[MMTK] MMTK NetCDF Format
n.jackson12 at imperial.ac.uk
Wed Jul 9 16:38:04 UTC 2014
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.
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:
> 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.
> 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.
> 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
> 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:
> It won't happen rapidly though, because it is very difficult
> to get
> funding for such work.
> mmtk maillist - mmtk at starship.python.net
> <mailto:mmtk at starship.python.net>
> Salomon Turgman Cohen
> Assistant Professor
> Chemical Engineering
> Kettering University
> (919) 341-9650
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