Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/src/temper.txt
2f298951cff2lammm-devel

Last Change
Raw File

temper.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
temper command :h3
[Syntax:]
temper N M temp fix-ID seed1 seed2 index :pre
N = total # of timesteps to run
M = attempt a tempering swap every this many steps
temp = initial temperature for this ensemble
fix-ID = ID of the fix that will control temperature during the run
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:]
temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w :pre
[Description:]
Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "Section 2.7"_Section_start.html#start_7 of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
(with and without included time integration) are supported. The command
will print an error message and abort, if the chosen fix is unsupported.
The desired temperature is specified by {temp}, 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 t world 300.0 310.0 320.0 330.0
fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382 :pre
would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.
As the tempering simulation runs for {N} timesteps, a temperature 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 Boltzmann-weighted Metropolis criterion which uses
{seed2} in the random number generator.
As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the "section on command-line
switches"_Section_start.html#start_7 for info on how to change these
names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
... :pre
The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
You can have each replica create its own dump file in the following
manner:
variable rep world 0 1 2 3 4 5 6 7
dump 1 all atom 1000 dump.temper.${rep} :pre
NOTE: Each replica's dump file will contain a continuous trajectory
for its atoms where the temperature varies over time as swaps take
place involving that replica. If you want a series of dump files,
each with snapshots (from all replicas) that are all at a single
temperature, then you will need to post-process the dump files using
the information from the log.lammps file. E.g. you could produce one
dump file with snapshots at 300K (from all replicas), another with
snapshots at 310K, etc. Note that these new dump files will not
contain "continuous trajectories" for individual atoms, because two
successive snapshots (in time) may be from different replicas.
The last argument {index} in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The {index} value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the {N} values listed in the log file for the previous
run for the replica temperatures at that timestep. 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 tempering command like the
example above with $w as the last argument.
:line
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"variable"_variable.html, "prd"_prd.html, "neb"_neb.html
[Default:] none
c4science · Help