forked from lijiext/lammps
186 lines
7.6 KiB
HTML
186 lines
7.6 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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</CENTER>
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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 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
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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. The <A HREF = "pair_style.html">pair_style soft</A> potential also
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changes its pair potential coefficients in this manner.
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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> 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 <A HREF = "print.html">print</A> command could be invoked or a <A HREF = "fix.html">fix</A>
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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 <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#4_10">this
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section</A> of the documentation for ideas about
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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 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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</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, as in this example, the
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command can contain <A HREF = "variable.html">variables</A> which will be evaluated
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each time the command is invoked.
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</P>
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<P>IMPORTANT NOTE: For the <I>every</I> 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 <I>every</I> option must be the last keyword
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used.
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</P>
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<P>IMPORTANT NOTE: For the <I>every</I> option, if the command includes a
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variable (e.g. $x or ${abc}), and you want the variable to be
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evaluated afresh each time the command is invoked, then you should
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enclose that command argument in double quotes, as in the "Protein Rg
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= $r" example above. If you don't do this, then the variable will be
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substituted for only once initially when the run command is parsed,
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just as occurs for any other command containing a variable.
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</P>
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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><B>Restrictions:</B> none
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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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