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.