[MMTK] MMTK NetCDF Format

Salomon Turgman Cohen sturgman at gmail.com
Wed Jul 9 16:12:06 UTC 2014


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>
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.
>>
>
>
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-- 
Salomon Turgman Cohen
Assistant Professor
Chemical Engineering
Kettering University
(919) 341-9650
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