From 2bc8b55c790315b434daf0b3bae29b6bd2b9ed2c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 7 Jun 2012 16:10:22 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8233 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/rerun.html | 189 +++++++++++++++++++++++++++++++++++++++++++++++++ doc/rerun.txt | 181 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 370 insertions(+) create mode 100644 doc/rerun.html create mode 100644 doc/rerun.txt diff --git a/doc/rerun.html b/doc/rerun.html new file mode 100644 index 0000000000..abb5d6746a --- /dev/null +++ b/doc/rerun.html @@ -0,0 +1,189 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

rerun command +

+

Syntax: +

+
rerun file1 file2 ... keyword args ... 
+
+ +

Examples: +

+
rerun dump.file dump x y z vx vy vz
+rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z
+rerun ../run7/dump.file.gz skip 2 dump x y z box yes 
+
+

Description: +

+

Perform a psuedo simulation run where atom information is read one +snapshot at a time from a dump file(s), and energies and forces are +computed on the shapshot to produce thermodynamic or other output. +

+

This can be useful in the following kinds of scenarios, after an +initial simulation produced the dump file: +

+ +

Conceptually, using the rerun command is like running an input script +that has a loop in it (see the next and jump +commands). Each iteration of the loop reads one snapshot from the +dump file via the read_dump command, sets the timestep to +the appropriate value, and then invokes a run command for +zero timesteps to simply compute energy and forces, and any other +thermodynamic output 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 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, +read_data, or read_restart +commands. +

+

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 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 command, before +using the rerun command. +

+
+ +

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 command. They only need to be defined if (a) you +are using a fix 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 +command. The first argument following the dump keyword should be +the field1 argument of the "read_dump" command. See the +read_dump 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. +

+
+ +

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 command. There are a few exceptions and +points to consider, as discussed here. +

+

Fixes that perform time integration, such as fix nve or +fix npt 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 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 and fix dt/reset fixes +are in this category. They also make no sense to use with a rerun +command. +

+

If time-averaging fixes like fix ave/time 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 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, +dump, and restart 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. +

+
+ +

Restrictions: +

+

To read gzipped dump files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the Making +LAMMPS section of the documentation. +

+

Related commands: +

+

read_dump +

+

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; +

+ diff --git a/doc/rerun.txt b/doc/rerun.txt new file mode 100644 index 0000000000..7f807732a1 --- /dev/null +++ b/doc/rerun.txt @@ -0,0 +1,181 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +rerun command :h3 + +[Syntax:] + +rerun file1 file2 ... keyword args ... :pre + +file1,file2,... = dump file(s) to read :ulb,l +one or more keywords may be appended, keyword {dump} must appear and be last :l +keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump} + {first} args = Nfirts + Nfirst = dump timestep to start on + {last} args = Nlast + Nlast = dumptimestep to stop on + {every} args = Nevery + Nevery = read snapshots matching every this many timesteps + {skip} args = Nskip + Nskip = read one out of every Nskip snapshots + {start} args = Nstart + Nstart = timestep on which pseudo run will start + {stop} args = Nstop + Nstop = timestep to which pseudo run will end + {dump} args = same as "read_dump"_read_dump.html command starting with its field arguments :pre +:ule + +[Examples:] + +rerun dump.file dump x y z vx vy vz +rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z +rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre + +[Description:] + +Perform a psuedo simulation run where atom information is read one +snapshot at a time from a dump file(s), and energies and forces are +computed on the shapshot to produce thermodynamic or other output. + +This can be useful in the following kinds of scenarios, after an +initial simulation produced the dump file: + +Compute the energy and forces of snaphots using a different potential. +:ulb,l + +Calculate one or more diagnostic quantities on the snapshots that +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, +"read_data"_read_data.html, or "read_restart"_read_restart.html +commands. + +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;