Issue 11: Remove incorrect calls to Atoms.get_number_of_atoms()
Remove incorrect calls to Atoms.get_number_of_atoms(), and amend the docstring of that method to make it clearer that it should not be used as a general alternative to len(atoms).
I will keep an eye open for eliminating it completely, if it can be done without adding unduely to the complexity of Asap.
Closes issue #11 (closed).