forked from lijiext/lammps
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This commit is contained in:
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<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>rerun command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>rerun file1 file2 ... keyword args ...
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</PRE>
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<UL><LI>file1,file2,... = dump file(s) to read
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<LI>one or more keywords may be appended, keyword <I>dump</I> must appear and be last
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<PRE>keyword = <I>first</I> or <I>last</I> or <I>every</I> or <I>skip</I> or <I>start</I> or <I>stop</I> or <I>dump</I>
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<I>first</I> args = Nfirts
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Nfirst = dump timestep to start on
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<I>last</I> args = Nlast
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Nlast = dumptimestep to stop on
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<I>every</I> args = Nevery
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Nevery = read snapshots matching every this many timesteps
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<I>skip</I> args = Nskip
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Nskip = read one out of every Nskip snapshots
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<I>start</I> args = Nstart
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Nstart = timestep on which pseudo run will start
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<I>stop</I> args = Nstop
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Nstop = timestep to which pseudo run will end
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<I>dump</I> args = same as <A HREF = "read_dump.html">read_dump</A> command starting with its field arguments
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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>rerun dump.file dump x y z vx vy vz
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rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
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rerun ../run7/dump.file.gz skip 2 dump x y z box yes
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Perform a psuedo simulation run where atom information is read one
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snapshot at a time from a dump file(s), and energies and forces are
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computed on the shapshot to produce thermodynamic or other output.
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</P>
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<P>This can be useful in the following kinds of scenarios, after an
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initial simulation produced the dump file:
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</P>
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<UL><LI>Compute the energy and forces of snaphots using a different potential.
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<LI>Calculate one or more diagnostic quantities on the snapshots that
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weren't computed in the initial run. These can also be computed with
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settings not used in the initial run, e.g. computing an RDF via the
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<A HREF = "compute.rdf.html">compute rdf</A> command with a longer cutoff than was
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used initially.
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<LI>Calculate the portion of per-atom forces resulting from a subset of
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the potential. E.g. compute only Coulombic forces. This can be done
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by only defining only a Coulombic pair style in the rerun script.
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Doing this in the original script would result in different (bad)
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dynamics.
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</UL>
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<P>Conceptually, using the rerun command is like running an input script
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that has a loop in it (see the <A HREF = "next.html">next</A> and <A HREF = "jump.html">jump</A>
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commands). Each iteration of the loop reads one snapshot from the
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dump file via the <A HREF = "read_dump">read_dump</A> command, sets the timestep to
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the appropriate value, and then invokes a <A HREF = "run.html">run</A> command for
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zero timesteps to simply compute energy and forces, and any other
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<A HREF = "thermo_style.html">thermodynamic output</A> or diagnostic info you have
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defined. This computation also invokes any fixes you have defined
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that apply constraints to the system, such as <A HREF = "fix_shake.html">fix
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shake</A> or "fix indent-_fix_indent.html.
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</P>
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<P>Note that a simulation box must already be defined before using the
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rerun command. This can be done by the <A HREF = "create_box.html">create_box</A>,
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<A HREF = "read_data.html">read_data</A>, or <A HREF = "read_restart.html">read_restart</A>
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commands.
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</P>
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<P>Also note that reading per-atom information from dump snapshots is
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limited to the atom coordinates, velocities and image flags as
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explained in the <A HREF = "read_dump.html">read_dump</A> command. Other atom
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properties, which may be necessary to compute energies and forces,
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such as atom charge, or bond topology information for a molecular
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system, are not read from (or even contained in) dump files. Thus
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this auxiliary information should be defined in the usual way, e.g. in
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a data file read in by a <A HREF = "read_data.html">read_data</A> command, before
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using the rerun command.
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</P>
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<HR>
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<P>If more than one dump file is specified, the dump files are read one
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after the other. It is assumed that snapshot timesteps will be in
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ascending order.
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</P>
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<P>The <I>first</I>, <I>last</I>, <I>every</I>, <I>skip</I> keywords determine which
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snapshots are read from the dump file(s). Snapshots are skipped until
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they have a timestamp >= <I>Nfirst</I>. When a snapshot with a timestamp >
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<I>Nlast</I> is encountered, the rerun command finishes. Note below that
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the defaults for <I>first</I> and <I>last</I> are to read all snapshots. If the
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<I>every</I> keyword is set to a value > 0, then only snapshots with
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timestamps that are a multiple of <I>Nevery</I> are read (the first
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snapshot is always read). If <I>Nevery</I> = 0, then this criterion is
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ignored, i.e. every snapshot is read that meets the other criteria.
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If the <I>skip</I> keyword is used, then after the first snapshot is read,
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every Nth snapshot is read, where N = <I>Nskip</I>. E.g. if <I>Nskip</I> = 3,
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then only 1 out of every 3 snapshots is read, assuming the snapshot
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timestamp is also consistent with the other criteria.
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</P>
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<P>The <I>start</I> and <I>stop</I> keywords have the same meaning that they do for
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the <A HREF = "run.html">run</A> command. They only need to be defined if (a) you
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are using a <A HREF = "fix.html">fix</A> command that changes some value over time,
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and (b) you want the reference point for elapsed time (from start to
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stop) to be different than the <I>first</I> and <I>last</I> settings. See the
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doc page for individual fixes to see which ones can be used with the
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<I>start/stop</I> keywords. Note that if you define neither of the
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<I>start</I>/<I>stop</I> or <I>first</I>/<I>last</I> keywords, then LAMMPS treats the
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pseudo run as going from 0 to a huge value (effectively infinity).
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This means that any quantity that a fix scales as a fraction of
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elapsed time in the run, will essentially remain at its intiial value.
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</P>
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<P>The <I>dump</I> keyword is required and must be the last keyword specified.
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Its arguments are passed internally to the <A HREF = "read_dump.html">read_dump</A>
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command. The first argument following the <I>dump</I> keyword should be
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the <I>field1</I> argument of the "read_dump" command. See the
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<A HREF = "read_dump.html">read_dump</A> doc page for details on the various options
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it allows for extracting information from the dump file snapshots, and
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for using that information to alter the LAMMPS simulation.
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</P>
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<HR>
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<P>In general, a LAMMPS input script that uses a rerun command can
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include and perform all the usual operations of an input script that
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uses the <A HREF = "run.html">run</A> command. There are a few exceptions and
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points to consider, as discussed here.
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</P>
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<P>Fixes that perform time integration, such as <A HREF = "fix_nve.html">fix nve</A> or
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<A HREF = "fix_nh.html">fix npt</A> are not invoked, since no time integration is
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performed.
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</P>
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<P>Every time a snapshot is read, the timestep for the simulation is
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reset, as if the <A HREF = "reset_timestep.html<A HREF = "fix_deposit.html">>reset_timestep</A> command were
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used. This command has some restrictions as to what fixes can be
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defined. See its doc page for details. For example, the fix
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deposit</A> and <A HREF = "fix_dt_reset.html">fix dt/reset</A> fixes
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are in this category. They also make no sense to use with a rerun
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command.
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</P>
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<P>If time-averaging fixes like <A HREF = "fix_ave_time.html">fix ave/time</A> are
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used, they are invoked on timesteps that are a function of their
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<I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> settings. As an example, see the
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<A HREF = "fix_ave_time.html">fix ave/time</A> doc page for details. You must
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insure those settings are consistent with the snapshot timestamps that
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are read from the dump file(s). If an averaging fix is not invoked on
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a timestep it expects to be, LAMMPS will flag an error.
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</P>
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<P>The various forms of LAMMPS output, as defined by the
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<A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "thermo.html">thermo</A>,
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<A HREF = "dump.html">dump</A>, and <A HREF = "restart.html">restart</A> commands occur on
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specific timesteps. If successvive dump snapshots skip those
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timesteps, then no output will be produced. E.g. if you request
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thermodynamic output every 100 steps, but the dump file snapshots are
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every 1000 steps, then you will only see thermodynamic output every
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1000 steps.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>To read gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
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LAMMPS</A> section of the documentation.
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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 = "readdump.html">read_dump</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 first = 0, last = a huge value (effectively
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infinity), start = same as first, stop = same as last, every = 0, skip
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= 1;
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</P>
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</HTML>
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@ -0,0 +1,181 @@
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"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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rerun command :h3
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[Syntax:]
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rerun file1 file2 ... keyword args ... :pre
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file1,file2,... = dump file(s) to read :ulb,l
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one or more keywords may be appended, keyword {dump} must appear and be last :l
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keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump}
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{first} args = Nfirts
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Nfirst = dump timestep to start on
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{last} args = Nlast
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Nlast = dumptimestep to stop on
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{every} args = Nevery
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Nevery = read snapshots matching every this many timesteps
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{skip} args = Nskip
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Nskip = read one out of every Nskip snapshots
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{start} args = Nstart
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Nstart = timestep on which pseudo run will start
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{stop} args = Nstop
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Nstop = timestep to which pseudo run will end
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{dump} args = same as "read_dump"_read_dump.html command starting with its field arguments :pre
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:ule
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[Examples:]
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rerun dump.file dump x y z vx vy vz
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rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
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rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre
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|
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[Description:]
|
||||
|
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Perform a psuedo simulation run where atom information is read one
|
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snapshot at a time from a dump file(s), and energies and forces are
|
||||
computed on the shapshot to produce thermodynamic or other output.
|
||||
|
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This can be useful in the following kinds of scenarios, after an
|
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initial simulation produced the dump file:
|
||||
|
||||
Compute the energy and forces of snaphots using a different potential.
|
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:ulb,l
|
||||
|
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Calculate one or more diagnostic quantities on the snapshots that
|
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weren't computed in the initial run. These can also be computed with
|
||||
settings not used in the initial run, e.g. computing an RDF via the
|
||||
"compute rdf"_compute.rdf.html command with a longer cutoff than was
|
||||
used initially. :l
|
||||
|
||||
Calculate the portion of per-atom forces resulting from a subset of
|
||||
the potential. E.g. compute only Coulombic forces. This can be done
|
||||
by only defining only a Coulombic pair style in the rerun script.
|
||||
Doing this in the original script would result in different (bad)
|
||||
dynamics. :l,ule
|
||||
|
||||
Conceptually, using the rerun command is like running an input script
|
||||
that has a loop in it (see the "next"_next.html and "jump"_jump.html
|
||||
commands). Each iteration of the loop reads one snapshot from the
|
||||
dump file via the "read_dump"_read_dump command, sets the timestep to
|
||||
the appropriate value, and then invokes a "run"_run.html command for
|
||||
zero timesteps to simply compute energy and forces, and any other
|
||||
"thermodynamic output"_thermo_style.html or diagnostic info you have
|
||||
defined. This computation also invokes any fixes you have defined
|
||||
that apply constraints to the system, such as "fix
|
||||
shake"_fix_shake.html or "fix indent-_fix_indent.html.
|
||||
|
||||
Note that a simulation box must already be defined before using the
|
||||
rerun command. This can be done by the "create_box"_create_box.html,
|
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"read_data"_read_data.html, or "read_restart"_read_restart.html
|
||||
commands.
|
||||
|
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Also note that reading per-atom information from dump snapshots is
|
||||
limited to the atom coordinates, velocities and image flags as
|
||||
explained in the "read_dump"_read_dump.html command. Other atom
|
||||
properties, which may be necessary to compute energies and forces,
|
||||
such as atom charge, or bond topology information for a molecular
|
||||
system, are not read from (or even contained in) dump files. Thus
|
||||
this auxiliary information should be defined in the usual way, e.g. in
|
||||
a data file read in by a "read_data"_read_data.html command, before
|
||||
using the rerun command.
|
||||
|
||||
:line
|
||||
|
||||
If more than one dump file is specified, the dump files are read one
|
||||
after the other. It is assumed that snapshot timesteps will be in
|
||||
ascending order.
|
||||
|
||||
The {first}, {last}, {every}, {skip} keywords determine which
|
||||
snapshots are read from the dump file(s). Snapshots are skipped until
|
||||
they have a timestamp >= {Nfirst}. When a snapshot with a timestamp >
|
||||
{Nlast} is encountered, the rerun command finishes. Note below that
|
||||
the defaults for {first} and {last} are to read all snapshots. If the
|
||||
{every} keyword is set to a value > 0, then only snapshots with
|
||||
timestamps that are a multiple of {Nevery} are read (the first
|
||||
snapshot is always read). If {Nevery} = 0, then this criterion is
|
||||
ignored, i.e. every snapshot is read that meets the other criteria.
|
||||
If the {skip} keyword is used, then after the first snapshot is read,
|
||||
every Nth snapshot is read, where N = {Nskip}. E.g. if {Nskip} = 3,
|
||||
then only 1 out of every 3 snapshots is read, assuming the snapshot
|
||||
timestamp is also consistent with the other criteria.
|
||||
|
||||
The {start} and {stop} keywords have the same meaning that they do for
|
||||
the "run"_run.html command. They only need to be defined if (a) you
|
||||
are using a "fix"_fix.html command that changes some value over time,
|
||||
and (b) you want the reference point for elapsed time (from start to
|
||||
stop) to be different than the {first} and {last} settings. See the
|
||||
doc page for individual fixes to see which ones can be used with the
|
||||
{start/stop} keywords. Note that if you define neither of the
|
||||
{start}/{stop} or {first}/{last} keywords, then LAMMPS treats the
|
||||
pseudo run as going from 0 to a huge value (effectively infinity).
|
||||
This means that any quantity that a fix scales as a fraction of
|
||||
elapsed time in the run, will essentially remain at its intiial value.
|
||||
|
||||
The {dump} keyword is required and must be the last keyword specified.
|
||||
Its arguments are passed internally to the "read_dump"_read_dump.html
|
||||
command. The first argument following the {dump} keyword should be
|
||||
the {field1} argument of the "read_dump" command. See the
|
||||
"read_dump"_read_dump.html doc page for details on the various options
|
||||
it allows for extracting information from the dump file snapshots, and
|
||||
for using that information to alter the LAMMPS simulation.
|
||||
|
||||
:line
|
||||
|
||||
In general, a LAMMPS input script that uses a rerun command can
|
||||
include and perform all the usual operations of an input script that
|
||||
uses the "run"_run.html command. There are a few exceptions and
|
||||
points to consider, as discussed here.
|
||||
|
||||
Fixes that perform time integration, such as "fix nve"_fix_nve.html or
|
||||
"fix npt"_fix_nh.html are not invoked, since no time integration is
|
||||
performed.
|
||||
|
||||
Every time a snapshot is read, the timestep for the simulation is
|
||||
reset, as if the "reset_timestep"_reset_timestep.html command were
|
||||
used. This command has some restrictions as to what fixes can be
|
||||
defined. See its doc page for details. For example, the fix
|
||||
deposit"_fix_deposit.html and "fix dt/reset"_fix_dt_reset.html fixes
|
||||
are in this category. They also make no sense to use with a rerun
|
||||
command.
|
||||
|
||||
If time-averaging fixes like "fix ave/time"_fix_ave_time.html are
|
||||
used, they are invoked on timesteps that are a function of their
|
||||
{Nevery}, {Nrepeat}, and {Nfreq} settings. As an example, see the
|
||||
"fix ave/time"_fix_ave_time.html doc page for details. You must
|
||||
insure those settings are consistent with the snapshot timestamps that
|
||||
are read from the dump file(s). If an averaging fix is not invoked on
|
||||
a timestep it expects to be, LAMMPS will flag an error.
|
||||
|
||||
The various forms of LAMMPS output, as defined by the
|
||||
"thermo_style"_thermo_style.html, "thermo"_thermo.html,
|
||||
"dump"_dump.html, and "restart"_restart.html commands occur on
|
||||
specific timesteps. If successvive dump snapshots skip those
|
||||
timesteps, then no output will be produced. E.g. if you request
|
||||
thermodynamic output every 100 steps, but the dump file snapshots are
|
||||
every 1000 steps, then you will only see thermodynamic output every
|
||||
1000 steps.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
To read gzipped dump files, you must compile LAMMPS with the
|
||||
-DLAMMPS_GZIP option - see the "Making
|
||||
LAMMPS"_Section_start.html#start_2 section of the documentation.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"read_dump"_readdump.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are first = 0, last = a huge value (effectively
|
||||
infinity), start = same as first, stop = same as last, every = 0, skip
|
||||
= 1;
|
||||
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