[MMTK] MMTK NetCDF Format

Niall Jackson n.jackson12 at imperial.ac.uk
Wed Jul 9 16:38:04 UTC 2014


Dear Salomon,

We're looking to calculate some structure factors. I know the the dynsf 
code can read LAMMPS files directly, but we're working with a group that 
has a lot of experience already with nMOLDYN. In fact, nMOLDYN includes 
a LAMMPS to MMTK converter, but we're having some trouble making it 
work. I'll inspect the source and see how they go about it.

Being able to look at a converted DLPOLY file could be extremely useful, 
if you don't mind.

Thanks,
Niall

On 09/07/14 17:12, Salomon Turgman Cohen wrote:
> Hey Niall,
>
> Just out of curiosity, what particular functionality of nMOLDYN are 
> you looking to use? I was following the same approach you will be 
> pursuing with DLPOLY trajectories (nMOLDYN comes with a converter), 
> but it is a very painful process for very large trajectories.
>
> In case you are not aware, you can look at the exact structure of a 
> MMTK trajectory from the linux command line with the ncdump tool:
>
> http://www.unidata.ucar.edu/software/netcdf/workshops/2011/utilities/Ncdump.html
>
> I also have some of the trajectory files of multi-atom molecule system 
> in mmtk format that I converted from DLPOLY, if you want to see the 
> final result of the conversion. I would have to generate one with a 
> smaller size for an example.
>
> Salomon
>
>
> On Wed, Jul 9, 2014 at 12:02 PM, Niall Jackson 
> <n.jackson12 at imperial.ac.uk <mailto:n.jackson12 at imperial.ac.uk>> wrote:
>
>     Dear Konrad,
>
>     Thank you for your reply. I suspected that this might be the case
>     - I'll have a look into writing a Python script to interpret
>     LAMMPS output files and feed them into MMTK.
>
>     Cheers,
>     Niall
>
>     On 09/07/14 17:01, Konrad Hinsen wrote:
>
>         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.
>
>
>
>     _______________________________________________
>     mmtk maillist  - mmtk at starship.python.net
>     <mailto:mmtk at starship.python.net>
>     http://starship.python.net/mailman/listinfo/mmtk
>
>
>
>
> -- 
> Salomon Turgman Cohen
> Assistant Professor
> Chemical Engineering
> Kettering University
> (919) 341-9650

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