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"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
dump vtk command :h3
[Syntax:]
dump ID group-ID vtk N file args :pre
ID = user-assigned name for the dump
group-ID = ID of the group of atoms to be dumped
vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
N = dump every this many timesteps
file = name of file to write dump info to
args = same as arguments for "dump_style custom"_dump.html :ul
[Examples:]
dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx
dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre
[Description:]
Dump a snapshot of atom quantities to one or more files every N
timesteps in a format readable by the "VTK visualization
toolkit"_http://www.vtk.org or other visualization tools that use it,
e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump
output is written can also be controlled by a variable; see the
"dump_modify every"_dump_modify.html command for details.
This dump style is similar to "dump_style custom"_dump.html but uses
the VTK library to write data to VTK simple legacy or XML format
depending on the filename extension specified for the dump file. This
can be either {*.vtk} for the legacy format or {*.vtp} and {*.vtu},
respectively, for XML format; see the "VTK
homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), the
"dump_modify binary"_dump_modify.html command allows setting of a
binary option for this dump style explicitly.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also
alter what atoms are included; see details below.
As described below, special characters ("*", "%") in the filename
determine the kind of output.
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
is invoked, the lines of atom information written to dump files will
be in an indeterminate order for each snapshot. This is even true
when running on a single processor, if the "atom_modify
sort"_atom_modify.html option is on, which it is by default. In this
case atoms are re-ordered periodically during a simulation, due to
spatial sorting. It is also true when running in parallel, because
data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.
For the {vtk} style, sorting is off by default. See the
"dump_modify"_dump_modify.html doc page for details.
:line
The dimensions of the simulation box are written to a separate file
for each snapshot (either in legacy VTK or XML format depending on the
format of the main dump file) with the suffix {_boundingBox} appended
to the given dump filename.
For an orthogonal simulation box this information is saved as a
rectilinear grid (legacy .vtk or .vtr XML format).
Triclinic simulation boxes (non-orthogonal) are saved as
hexahedrons in either legacy .vtk or .vtu XML format.
Style {vtk} allows you to specify a list of atom attributes to be
written to the dump file for each atom. The list of possible attributes
is the same as for the "dump_style custom"_dump.html command; see
its doc page for a listing and an explanation of each attribute.
NOTE: Since position data is required to write VTK files the atom
attributes "x y z" do not have to be specified explicitly; they will
be included in the dump file regardless. Also, in contrast to the
{custom} style, the specified {vtk} attributes are rearranged to
ensure correct ordering of vector components (except for computes and
fixes - these have to be given in the right order) and duplicate
entries are removed.
The VTK format uses a single snapshot of the system per file, thus
a wildcard "*" must be included in the filename, as discussed below.
Otherwise the dump files will get overwritten with the new snapshot
each time.
:line
Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command.
The "dump_modify every"_dump_modify.html command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
"dump_modify first"_dump_modify.html command is used.
Dump filenames can contain two wildcard characters. If a "*"
character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.
If a "%" character appears in the filename, then each of P processors
writes a portion of the dump file, and the "%" character is replaced
with the processor ID from 0 to P-1 preceded by an underscore character.
For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
mode of output on parallel machines that support parallel I/O for output.
By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the {nfile} or
{fileper} keywords of the "dump_modify"_dump_modify.html command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.
For the legacy VTK format "%" is ignored and P = 1, i.e., only
processor 0 does write files.
Note that using the "*" and "%" characters together can produce a
large number of small dump files!
If {dump_modify binary} is used, the dump file (or files, if "*" or
"%" is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically
write out much faster.
:line
[Restrictions:]
The {vtk} style does not support writing of gzipped dump files.
The {vtk} dump style is part of the USER-VTK package. It is
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
To use this dump style, you also must link to the VTK library. See
the info in lib/vtk/README and insure the Makefile.lammps file in that
directory is appropriate for your machine.
The {vtk} dump style supports neither buffering or custom format
strings.
[Related commands:]
"dump"_dump.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "undump"_undump.html
[Default:]
By default, files are written in ASCII format. If the file extension
is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
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