TODO

Get rid of all global variables.
Break main() into smaller chunks; operations that are timed should become independent functions.
Dynamically allocate the big arrays.
Create a key-value config file reader to replace the external parameter files.
Remove all ifdef blocks, options should be selected in the config file.
Optional HDF5 output.
In the config file let choose number of digits for ASCII output and 32 or 64-bit floats for HDF5.