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[h5md-user] New User

From: Hart, David Blaine
Subject: [h5md-user] New User
Date: Mon, 28 Apr 2014 21:02:53 +0000


I wanted to introduce myself, since I realize I didn't do so when I asked my first question of the group. My name is David Hart, and I am a member of technical staff at Sandia National Laboratories, in New Mexico, USA. I work with the geochemistry department doing MD simulation analyses and code development. Most of my work has been with the LAMMPS code (developed at Sandia), though our group uses Towhee, VASP, Gaussian and MaterialsStudio as well. I have worked mostly with clays and mineral surface simulations, although our group does work with MOFs and glasses as well.

As some of you know, LAMMPS dumps its output in text files, which get unwieldy in a hurry. I originally started developing my own HDF5-based format for storing the LAMMPS dumps as a post-run conversion as we worked to improve the 'pizza.py' analysis tools that the LAMMPS group wrote a while back. I stumbled across the H5MD specification, and I really like it. My personal goal would be to write a LAMMPS extension that can output H5MD formatted files directly, so I can skip the conversion steps, and as such I'm particularly interested in the concept of the different modules that H5MD provides, since LAMMPS has some quirks that other codes do not (like the box definitions which use tilt factors and hi-low bounds rather than the normal A/B/C vectors).

Thanks, and I look forward to talking to all of you.


David B. Hart
Geochemistry Department
Sandia National Laboratories
PO Box 5800 MS 0751
Albuquerque, NM 87185-0751

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