added documention, re-ran temper_grem example

"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

grem command :h3

[Syntax:]

grem N M lambda fix-ID thermostat-ID seed1 seed2 index :pre

N = total # of timesteps to run

M = attempt a tempering swap every this many steps

lambda = initial lambda for this ensemble

fix-ID = ID of fix_grem

thermostat-ID = ID of the thermostat that controls kinetic temperature

seed1 = random # seed used to decide on adjacent temperature to partner with

seed2 = random # seed for Boltzmann factor in Metropolis swap

index = which temperature (0 to N-1) I am simulating (optional) :ul

[Examples:]

grem 100000 100 ${lambda} fxgREM fxnvt 0 58728

grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 $w :pre

[Description:]

Run a parallel tempering or replica exchange simulation using multiple

generalized replicas (ensembles) of a system defined by 

"fix_grem"_fix_grem.html. Two or more replicas must be used. 

This command is a modification of the "temper"_temper.html command and has the 

same dependencies, restraints, and input variables which are discussed there

in detail.

Instead of temperature, this command performs replica exchanges in lambda

as per the generalized ensemble enforced by "fix_grem"_fix_grem.html.

The desired lambda is specified by {lambda}, which is typically a

variable previously set in the input script, so that each partition is

assigned a different temperature.  See the "variable"_variable.html

command for more details.  For example:

variable lambda world 400 420 440 460

fix fxnvt all nvt temp 300.0 300.0 100.0

fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt

temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre

would define 4 lambdas with constant kinetic temperature, and assign one

of them to "fix_grem"_fix_grem.html used by each replica, and to the grem

command.

As the gREM simulation runs for {N} timesteps, a swap

between adjacent ensembles will be attempted every {M} timesteps.  If

{seed1} is 0, then the swap attempts will alternate between odd and

even pairings.  If {seed1} is non-zero then it is used as a seed in a

random number generator to randomly choose an odd or even pairing each

time.  Each attempted swap of temperatures is either accepted or

rejected based on a Metropolis criterion, derived for gREM by 

"(Kim)"_#Kim, which uses {seed2} in the random number generator.

File management works identical to the "temper"_temper.html command.

Dump files created by this fix contain continuous trajectories and

require post-processing to obtain per-replica information.

The last argument {index} in the grem command is optional and is

used when restarting a run from a set of restart files (one

for each replica) which had previously swapped to new lambda.

This is done using a variable. For example if the

log file listed the following for a simulation with 5 replicas:

500000 2 4 0 1 3 :pre

then a setting of

variable w world 2 4 0 1 3 :pre

would be used to restart the run with a grem command like the

example above with $w as the last argument. This functionality

is identical to "temper"_temper.html.

:line

[Restrictions:]

This command can only be used if LAMMPS was built with the USER-MISC

package.  See the "Making LAMMPS"_Section_start.html#start_3 section

for more info on packages.

This command must be used with "fix_grem"_fix_grem.html.

[Related commands:]

"fix_grem"_fix_grem.html, "temper"_temper.html, "variable"_variable.html

[Default:] none

:link(Kim)

[(Kim)] Kim, Keyes, Straub, J. Chem. Phys., 132, 224107 (2010).