forked from lijiext/lammps
181 lines
6.9 KiB
Plaintext
181 lines
6.9 KiB
Plaintext
"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
|
|
|
|
run command :h3
|
|
|
|
[Syntax:]
|
|
|
|
run N keyword values ... :pre
|
|
|
|
N = # of timesteps :ulb,l
|
|
zero or more keyword/value pairs may be appended :l
|
|
keyword = {upto} or {start} or {stop} or {pre} or {post} or {every} :l
|
|
{upto} value = none
|
|
{start} value = N1
|
|
N1 = timestep at which 1st run started
|
|
{stop} value = N2
|
|
N2 = timestep at which last run will end
|
|
{pre} value = {no} or {yes}
|
|
{post} value = {no} or {yes}
|
|
{every} values = M c1 c2 ...
|
|
M = break the run into M-timestep segments and invoke one or more commands between each segment
|
|
c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
|
|
c1 = NULL means no command will be invoked :pre
|
|
:ule
|
|
|
|
[Examples:]
|
|
|
|
run 10000
|
|
run 1000000 upto
|
|
run 100 start 0 stop 1000
|
|
run 1000 pre no post yes
|
|
run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
|
|
run 100000 every 1000 NULL :pre
|
|
|
|
[Description:]
|
|
|
|
Run or continue dynamics for a specified number of timesteps.
|
|
|
|
When the "run style"_run_style.html is {respa}, N refers to outer
|
|
loop (largest) timesteps.
|
|
|
|
A value of N = 0 is acceptable; only the thermodynamics of the system
|
|
are computed and printed without taking a timestep.
|
|
|
|
The {upto} keyword means to perform a run starting at the current
|
|
timestep up to the specified timestep. E.g. if the current timestep
|
|
is 10,000 and "run 100000 upto" is used, then an additional 90,000
|
|
timesteps will be run. This can be useful for very long runs on a
|
|
machine that allocates chunks of time and terminate your job when time
|
|
is exceeded. If you need to restart your script multiple times
|
|
(reading in the last restart file), you can keep restarting your
|
|
script with the same run command until the simulation finally
|
|
completes.
|
|
|
|
The {start} or {stop} keywords can be used if multiple runs are being
|
|
performed and you want a "fix"_fix.html command that changes some
|
|
value over time (e.g. temperature) to make the change across the
|
|
entire set of runs and not just a single run. See the doc page for
|
|
individual fixes to see which ones can be used with the {start/stop}
|
|
keywords.
|
|
|
|
For example, consider this fix followed by 10 run commands:
|
|
|
|
fix 1 all nvt 200.0 300.0 1.0
|
|
run 1000 start 0 stop 10000
|
|
run 1000 start 0 stop 10000
|
|
...
|
|
run 1000 start 0 stop 10000 :pre
|
|
|
|
The NVT fix ramps the target temperature from 200.0 to 300.0 during a
|
|
run. If the run commands did not have the start/stop keywords (just
|
|
"run 1000"), then the temperature would ramp from 200.0 to 300.0
|
|
during the 1000 steps of each run. With the start/stop keywords, the
|
|
ramping takes place over the 10000 steps of all runs together.
|
|
|
|
The {pre} and {post} keywords can be used to streamline the setup,
|
|
clean-up, and associated output to the screen that happens before and
|
|
after a run. This can be useful if you wish to do many short runs in
|
|
succession (e.g. LAMMPS is being called as a library which is doing
|
|
other computations between successive short LAMMPS runs).
|
|
|
|
By default (pre and post = yes), LAMMPS creates neighbor lists,
|
|
computes forces, and imposes fix constraints before every run. And
|
|
after every run it gathers and prints timings statistics. If a run is
|
|
just a continuation of a previous run (i.e. no settings are changed),
|
|
the initial computation is not necessary; the old neighbor list is
|
|
still valid as are the forces. So if {pre} is specified as "no" then
|
|
the initial setup is skipped, except for printing thermodynamic info.
|
|
Note that if {pre} is set to "no" for the very 1st run LAMMPS
|
|
performs, then it is overridden, since the initial setup computations
|
|
must be done.
|
|
|
|
IMPORTANT NOTE: If your input script changes settings between 2 runs
|
|
(e.g. adds a "fix"_fix.html or "dump"_dump.html or
|
|
"compute"_compute.html or changes a "neighbor"_neigh_modify.html list
|
|
parameter), then the initial setup must be performed. LAMMPS does not
|
|
check for this, but it would be an error to use the {pre no} option in
|
|
this case.
|
|
|
|
If {post} is specified as "no", the full timing summary is skipped;
|
|
only a one-line summary timing is printed.
|
|
|
|
The {every} keyword provides a means of breaking a LAMMPS run into a
|
|
series of shorter runs. Optionally, one or more LAMMPS commands (c1,
|
|
c2, ..., cN) will be executed in between the short runs. If used, the
|
|
{every} keyword must be the last keyword, since it has a variable
|
|
number of arguments. Each of the trailing arguments is a single
|
|
LAMMPS command, and each command should be enclosed in quotes, so that
|
|
the entire command will be treated as a single argument. This will
|
|
also prevent any variables in the command from being evaluated until
|
|
it is executed multiple times during the run. Note that if a command
|
|
itself needs one of its arguments quoted (e.g. the "print"_print.html
|
|
command), then you can use a combination of single and double quotes,
|
|
as in the example above or below.
|
|
|
|
The {every} keyword is a means to avoid listing a long series of runs
|
|
and interleaving commands in your input script. For example, a
|
|
"print"_print.html command could be invoked or a "fix"_fix.html could
|
|
be redefined, e.g. to reset a thermostat temperature. Or this could
|
|
be useful for invoking a command you have added to LAMMPS that wraps
|
|
some other code (e.g. as a library) to perform a computation
|
|
periodically during a long LAMMPS run. See "this
|
|
section"_Section_modify.html of the documentation for info about how
|
|
to add new commands to LAMMPS. See "this
|
|
section"_Section_howto.html#4_10 of the documentation for ideas about
|
|
how to couple LAMMPS to other codes.
|
|
|
|
With the {every} option, N total steps are simulated, in shorter runs
|
|
of M steps each. After each M-length run, the specified commands are
|
|
invoked. If only a single command is specified as NULL, then no
|
|
command is invoked. Thus these lines:
|
|
|
|
variable q equal x\[100\]
|
|
run 6000 every 2000 "print Coord = $q" :pre
|
|
|
|
are the equivalent of:
|
|
|
|
variable q equal x\[100\]
|
|
run 2000
|
|
print Coord = $q
|
|
run 2000
|
|
print Coord = $q
|
|
run 2000
|
|
print Coord = $q :pre
|
|
|
|
which does 3 runs of 2000 steps and prints the x-coordinate of a
|
|
particular atom between runs. Note that the variable "$q" will
|
|
be evaluated afresh each time the print command is executed.
|
|
|
|
Note that by using the line continuation character "&", the run every
|
|
command can be spread across many lines, though it is still a single
|
|
command:
|
|
|
|
run 100000 every 1000 &
|
|
"print 'Minimum value = $a'" &
|
|
"print 'Maximum value = $b'" &
|
|
"print 'Temp = $c'" &
|
|
"print 'Press = $d'" :pre
|
|
|
|
If the {pre} and {post} options are set to "no" when used with the
|
|
{every} keyword, then the 1st run will do the full setup and the last
|
|
run will print the full timing summary, but these operations will be
|
|
skipped for intermediate runs.
|
|
|
|
[Restrictions:] none
|
|
|
|
[Related commands:]
|
|
|
|
"minimize"_minimize.html, "run_style"_run_style.html,
|
|
"temper"_temper.html
|
|
|
|
[Default:]
|
|
|
|
The option defaults are start = the current timestep, stop = current
|
|
timestep + N, pre = yes, and post = yes.
|