[MMTK] MMTK NetCDF Format

Konrad Hinsen research at khinsen.fastmail.net
Wed Jul 9 16:01:22 UTC 2014


Niall Jackson writes:

 > We are trying to use nMOLDYN with LAMMPS trajectories. Ideally, we would 
 > like to produce a new LAMMPS dump style that generates MMTK style dump 
 > files directly. Is there a document or manual section which outlines the 
 > structure of the MMTK style NetCDF file?

Unfortunately not, and for a reason: it is probably very difficult to
generate such netCDF files without using MMTK.

Most of the contents of a trajectory file are plain netCDF arrays that
hardly require much documentation. But there is also the variable
"description", which contains a string that defines the complete
universe for which the simulation was run. That string is a Python
expression that gets evaluated in the right context to reconstruct the
system. This is a nice trick, and quite efficient, but not at all
portable. At the very least, you need Python and a class hierarchy
with a similar structure to MMTK's.

For this reason, all trajectory converters to or from MMTK's format
that I know of are written in Python and use MMTK.

My long-term plan is to transition to a new format that is fully
documented, more flexible, and has better performance:

  https://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html

It won't happen rapidly though, because it is very difficult to get
funding for such work.

Konrad.
-- 
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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