[MMTK] pMoldyn scripting problems

Wed Aug 16 17:20:05 CEST 2006


I'm not sure if this is the correct mailing list for a problem like this,
however it seems some of your have worked on both codes. Please disgregard this
if it is not a relevent topic.

I have recently started using nMoldyn on some simulation data from
VASP that I translated into netCDF through python and MMTK. I am mainly
interested in extracting incoherent scattering data from specific atoms within
my system, as well as the half-width half-maximum of the spectrum for different
Q values. 

However, I am running into a few problems finding documentation on constructing
pMoldyn scripts. I am having trouble in extracting units from the nc files that
are produced (ncdump shows no units for frequency or Q). Looking through the
nMoldyn source I haven't been able to find the "units_q" variable that is set
within the xMoldyn GUI when preparing a simulation. I haven't been able to sift
through it all too well as I am relatively new at Python, but I also am at a
loss as to why the frequency units are not being set as well. I have been using
the default input file generated by xMoldyn as a stepping stone to figuring out
these problems, but can not find any other documentation on how to construct
these input files other than some small examples.

My second issue arises from filtering the data so I see the contribution of only
certain specific atoms to the spectra, however I feel it more pertinent to get
accurate scale on my data before specifying more complicated specifications.

If you can help me with any of these issues, or maybe direct me to some
documentation or guides available for the code, I would greatly appreciate it.

Thank you,
Alejandro Suarez
Graduate Student
Department of Physics

More information about the mmtk mailing list