Modified to use a preferences file input.

Instead of 5 bazillion command line options, just have
a simple prefs file now. Check out the file itself for
the order of the prefs.
Modification to allow text-string identifiers.

Previously entries in atoms.list had to be numbers,
they can now be strings.
The atomic energies file can now be specified.

Previously this was assumed to be called "atom_energies.txt"
which was a bit annoying if you had different species
with different energies in the same simulation.
Fixed array/number problem

Previously if one of the files used by this script
had length 1, it would store the contents in a number
not an array (due to the behaviour of loadtxt). This is
now checked explicitly and always forced to an array.