Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature

as the lowest desired sampled enthalpy.  Further explanation can be

found in our recent papers "(Malolepsza)"_#Malolepsza.

This fix requires a Nose-Hoover thermostat reference passed to the grem

by {thermostat-ID}. Two distinct temperatures exist in this generalized

This fix requires a Nose-Hoover thermostat fix reference passed to the

grem as {thermostat-ID}. Two distinct temperatures exist in this generalized

ensemble, the effective temperature defined above, and a kinetic

temperature that controls the velocity distribution of particles as

usual. Either constant volume or constant pressure algorithms can be

used.

The fix enforces a generalized ensemble in a single replica only.

Typically, different replicas only differ by {lambda} for simplicity,

but this is not necessary. Multi-replica runs need to be run outside

of LAMMPS. An example of this can be found in examples/USER/misc/grem

The fix enforces a generalized ensemble in a single replica

only. Typically, this ideaology is combined with replica 

exchange with replicas differing by {lambda} only

for simplicity, but this is not required. A multi-replica 

simulation can be run within the LAMMPS environment using the

"grem"_temper_grem.html command. This utilizes LAMMPS partition

mode and requires the number of available processors be 

on the order of the number of desired replicas. A 100-replica

simulation would require at least 100 processors (1 per world

at minimum). If a many replicas are needed on a small number of

processors, multi-replica runs can be run outside of LAMMPS.

An example of this can be found in examples/USER/misc/grem and 

has no limit on the number of replicas per processor. However, 

this is very inefficient and error prone and should be avoided

if possible. 

In general, defining the generalized ensembles is unique for every

system. When starting a many-replica simulation without any knowledge of

[Related commands:]

"fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, "thermo_modify"_thermo_modify.html

"grem"_temper_grem.html, "fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, "thermo_modify"_thermo_modify.html

[Default:] none

"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 1000 ${lambda} fxgREM fxnvt 0 58728

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

[Description:]

Run a parallel tempering or replica exchange simulation in LAMMPS partition

mode 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 greater 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 but unique

generalized 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 walkers world 2 4 0 1 3 :pre

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

example above with ${walkers} 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).

timestep        1.0

fix             fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 

fix             fxgREM all grem 400 -.01 -30000 fxnvt

fix             fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 

fix             fxgREM all grem 400 -.01 -30000 fxnpt

thermo_modify   press fxgREM_press

run             1000

/run.sh

/screen.*

/log.lammps.*