VMD-L Mailing List

From: Pierre de Buyl (pierre.debuyl_at_chem.kuleuven.be)
Date: Thu Apr 23 2015 - 06:56:29 CDT

Hi vmd-l,

Here is a short follow-up on H5MD. I was not subscribed to vmd-l and cannot
reply in the proper thread, sorry about that.

H5MD is a file format for molecular data based on HDF5. It is currently used in
several groups: Felix Hoëfling (Stuttgart, Max Planck Institute
http://halmd.org/ ), Jonas Landsgesell (and others, I suppose at the Institute
for Computational Physics, http://espressomd.org/ ), Peter Colberg (Toronto) and
in Leuven (Jakub Krajniak and myself).

I have written a dump style for LAMMPS
https://github.com/pdebuyl/lammps/tree/start_dump_h5md/src/USER-H5MD
that requires to compile the bundled lib/ch5md and to enable the USER-H5MD
package. Then, it works mostly like a regular dump style in LAMMPS and operates
on the master cpu only.

I did advertise the dump style on lammps-users but had no reply.

For info, I also developed a Python library for H5MD that enables a basic
implementation in ESPResSo++. An example can be found here
https://github.com/pdebuyl/cg_md_polymerization/blob/master/code/chain_h5md.py

I hope this is of interest to the vmd community.

Regards,

Pierre