 -- Utility functions directory --

 * This is the directory containing functions that are used in the other 
   modules in the code.

 * Files:
   - depend.py: Deals with the dependency detection, value caching and 
      automatic updating of variables.
   - inputvalue.py: Contains the base classes used in reading the xml
      input file, and creating the restart file.
   - mathtools.py: Contains the algorithms used in various parts of the code.
   - messages.py: Contains the classes to generate info and warning messages
      to standard output during the simulation.
   - nmtransform.py: Contains the algorithms that deal with the normal mode
      and ring polymer contraction transformations.
   - prng.py: Deals with random number generation.
   - softexit: Contains the classes to deal with calls for a soft exit.
   - units.py: Holds atomic masses, fundamental constants, and unit conversions.

 * Directories:
   - io: Holds the modules that deal with reading and outputting files.
