dump netcdf command

dump netcdf/mpiio command

Syntax

dump ID group-ID netcdf N file args
dump ID group-ID netcdf/mpiio N file args
  • ID = user-assigned name for the dump
  • group-ID = ID of the group of atoms to be imaged
  • 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 doc page)
  • N = dump every this many timesteps
  • file = name of file to write dump info to
  • args = list of atom attributes, same as for dump_style custom

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
dump 1 all netcdf 1000 traj.*.nc id type x y z

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. All data is collected on one processor and then written to the dump file. Dump style netcdf/mpiio uses the parallel NetCDF library 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.

In addition to per-atom data, thermo data can be included in the dump file. The data included in the dump file is identical to the data specified by thermo_style.


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 for more info.