Changing the way atom lines are parsed in dump file.

Removing use of Atom/Atoms classes. Creating these
object instances in-real-time was too memory intensive.
Reverting code back to where each line of data is parsed
and stored in numpy array, similar to pizza.py approach.

The better solution now I think is to iterate through
the array data creating only one Atoms instance per snapshot.
Populate the Atoms instance with Atom instances for the given
snapshot, perform the structure analysis and store the
result. Repeat for each snapshot.