forked from lijiext/lammps
126 lines
5.2 KiB
Plaintext
126 lines
5.2 KiB
Plaintext
"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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dump_modify command :h3
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[Syntax:]
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dump_modify dump-ID keyword values ... :pre
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dump-ID = ID of dump to modify :ulb,l
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one or more keyword/value pairs may be appended :l
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keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {precision} or {region} or {thresh} :l
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{format} arg = C-style format string for one line of output
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{scale} arg = {yes} or {no}
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{image} arg = {yes} or {no}
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{flush} arg = {yes} or {no}
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{unwrap} arg = {yes} or {no}
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{every} arg = N
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N = dump every this many timesteps
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{precision} arg = power-of-10 value from 10 to 1000000
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{region} arg = region-ID or "none"
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{thresh} args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!="
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value = numeric value to compare to
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these 3 args can be replaced by the word "none" to turn off thresholding
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:pre
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:ule
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[Examples:]
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dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000 :pre
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[Description:]
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Modify the parameters of a previously defined dump command. Not all
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parameters are relevant to all dump styles.
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The text-based dump styles have a default C-style format string which
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simply specifies %d for integers and %g for real values. The {format}
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keyword can be used to override the default with a new C-style format
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string. Do not include a trailing "\n" newline character in the
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format string. This option has no effect on the {dcd} and {xtc} dump
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styles since they write binary files.
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The {scale} and {image} keywords apply only to the dump {atom} style.
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A scale value of {yes} means atom coords are written in normalized
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units from 0.0 to 1.0 in each box dimension. If the simluation box is
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triclinic (tilted), then all atom coords will still be between 0.0 and
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1.0. A value of {no} means they are written in absolute distance
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units (e.g. Angstroms or sigma).
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If the image value is {yes}, 3 flags are appended to each atom's
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coords which are the absolute box image of the atom in each dimension.
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For example, an x image flag of -2 with a normalized coord of 0.5
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means the atom is in the center of the box, but has passed thru the
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box boundary 2 times and is really 2 box lengths to the left of its
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current coordinate. Note that for dump style {custom} these various
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values can be printed in the dump file by using the appropriate atom
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attributes in the dump command itself.
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The {flush} option determines whether a flush operation in invoked
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after a dump snapshot is written to the dump file. A flush insures
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the output in that file is current (no buffering by the OS), even if
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LAMMPS halts before the simulation completes. Flushes cannot be
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performed with dump style {xtc}.
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The {unwrap} option only applies to the dump {dcd} and {xtc} styles.
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If set to {yes}, coordinates will be written "unwrapped" by the image
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flags for each atom. Unwrapped means that if the atom has passed thru
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a periodic boundary one or more times, the value is printed for what
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the coordinate would be if it had not been wrapped back into the
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periodic box. Note that these coordinates may thus be far outside the
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box size stored with the snapshot.
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The {every} option changes the dump frequency originally specified by
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the "dump"_dump.html command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump {dcd} style.
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The {precision} option only applies to the dump {xtc} style. A
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specified value of N means that coordinates are stored to 1/N
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nanometer accuracy, e.g. for N = 1000, the coordinates are written to
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1/1000 nanometer accuracy.
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The {region} keyword only applies to the dump {custom} style. If
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specified, only atoms in the region will be written to the dump file.
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Only one region can be applied as a filter (the last one specified).
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See the "region"_region.html command for more details. Note that a
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region can be defined as the "inside" or "outside" of a geometric
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shape, and it can be the "union" or "intersection" of a series of
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simpler regions.
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The {thresh} keyword only applies to the dump {custom} style.
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Multiple thresholds can be specified. Specifying "none" turns off
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all threshold criteria. If thresholds are specified, only atoms
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whose attributes meet all the threshold criteria are written to the
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dump file. The possible attributes that can be tested for are the
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same as those that can be specified in the "dump custom"_dump.html
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command. Note that different attributes can be output by the dump
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custom command than are used as threshold criteria by the dump_modify
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command. E.g. you can output the coordinates and stress of atoms
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whose energy is above some threshold.
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[Restrictions:] none
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[Related commands:]
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"dump"_dump.html, "undump"_undump.html
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[Default:]
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The option defaults are format = %d and %g for each integer or
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floating point value, scale = yes, image = no, flush = yes (except for
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the dump {xtc} style), unwrap = no, every = whatever it was set to via
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the "dump"_dump.html command, precision = 1000, region = none, and
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thresh = none.
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