[MMTK] convert DLPOLY trajectory to ncd file UPDATE

JAVIER SACRISTAN jus29 at psu.edu
Fri May 19 19:31:11 CEST 2006


Hi, 
I am sorry to bother you once again, but after adding the new Q atom to
MMTKdatabase, and convert DLPOLY trajectory to ncd file, I found this error
Traceback (most recent call last):
  File "C:\Python23\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py",
line 310, in RunScript
    exec codeObject in __main__.__dict__
  File "C:\Python23\Scripts\dlpoly_to_nc.py", line 239, in ?
    data.writeTrajectory(nc_file, block_size)
  File "C:\Python23\Scripts\dlpoly_to_nc.py", line 159, in writeTrajectory
    nvectors = data[3]+1
  File "C:\Python23\Lib\site-packages\Scientific\IO\FortranFormat.py", line 122,
in __getitem__
    return self.data[i]
IndexError: list index out of range

Anyway using that trajectory file I tried to calculate MSD with nMoldyn and the
first thing is that the Trajectory file does not contain information about the
time.  If I run the script to calculate MSD I get this error on the MSD output
file.
'pMoldyn' is not recognized as an internal or external command,
operable program or batch file.

So  I have checked pMoldyn and I am getting a new error,  

>>>import nMoldyn

>>> import pMoldyn
Traceback (most recent call last):
  File "<interactive input>", line 1, in ?
  File "C:\Python23\Scripts\pMoldyn.py", line 3, in ?
    from nMoldyn.core import *
  File "c:\python23\Lib\site-packages\nMoldyn\core.py", line 20, in ?
    from os import system,getuid
ImportError: cannot import name getuid

Any help would be greatly appreciated

JAvier

Javier Sacristan Bermejo
115 Fenske Lab.
Computer Polymer Simulations



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