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lammps/doc/src/dump_nc.txt
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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 nc command :h3
dump nc/mpiio command :h3
[Syntax:]
dump ID group-ID nc N file.nc args
dump ID group-ID nc/mpiio N file.nc args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
{nc} or {nc/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.nc = name of file to write to :l
args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
[Examples:]
dump 1 all nc 100 traj.nc type x y z vx vy vz
dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
dump 1 all nc/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 {nc} uses the "standard NetCDF
library"_netcdf-home all data is collected on one processor and then
written to the dump file. Dump style {nc/mpiio} used the "parallel
NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
a larger number of processors. Note that 'nc' outputs all atoms sorted
by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
In addition to per-atom data, also global (i.e. not per atom, but per
frame) quantities can be included in the dump file. This can be
variables, output from computes or fixes data prefixed with v_, c_ and
f_, respectively. These properties are included via
"dump_modify"_dump_modify.html {global}.
:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
:line
[Restrictions:]
The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
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.
:line
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
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