1 -- Utility functions directory -- 2 3 * This is the directory containing functions that are used in the other 4 modules in the code. 5 6 * Files: 7 - depend.py: Deals with the dependency detection, value caching and 8 automatic updating of variables. 9 - inputvalue.py: Contains the base classes used in reading the xml 10 input file, and creating the restart file. 11 - mathtools.py: Contains the algorithms used in various parts of the code. 12 - messages.py: Contains the classes to generate info and warning messages 13 to standard output during the simulation. 14 - nmtransform.py: Contains the algorithms that deal with the normal mode 15 and ring polymer contraction transformations. 16 - prng.py: Deals with random number generation. 17 - softexit: Contains the classes to deal with calls for a soft exit. 18 - units.py: Holds atomic masses, fundamental constants, and unit conversions. 19 20 * Directories: 21 - io: Holds the modules that deal with reading and outputting files. 22