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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 netcdf command :h3
dump netcdf/mpiio command :h3
[Syntax:]
dump ID group-ID netcdf N file args
dump ID group-ID netcdf/mpiio N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
{netcdf} or {netcdf/mpiio} = 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) :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
[Examples:]
dump 1 all netcdf 100 traj.nc type x y z vx vy vz
dump_modify 1 append yes at -1 thermo yes
dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
[Description:]
Dump a snapshot of atom coordinates every N timesteps in Amber-style
NetCDF file format. NetCDF files are binary, portable and
self-describing. This dump style will write only one file on the root
node. The dump style {netcdf} uses the "standard NetCDF
library"_netcdf-home. All data is collected on one processor and then
written to the dump file. Dump style {netcdf/mpiio} uses the
"parallel NetCDF library"_pnetcdf-home and MPI-IO to write to the dump
file in parallel; it has better performance on a larger number of
processors. Note that style {netcdf} outputs all atoms sorted by atom
tag while style {netcdf/mpiio} outputs atoms in order of their MPI
rank.
NetCDF files can be directly visualized via the following tools:
Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
all extensions of this dump style. :ule,b
VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
contains a NetCDF reader that is not present in the standard
distribution of AtomEye. :l,ule
In addition to per-atom data, "thermo"_thermo.html data can be included in the
dump file. The data included in the dump file is identical to the data specified
by "thermo_style"_thermo_style.html.
:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
:line
[Restrictions:]
The {netcdf} and {netcdf/mpiio} dump styles are part of the
USER-NETCDF package. They are only enabled if LAMMPS was built with
that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
:line
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
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