1 -- Utility functions directory --
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3 * This is the directory containing functions that are used in the other
4   modules in the code.
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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.
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20 * Directories:
21   - io: Holds the modules that deal with reading and outputting files.
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