run command — LIGGGHTS v3.X documentation

# run command

## Syntax

run N keyword values ...

- N = # of timesteps
- zero or more keyword/value pairs may be appended
- keyword = upto or start or stop or pre or post or every

    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 LIGGGHTS(R)-PUBLIC commands, each enclosed in quotes
      c1 = NULL means no command will be invoked

## 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

## Description

Run or continue dynamics for a specified number of timesteps (“run”).

When the run style 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 command that changes some value over time 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.

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. LIGGGHTS(R)-PUBLIC is being called as a library which is doing other computations between successive short LIGGGHTS(R)-PUBLIC runs).

By default (pre and post = yes), LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC performs, then it is overridden, since the initial setup computations must be done.

Warning

If your input script changes settings between 2 runs (e.g. adds a fix or dump or compute or changes a neighbor list parameter), then the initial setup must be performed. LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC run into a series of shorter runs. Optionally, one or more LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC 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 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 command could be invoked or a fix could be redefined, e.g. to reset a thermostat temperature. Or this could be useful for invoking a command you have added to LIGGGHTS(R)-PUBLIC that wraps some other code (e.g. as a library) to perform a computation periodically during a long LIGGGHTS(R)-PUBLIC run. See this section of the documentation for info about how to add new commands to LIGGGHTS(R)-PUBLIC. See this section of the documentation for ideas about how to couple LIGGGHTS(R)-PUBLIC 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"

are the equivalent of:

    variable q equal x[100]
    run 2000
    print Coord = $q
    run 2000
    print Coord = $q
    run 2000
    print Coord = $q

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'"

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.

Warning

You might hope to specify a command that exits the run by jumping out of the loop, e.g.

    variable t equal temp
    run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"

Unfortunately this will not currently work. The run command simply executes each command one at a time each time it pauses, then continues the run. You can replace the jump command with a simple quit command and cause LIGGGHTS(R)-PUBLIC to exit during the middle of a run when the condition is met.

## Restrictions

The number of specified timesteps N must fit in a signed 32-bit integer, so you are limited to slightly more than 2 billion steps (2^31) in a single run. However, you can perform successive runs to run a simulation for any number of steps (ok, up to 2^63 steps).

## Related commands

run_style,

## Default

The option defaults are start = the current timestep, stop = current timestep + N, pre = yes, and post = yes.