Simulation results now saved in folders

Merged custom_functions() and world_builder() to become Entities().
Merged custom_functions() and world_builder into Entities()

Renamed 'p' to parameters
Removed get_cell() custom function
Fixed "World = world_builder()" leftover bug
Fixed "world_builder" in line 36 leftover bug
Fixed "World" parameter in line 173 leftover bug
Merge pull request #3 from clarencecastillo/master

Updated dose.py and SIM_01.py