read_dump command — LIGGGHTS v3.X documentation

# read_dump command

## Syntax

    read_dump file Nstep field1 field2 ... keyword values ...

- file = name of dump file to read
- Nstep = snapshot timestep to read from file
- one or more fields may be appended

    field = x or y or z or vx or vy or vz or q or ix or iy or iz
      x,*y*,*z* = atom coordinates
      vx,*vy*,*vz* = velocity components
      q = charge
      ix,*iy*,*iz* = image flags in each dimension

- zero or more keyword/value pairs may be appended
- keyword = box or replace or purge or trim or add or label or scaled or wrapped or format

    box value = yes or no = replace simulation box with dump box
    replace value = yes or no = overwrite atoms with dump atoms
    purge value = yes or no = delete all atoms before adding dump atoms
    trim value = yes or no = trim atoms not in dump snapshot
    add value = yes or no = add new dump atoms to system
    label value = field column
      field = one of the listed fields or id or type
      column = label on corresponding column in dump file
    scaled value = yes or no = coords in dump file are scaled/unscaled
    wrapped value = yes or no = coords in dump file are wrapped/unwrapped
    format values = format of dump file, must be last keyword if used
      native = native LIGGGHTS(R)-PUBLIC dump file
      xyz = XYZ file

## Examples

    read_dump dump.file 5000 x y z
    read_dump dump.xyz 5 x y z format xyz box no
    read_dump dump.file 5000 x y vx vy trim yes
    read_dump ../run7/dump.file.gz 10000 x y z box yes
    read_dump dump.xyz 5 x y z box no format xyz

## Description

Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and the simluation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the read_restart and read_data commands for alternative methods to do this. Also see the `rerun` command for a means of reading multiple snapshots from a dump file.

Note that a simulation box must already be defined before using the read_dump command. This can be done by the create_box, read_data, or read_restart commands. The read_dump command can reset the simulation box dimensions, as explained below.

Also note that reading per-atom information from a dump snapshot is limited to the atom coordinates, velocities and image flags, as explained below. Other atom properties, which may be necessary to run a valid simulation, 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 read_dump command, or by the set command, after the dump snapshot is read.

If the dump filename specified as file ends with ”.gz”, the dump file is read in gzipped format. You cannot (yet) read a dump file that was written in binary format with a ”.bin” suffix, or to multiple files via the “%” option in the dump file name. See the dump command for details.

The format of the dump file is selected through the format keyword. If specified, it must be the last keyword used, since all remaining arguments are passed on to the dump reader. The native format is for native LIGGGHTS(R)-PUBLIC dump files, written with a “dump atom”.html or dump custom command. The xyz format is for generic XYZ formatted dump files,

Support for other dump format readers may be added in the future.

Global information is first read from the dump file, namely timestep and box information.

The dump file is scanned for a snapshot with a time stamp that matches the specified Nstep. This means the LIGGGHTS(R)-PUBLIC timestep the dump file snapshot was written on for the native format. However, the xyz formats do not store the timestep. For these formats, timesteps are numbered logically, in a sequential manner, starting from 0. Thus to access the 10th snapshot in an xyz or mofile formatted dump file, use Nstep = 9.

The dimensions of the simulation box for the selected snapshot are also read; see the box keyword discussion below. For the native format, an error is generated if the snapshot is for a triclinic box and the current simulation box is orthogonal or vice versa. A warning will be generated if the snapshot box boundary conditions (periodic, shrink-wrapped, etc) do not match the current simulation boundary conditions, but the boundary condition information in the snapshot is otherwise ignored. See the “boundary” command for more details.

For the xyz format, no information about the box is available, so you must set the box flag to no. See details below.

Per-atom information from the dump file snapshot is then read from the dump file snapshot. This corresponds to the specified fields listed in the read_dump command. It is an error to specify a z-dimension field, namely z, vz, or iz, for a 2d simulation.

For dump files in native format, each column of per-atom data has a text label listed in the file. A matching label for each field must appear, e.g. the label “vy” for the field vy. For the x, y, z fields any of the following labels are considered a match:

    x, xs, xu, xsu for field x
    y, ys, yu, ysu for field y
    z, zs, zu, zsu for field z

The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and unwrapped) is explained on the dump command doc page. These labels are searched for in the list of column labels in the dump file, in order, until a match is found.

The dump file must also contain atom IDs, with a column label of “id”.

If the add keyword is specified with a value of yes, as discussed below, the dump file must contain atom types, with a column label of “type”.

If a column label you want to read from the dump file is not a match to a specified field, the label keyword can be used to specify the specific column label from the dump file to associate with that field. An example is if a time-averaged coordinate is written to the dump file via the fix ave/atom command. The column will then have a label corresponding to the fix-ID rather than “x” or “xs”. The label keyword can also be used to specify new column labels for fields id and type.

For dump files in xyz format, only the x, y, and z fields are supported. The dump file does not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms is consistent from snapshot to snapshot in the the XYZ dump file. See the dump_modify sort command if the XYZ dump file was written by LIGGGHTS(R)-PUBLIC.

Information from the dump file snapshot is used to overwrite or replace properties of the current system. There are various options for how this is done, determined by the specified fields and optional keywords.

The timestep of the snapshot becomes the current timestep for the simulation. See the reset_timestep command if you wish to change this after the dump snapshot is read.

If the box keyword is specified with a yes value, then the current simulation box dimensions are replaced by the dump snapshot box dimensions. If the box keyword is specified with a no value, the current simulatoin box is unchanged.

If the purge keyword is specified with a yes value, then all current atoms in the system are deleted before any of the operations invoked by the replace, trim, or add keywords take place.

If the replace keyword is specified with a yes value, then atoms with IDs that are in both the current system and the dump snapshot have their properties overwritten by field values. If the replace keyword is specified with a no value, atoms with IDs that are in both the current system and the dump snapshot are not modified.

If the trim keyword is specified with a yes value, then atoms with IDs that are in the current system but not in the dump snapshot are deleted. These atoms are unaffected if the trim keyword is specified with a no value.

If the add keyword is specified with a yes value, then atoms with IDs that are in the dump snapshot, but not in the current system are added to the system. These dump atoms are ignored if the add keyword is specified with a no value.

Note that atoms added via the add keyword will have only the attributes read from the dump file due to the field arguments. If x or y or z is not specified as a field, a value of 0.0 is used for added atoms. Added atoms must have an atom type, so this value must appear in the dump file.

Any other attributes (e.g. charge or particle diameter for spherical particles) will be set to default values, the same as if the create_atoms command were used.

Note that atom IDs are not preserved for new dump snapshot atoms added via the add keyword. The procedure for assigning new atom IDS to added atoms is the same as is described for the create_atoms command.

Atom coordinates read from the dump file are first converted into unscaled coordinates, relative to the box dimensions of the snapshot. These coordinates are then be assigned to an existing or new atom in the current simulation. The coordinates will then be remapped to the simulation box, whether it is the original box or the dump snapshot box. If periodic boundary conditions apply, this means the atom will be remapped back into the simulation box if necessary. If shrink-wrap boundary conditions apply, the new coordinates may change the simulation box dimensions. If fixed boundary conditions apply, the atom will be lost if it is outside the simulation box.

For native format dump files, the 3 xyz image flags for an atom in the dump file are set to the corresponding values appearing in the dump file if the ix, iy, iz fields are specified. If not specified, the image flags for replaced atoms are not changed and image flags for new atoms are set to default values. If coordinates read from the dump file are in unwrapped format (e.g. xu) then the image flags for read-in atoms are also set to default values. The remapping procedure described in the previous paragraph will then change images flags for all atoms (old and new) if periodic boundary conditions are applied to remap an atom back into the simulation box.

Warning

If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms now have inconsistent image flags. As discussed in Section errors this may or may not cause problems for subsequent simulations, One way this can happen is if you read image flag fields from the dump file but do not also use the dump file box parameters.

LIGGGHTS(R)-PUBLIC knows how to compute unscaled and remapped coordinates for the snapshot column labels discussed above, e.g. x, xs, xu, xsu. If another column label is assigned to the x or y or z field via the label keyword, e.g. for coordinates output by the fix ave/atom command, then LIGGGHTS(R)-PUBLIC needs to know whether the coordinate information in the dump file is scaled and/or wrapped. This can be set via the scaled and wrapped keywords. Note that the value of the scaled and wrapped keywords is ignored for fields x or y or z if the label keyword is not used to assign a column label to that field.

The scaled/unscaled and wrapped/unwrapped setting must be identical for any of the x, y, z fields that are specified. Thus you cannot read xs and yu from the dump file. Also, if the dump file coordinates are scaled and the simulation box is triclinic, then all 3 of the x, y, z fields must be specified, since they are all needed to generate absolute, unscaled coordinates.

## Restrictions

To read gzipped dump files, you must compile LIGGGHTS(R)-PUBLIC with the -DLAMMPS_GZIP option - see the Making LIGGGHTS(R)-PUBLIC section of the documentation.

## Related commands

dump, read_data, read_restart, `rerun`

## Default

The option defaults are box = yes, replace = yes, purge = no, trim = no, add = no, scaled = no, wrapped = yes, and format = native.