forked from lijiext/lammps
207 lines
8.4 KiB
HTML
207 lines
8.4 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>run command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>run N keyword values ...
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</PRE>
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<UL><LI>N = # of timesteps
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>upto</I> or <I>start</I> or <I>stop</I> or <I>pre</I> or <I>post</I> or <I>every</I>
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<PRE> <I>upto</I> value = none
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<I>start</I> value = N1
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N1 = timestep at which 1st run started
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<I>stop</I> value = N2
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N2 = timestep at which last run will end
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<I>pre</I> value = <I>no</I> or <I>yes</I>
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<I>post</I> value = <I>no</I> or <I>yes</I>
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<I>every</I> values = M c1 c2 ...
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M = break the run into M-timestep segments and invoke one or more commands between each segment
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c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
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c1 = NULL means no command will be invoked
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Run or continue dynamics for a specified number of timesteps.
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</P>
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<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, N refers to outer
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loop (largest) timesteps.
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</P>
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<P>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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</P>
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<P>The <I>upto</I> 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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</P>
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<P>The <I>start</I> or <I>stop</I> keywords can be used if multiple runs are being
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performed and you want a <A HREF = "fix.html">fix</A> 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 <I>start/stop</I>
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keywords.
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</P>
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<P>For example, consider this fix followed by 10 run commands:
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</P>
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<PRE>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
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</PRE>
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<P>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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</P>
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<P>The <I>pre</I> and <I>post</I> 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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</P>
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<P>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 <I>pre</I> 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 <I>pre</I> 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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</P>
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<P>IMPORTANT NOTE: If your input script changes settings between 2 runs
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(e.g. adds a <A HREF = "fix.html">fix</A> or <A HREF = "dump.html">dump</A> or
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<A HREF = "compute.html">compute</A> or changes a <A HREF = "neigh_modify.html">neighbor</A> 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 <I>pre no</I> option in
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this case.
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</P>
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<P>If <I>post</I> 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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</P>
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<P>The <I>every</I> keyword provides a means of breaking a LAMMPS run into a
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series of shorter runs. Optionally, one or more LAMMPS commands (c1,
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c2, ..., cN) will be executed in between the short runs. If used, the
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<I>every</I> keyword must be the last keyword, since it has a variable
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number of arguments. Each of the trailing arguments is a single
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LAMMPS command, and each command should be enclosed in quotes, so that
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the entire command will be treated as a single argument. This will
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also prevent any variables in the command from being evaluated until
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it is executed multiple times during the run. Note that if a command
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itself needs one of its arguments quoted (e.g. the <A HREF = "print.html">print</A>
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command), then you can use a combination of single and double quotes,
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as in the example above or below.
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</P>
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<P>The <I>every</I> keyword is a means to avoid listing a long series of runs
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and interleaving commands in your input script. For example, a
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<A HREF = "print.html">print</A> command could be invoked or a <A HREF = "fix.html">fix</A> could
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be redefined, e.g. to reset a thermostat temperature. Or this could
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be useful for invoking a command you have added to LAMMPS that wraps
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some other code (e.g. as a library) to perform a computation
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periodically during a long LAMMPS run. See <A HREF = "Section_modify.html">this
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section</A> of the documentation for info about how
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to add new commands to LAMMPS. See <A HREF = "Section_howto.html#howto_10">this
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section</A> of the documentation for ideas
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about how to couple LAMMPS to other codes.
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</P>
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<P>With the <I>every</I> option, N total steps are simulated, in shorter runs
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of M steps each. After each M-length run, the specified commands are
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invoked. If only a single command is specified as NULL, then no
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command is invoked. Thus these lines:
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</P>
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<PRE>variable q equal x[100]
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run 6000 every 2000 "print 'Coord = $q'"
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</PRE>
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<P>are the equivalent of:
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</P>
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<PRE>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 = $q"
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</PRE>
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<P>which does 3 runs of 2000 steps and prints the x-coordinate of a
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particular atom between runs. Note that the variable "$q" will
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be evaluated afresh each time the print command is executed.
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</P>
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<P>Note that by using the line continuation character "&", the run every
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command can be spread across many lines, though it is still a single
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command:
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</P>
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<PRE>run 100000 every 1000 &
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"print 'Minimum value = $a'" &
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"print 'Maximum value = $b'" &
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"print 'Temp = $c'" &
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"print 'Press = $d'"
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</PRE>
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<P>If the <I>pre</I> and <I>post</I> options are set to "no" when used with the
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<I>every</I> keyword, then the 1st run will do the full setup and the last
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run will print the full timing summary, but these operations will be
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skipped for intermediate runs.
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</P>
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<P>IMPORTANT NOTE: You might hope to specify a command that exits the run
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by jumping out of the loop, e.g.
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</P>
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<PRE>variable t equal temp
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run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'"
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</PRE>
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<P>Unfortunately this will not currently work. The run command simply
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executes each command one at a time each time it pauses, then
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continues the run. You can replace the jump command with a simple
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<A HREF = "quit.html">quit</A> command and cause LAMMPS to exit during the
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middle of a run when the condition is met.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The number of specified timesteps N must fit in a signed 32-bit
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integer, so you are limited to slightly more than 2 billion steps
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(2^31) in a single run. However, you can perform successive runs to
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run a simulation for any number of steps (ok, up to 2^63 steps).
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "minimize.html">minimize</A>, <A HREF = "run_style.html">run_style</A>,
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<A HREF = "temper.html">temper</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>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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</P>
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</HTML>
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