dump nc command
dump nc/mpiio command
dump ID group-ID nc N file.nc args dump ID group-ID nc/mpiio N file.nc args
- ID = user-assigned name for the dump
- group-ID = ID of the group of atoms to be imaged
- 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 doc page)
- N = dump every this many timesteps
- file.nc = name of file to write to
- args = list of per atom data elements to dump, same as for the ‘custom’ dump style.
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 dump 1 all nc/mpiio 1000 traj.nc id type x y z
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 all data is collected on one processor and then written to the dump file. Dump style nc/mpiio used the parallel NetCDF library 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 global.
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 for more info.