not moving.
In the second case, the same 100000 swaps are spread across 100
timesteps. This will require 100 neighbor list builds (once each time
the fix is invoked, which should still be relatively cheap), but also
allows you to monitor or analyze various quantities such as the
evolution of the system energy as a function of timestep, as if the
system were evolving over time.
[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 2, which can be accessed
by various "output commands"_Section_howto.html#howto_15. The vector
values are the following global cumulative quantities:
1 = swap attempts
2 = swap 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.
[Related commands:]
"fix bond/swap"_fix_bond_swap.html, "fix_nvt"_fix_nvt.html,
"neighbor"_neighbor.html, "fix_deposit"_fix_deposit.html,
"fix_evaporate"_fix_evaporate.html, "delete_atoms"_delete_atoms.html,
"fix_gcmc"_fix_gcmc.html
[Default:]
The option defaults are ke = yes, semi-grand = no.
c4science · Help