Cleaned up code

Cleaned up old things I tried in this branch in run.py
Added conditional statement to real z calculation

Added if statement to the end of the loop in run.py to control whether or not to bother calculating the real z coordinate for the drifters. In the case of surface-only drifters, I suspect that no one cares what the real z depth is as the drifters bob up and down on the surface.
Added ability to control xlim/ylim in pcolor hist

Now xlim and ylim values can be input to the pcolor histogram for ease of plotting various magnifications.
small change to plotting