proposed new dump style, HDF5 based

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1

Dear lammps-list,

I attach a new dump style that writes H5MD files http://nongnu.org/h5md/
H5MD is a file format based on HDF5 that is structured to contain molecular
data.

H5MD is a recent effort to develop a (hopefully) widespread binary, portable,
structured and self-describing file format for molecular simulations (and
experimental data too).

The dump style is currently serial and only dumps the coordinates and box
information.

The attached archive contains a lib/ch5md that provides proxy routines to HDF5
and is written in C. The dump style is in USER-H5MD. Given that the compilation
of ch5md requires a call to h5cc (instead of a C++ compiler), I preferred to
separate it in a library.

There is also a doc/dump_h5md.{txt,html} file.

Let me know if this is of interest to lammps.

Regards,

Pierre de Buyl

user-h5md-dump-style.tgz (8.53 KB)

2

thanks - I’ll take a look

Steve

3

Dear Steve,

Thanks for the reply. I'd like to note that this first version is not well
suited to an inclusion in lammps. It is functional, so interested users can use
it already to explore its use but it is limited, as of now, and I didn't
organize the error handling.

A more complete form would be

dump dumpID groupID h5md file filename.h5 [data interval] [data interval]...

where data can be position, image, velocity, force, mass, species, id with each
its dump interval. several items could be specified.

Comments are welcome. I tried to follow the organization of other USER packages.
For anyone interested in the development, I host it at
https://github.com/pdebuyl/lammps/tree/start_dump_h5md

Regards,

Pierre