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: timestep at which 1st run started

    • stop value = 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 SPARTA 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 'Temp = $t'"
run 100000 every 1000 NULL

Description:

Run or continue a simulation for a specified number of timesteps.

A value of N = 0 is acceptable; only the statistics 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 variable or fix command that changes some value over time (e.g. target temperature) to make the change across the entire set of runs and not just a single run.

For example, consider these commands followed by 10 run commands:

variable     myTemp equal ramp(300,500)
surf_collide 1 diffuse v_myTemp 0.5
run      1000 start 0 stop 10000
run      1000 start 0 stop 10000
...
run      1000 start 0 stop 10000

The ramp() function in the variable and its use in the “surf_collide” command will ramp the target temperature from 300 to 500 during a run. If the run commands did not have the start/stop keywords (just “run 1000”), then the temperature would ramp from 300 to 500 during the 1000 steps of each run. With the start/stop keywords, the ramping takes place smoothly over the 10000 steps of all the 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. SPARTA is being called as a library which is doing other computations between successive short SPARTA runs).

By default (pre and post = yes), SPARTA zeroes statistical counts before every run and initializes other fixes and computes as needed. 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. So if pre is specified as “no” then the initial setup is skipped, except for printing statistical info. Note that if pre is set to “no” for the very 1st run SPARTA performs, then it is overridden, since the initial setup computations must be done.

Important

If your input script changes settings between 2 runs (e.g. adds a fix or compute), then the initial setup must be performed. SPARTA 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 and statistical output is skipped; only a one-line summary timing is printed.

The every keyword provides a means of breaking a SPARTA run into a series of shorter runs. Optionally, one or more SPARTA 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 SPARTA 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 load balancing parameter. Or this could be useful for invoking a command you have added to SPARTA that wraps some other code (e.g. as a library) to perform a computation periodically during a long SPARTA run. See Section 8 of the manual for info about how to add new commands to SPARTA. See Section 6.7 of the manual for ideas about how to couple SPARTA 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:

compute t temp
variable myT equal c_t
run 6000 every 2000 "print 'Temp = $myT'"

are the equivalent of:

compute t temp
variable myT equal c_t
run 2000
print "Temp = $myT"
run 2000
print "Temp = $myT"
run 2000
print "Temp = $myT"

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'"

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.

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

compute t temp
variable T equal c_t
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 SPARTA 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).

Default:

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