Package nMOLDYN :: Package Core :: Module IOFiles
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Module IOFiles

source code

This module implements IO-related classes, functions and procedures.

Classes:
    * TemporaryFile            : creates a temporary file stroring the evolution of an analysis.
    * EndOfFile                : an empty dummy class used by |DCDReader|.
    * FortranBinaryFile        : sets up a binary file reader.
    * DCDFile                  : sets up a DCD file reader.
    * AmberNetCDFConverter     : converts a trajectory from Amber > 9 to a MMTK NetCDF trajectory.
    * CHARMMConverter          : converts a trajectory from CHARMM to a MMTK NetCDF trajectory.
    * DL_POLYConverter         : converts a trajectory from DL_POLY > 9 to a MMTK NetCDF trajectory.
    * MaterialsStudioConverter : converts a trajectory from MaterialsStudio > 9 to a MMTK NetCDF trajectory.
    * NAMDConverter            : converts a trajectory from NAMD to a MMTK NetCDF trajectory.
    * VASPConverter            : converts a trajectory from VASP > 9 to a MMTK NetCDF trajectory.
        
Procedures:
    * convertNetCDFToASCII: converts a NetCDF file into an ASCII file.
    * convertASCIIToNetCDF: converts an ASCII file into a NetCDF file.

Classes [hide private]
  TemporaryFile
Creates a temporary file used to monitor (progress, start, end ...) an analysis.
  EndOfFile
  FortranBinaryFile
Sets up a Fortran binary file reader.
  DCDFile
Sets up a DCD file reader.
  AmberNetCDFConverter
Converts an Amber NetCDF Trajectory into a MMTK NetCDFFile.
  CHARMMConverter
Converts a CHARMM Trajectory into a MMTK NetCDFFile.
  DL_POLYConverter
Converts a DL_POLY Trajectory into a MMTK NetCDFFile.
  MaterialsStudioConverter
Converts a MaterialsStudio Discover or Forcite Trajectory into a MMTK NetCDFFile.
  NAMDConverter
Converts a NAMD Trajectory into a MMTK NetCDFFile.
  VASPConverter
Converts a VASP Trajectory into a MMTK NetCDFFile.
Functions [hide private]
 
convertNetCDFToASCII(inputFile, outputFile, variables, floatPrecision=9, doublePrecision=17)
Converts a file in NetCDF format to a file in ASCII/CDL format using the ncdump program provided with the netcdf library.
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convertASCIIToNetCDF(inputFile, outputFile)
Converts a file in ASCII format to a file in NetCDF format using the ncgen program provided with the netcdf library.
source code
Function Details [hide private]

convertNetCDFToASCII(inputFile, outputFile, variables, floatPrecision=9, doublePrecision=17)

source code 

Converts a file in NetCDF format to a file in ASCII/CDL format using the ncdump program provided with the netcdf library.

Parameters:
  • inputFile (string) - the name of the NetCDF input file.
  • outputFile (string) - the name of the CDL output file.
  • variables (list) - list of the NetCDF variables names (string) to extract from the NetCDF file for conversion.
  • floatPrecision (integer) - the precision on the float numbers.
  • doublePrecision (integer) - the precision on the double numbers.

convertASCIIToNetCDF(inputFile, outputFile)

source code 

Converts a file in ASCII format to a file in NetCDF format using the ncgen program provided with the netcdf library.

Parameters:
  • inputFile (string) - the name of the NetCDF input file.
  • outputFile (string) - the name of the CDL output file.