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