rerun command — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# rerun command

## Syntax

    rerun file1 file2 ... keyword args ...

- file1,file2,… = dump file(s) to read

- one or more keywords may be appended, keyword dump must appear and be last

      keyword = first or last or every or skip or start or stop or post or dump
       first args = Nfirst
         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
       post value = yes or no
       dump args = same as read_dump command starting with its field arguments

## 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 dump.vels dump x y z vx vy vz box yes format molfile lammpstrj
    rerun dump.dcd dump x y z box no format molfile dcd
    rerun ../run7/dump.file.gz skip 2 dump x y z box yes
    rerun dump.bp dump x y z box no format adios
    rerun dump.bp dump x y z vx vy vz format adios timeout 10.0

## Description

Perform a pseudo 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 snapshots using a different potential.

- Calculate one or more diagnostic quantities on the snapshots that were not 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 command with a longer cutoff than was used initially.

- 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.

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.

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.

Also note that the frequency of thermodynamic or dump output from the rerun simulation will depend on settings made in the rerun script, the same as for output from any LAMMPS simulation. See further info below as to what that means if the timesteps for snapshots read from dump files do not match the specified output frequency.

If more than one dump file is specified, the dump files are read one after the other in the order specified. It is assumed that snapshot timesteps will be in ascending order. If a snapshot is encountered that is not in ascending order, it will skip the snapshot until it reads one that is. This allows skipping of a duplicate snapshot (same timestep), e.g. that appeared at the end of one file and beginning of the next. However if you specify a series of dump files in an incorrect order (with respect to the timesteps they contain), you may skip large numbers of snapshots.

Note that the dump files specified as part of the dump keyword can be parallel files, i.e. written as multiple files either per processor and/or per snapshot. If that is the case they will also be read in parallel which can make the rerun command operate dramatically faster for large systems. See the page for the read_dump and dump commands which describe how to read and write parallel dump files.

The first, last, every, skip keywords determine which snapshots are read from the dump file(s). Snapshots are skipped until they have a timestep >= Nfirst. When a snapshot with a timestep > Nlast is encountered, the rerun command finishes. Note 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 timesteps 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 timestep is also consistent with the other criteria.

Note

Not all dump formats contain the timestep and not all dump readers support reading it. In that case individual snapshots are assigned consecutive timestep numbers starting at 1.

The start and stop keywords do not affect which snapshots are read from the dump file(s). Rather, they 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 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 initial value. Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the stop setting you have specified.

The post keyword can be used to minimize the output to the screen that happens after a rerun command, similar to the post keyword of the run command. It is set to no by default.

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 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. Fixes that perturb or constrain the forces on atoms will be invoked, just as they would during a normal run. Examples are fix indent and fix langevin. So you should think carefully as to whether that makes sense for the manner in which you are reprocessing the dump snapshots.

If you only want the rerun script to perform an analysis that does not involve pair interactions, such as use compute msd to calculated displacements over time, you do not need to define a pair style, which may also mean neighbor lists will not need to be calculated which saves time. The comm_modify cutoff command can also be used to ensure ghost atoms are acquired from far enough away for operations like bond and angle evaluations, if no pair style is being used.

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 documentation 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 page for details. You must ensure 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 with specified frequency, e.g. every N steps. If the timestep for a dump snapshot is not a multiple of N, then it will be read and processed, but no output will be produced. If you want output for every dump snapshot, you can simply use N=1 for an output frequency, e.g. for thermodynamic output or new dump file output.

## Restrictions

The rerun command is subject to all restrictions of the read_dump command.

## 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, post = no;