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### dump_modify command

Syntax:

    dump_modify dump-ID keyword values ...

- dump-ID = ID of dump to modify
- one or more keyword/value pairs may be appended
- keyword = append or every or flush or format or image or label or precision or region or scale or sort or thresh or unwrap

        append arg = yes or no
        element args = E1 E2 ... EN, where N = # of atom types
          E1,...,EN = element name, e.g. C or Fe or Ga
        every arg = N
          N = dump every this many timesteps
        first arg = yes or no
        format arg = C-style format string for one line of output
        flush arg = yes or no
        image arg = yes or no
        label arg = string
          string = character string (e.g. BONDS) to use in header of dump local file
        precision arg = power-of-10 value from 10 to 1000000
        region arg = region-ID or "none"
        scale arg = yes or no
        sort arg = yes or no
        thresh args = attribute operation value
          attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
          operation = "<" or "<=" or ">" or ">=" or "==" or "!="
          value = numeric value to compare to
          these 3 args can be replaced by the word "none" to turn off thresholding
        unwrap arg = yes or no

Examples:

    dump_modify 1 format "%d %d %20.15g %g %g" scale yes
    dump_modify myDump image yes scale no flush yes
    dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
    dump_modify xtcdump precision 10000

Description:

Modify the parameters of a previously defined dump command. Not all parameters are relevant to all dump styles.

The append keyword applies to all dump styles except cfg and xtc and dcd. It also applies only to text output files, not to binary or gzipped files. If specified as yes, then dump snapshots are appended to the end of an existing dump file. If specified as no, then a new dump file will be created which will overwrite an existing file with the same name. This keyword can only take effect if the dump_modify command is used after the dump command, but before the first command that causes dump snapshots to be output, e.g. a run or minimize command. Once the dump file has been opened, this keyword has no further effect.

The element keyword applies only to the the dump cfg style. It associates element names (e.g. H, C, Fe) with LAMMPS atom types, so that the AtomEye visualization package can render atoms with the appropriate size and color. An element name is specified for each atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types.

The every keyword changes the dump frequency originally specified by the dump command to a new value which must be > 0. The dump frequency cannot be changed for the dump dcd style.

The first keyword determines whether a dump snapshot is written on the very first timestep after the dump command is invoked. This will always occur if the current timestep is a multiple of N, the frequency specified in the dump command, including timestep 0. But if this is not the case, a dump snapshot will only be written if the setting of this keyword is yes. If it is no, which is the default, then it will not be written.

The flush keyword determines whether a flush operation in invoked after a dump snapshot is written to the dump file. A flush insures the output in that file is current (no buffering by the OS), even if LAMMPS halts before the simulation completes. Flushes cannot be performed with dump style xtc.

The text-based dump styles have a default C-style format string which simply specifies %d for integers and %g for real values. The format keyword can be used to override the default with a new C-style format string. Do not include a trailing "\n" newline character in the format string. This option has no effect on the dcd and xtc dump styles since they write binary files. Note that for the cfg style, the first two fields (atom id and type) are not actually written into the CFG file, though you must include formats for them in the format string.

The image keyword applies only to the dump atom style. If the image value is yes, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed thru the box boundary 2 times and is really 2 box lengths to the left of its current coordinate. Note that for dump style custom these various values can be printed in the dump file by using the appropriate atom attributes in the dump command itself.

The label keyword applies only to the dump local style. When it writes local informatoin, such as bond or angle topology to a dump file, it will use the specified label to format the header. By default this includes 2 lines:

    ITEM: NUMBER OF ENTRIES
    ITEM: ENTRIES ...

The word "ENTRIES" will be replaced with the string specified, e.g. BONDS or ANGLES.

The precision keyword only applies to the dump xtc style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to 1/1000 nanometer accuracy.

The region keyword only applies to the dump custom and cfg styles. If specified, only atoms in the region will be written to the dump file. Only one region can be applied as a filter (the last one specified). See the region command for more details. Note that a region can be defined as the "inside" or "outside" of a geometric shape, and it can be the "union" or "intersection" of a series of simpler regions.

The scale keyword applies only to the dump atom style. A scale value of yes means atom coords are written in normalized units from 0.0 to 1.0 in each box dimension. If the simluation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. A value of no means they are written in absolute distance units (e.g. Angstroms or sigma).

The sort keyword applies only to the dump cfg style. A sort value of yes means atoms will be written into the CFG file in sorted order, sorted by the atom ID. A value of no means a sort will not be performed and that atoms may be in an indeterminate order, depending on which processor owns which atoms.

The thresh keyword only applies to the dump custom and cfg styles. Multiple thresholds can be specified. Specifying "none" turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file. The possible attributes that can be tested for are the same as those that can be specified in the dump custom command. Note that different attributes can be output by the dump custom command than are used as threshold criteria by the dump_modify command. E.g. you can output the coordinates and stress of atoms whose energy is above some threshold.

The unwrap keyword only applies to the dump dcd and xtc styles. If set to yes, coordinates will be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed thru a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot.

Restrictions: none

Related commands:

dump, undump

Default:

The option defaults are

- append = no
- element = "C" for every atom type
- every = whatever it was set to via the dump command
- first = no
- flush = yes (except for the dump xtc style)
- format = %d and %g for each integer or floating point value
- image = no
- label = ENTRIES
- precision = 1000
- region = none
- scale = yes
- sort = no
- thresh = none
- unwrap = no