Package nMOLDYN :: Package Core :: Module IOFiles :: Class MaterialsStudioConverter
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Class MaterialsStudioConverter

source code

Converts a MaterialsStudio Discover or Forcite Trajectory into a MMTK NetCDFFile.

Instance Methods [hide private]
 
__init__(self, module, xtdxsdFile, histrjFile, outputFile, subselection=None)
The constructor.
source code
 
createCluster(self, at, clust) source code
 
readXTDFile(self)
Reads the Materials Studio XTD or XSD file and set up the universe from which the NetCDF MMTK trajectory will be written.
source code
 
readHISFile(self)
Reads a Materials Studio HIS file and fills up the NetCDF trajectory file.
source code
 
readTRJFile(self)
Reads a Materials Studio HIS file and fills up the NetCDF trajectory file.
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__convert(self)
Performs the actual conversion.
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Class Variables [hide private]
  atomLineFormat = FortranFormat('A5,1X,F14.9,1X,F14.9,1X,F14.9,...
Method Details [hide private]

__init__(self, module, xtdxsdFile, histrjFile, outputFile, subselection=None)
(Constructor)

source code 

The constructor. Will do the conversion.

Parameters:
  • module (string) - a string being one of 'Discover' or 'Forcite' specifying which module of MaterialsStudio the trajectory is coming from.
  • xtdxsdFile (string) - the MaterialsStudio XTD or XSD file name of the trajectory to convert.
  • histrjFile (string) - the MaterialsStudio HIS (Discover) or TRJ (Forcite) file name of the trajectory to convert.
  • outputFile (string) - the name of MMTK NetCDF trajectory output file.
  • subselection (list) - if not None, list of the indexes (integer >= 1) of the atoms to select when writing out the MMTK trajectory. The order being the one defined in the XTD/XSD file.

readXTDFile(self)

source code 

Reads the Materials Studio XTD or XSD file and set up the universe from which the NetCDF MMTK trajectory will be written.

Note: the XTD and XSD file are xml file.


Class Variable Details [hide private]

atomLineFormat

Value:
FortranFormat('A5,1X,F14.9,1X,F14.9,1X,F14.9,1X,A4,1X,A7,A7,1X,A2,1X,F\
6.3')