dump h5md command

Syntax:

dump ID group-ID h5md N file.h5

• ID = user-assigned name for the dump
• group-ID = ID of the group of atoms to be imaged
• h5md = 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.h5 = name of file to write to

Examples:

dump h5md1 all h5md 100 dump_h5md.h5

Description:

Dump a snapshot of atom coordinates every N timesteps in the HDF5 based H5MD file format.

This dump style will write only one file, on the root node.

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.

Restrictions:

The h5md dump style is part of the USER-H5MD package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. It also requires (i) building the ch5md library provided with LAMMPS (See the Making LAMMPS section for more info.) and (ii) having the HDF5 library installed (C bindings are sufficient). The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.

Related commands:

dump, dump_modify, undump