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dump h5md command

Syntax

dump ID group-ID h5md N file.h5 args

  • 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

  • args = position options or image or velocity options or force options or species options or file_from ID or box value or create_group value or author value = list of data elements to dump, with their dump “sub-intervals”

    position options
image
velocity options
force options
species options
file_from ID = do not open a new file, re-use the already opened file from dump ID
box value = yes or no
create_group value = yes or no
author value = quoted string

Note that at least one element must be specified and that image may only be present if position is specified first.

For the elements position, velocity, force and species, a sub-interval may be specified to write the data only every N_element iterations of the dump (i.e. every N*N_element time steps). This is specified by this option directly following the element declaration:

options = every N_element

Examples

dump h5md1 all h5md 100 dump_h5md.h5 position image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"

Description

Dump a snapshot of atom coordinates every N timesteps in the HDF5 based H5MD file format (de Buyl). HDF5 files are binary, portable and self-describing. This dump style will write only one file, on the root node.

Several dumps may write to the same file, by using file_from and referring to a previously defined dump. Several groups may also be stored within the same file by defining several dumps. A dump that refers (via file_from) to an already open dump ID and that concerns another particle group must specify create_group yes.

Each data element is written every N*N_element steps. For image, no sub-interval is needed as it must be present at the same interval as position. image must be given after position in any case. The box information (edges in each dimension) is stored at the same interval than the position element, if present. Else it is stored every N steps.

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.

Use from write_dump:

It is possible to use this dump style with the write_dump command. In this case, the sub-intervals must not be set at all. The write_dump command can be used either to create a new file or to add current data to an existing dump file by using the file_from keyword.

Typically, the species data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and store once the species data in the same file.

dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species

Restrictions

The number of atoms per snapshot cannot change with the h5md style. The position data is stored wrapped (box boundaries not enforced, see note above). Only orthogonal domains are currently supported. This is a limitation of the present dump h5md command and not of H5MD itself.

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