utils

README

- 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.