renaming dose_entities class in dose.py into dose_functions or simulation_functions

[mauriceling]

1. dose_entities class in dose.py is a class to hold all the user-defined functions/methods for simulation.
2. dose_entities class is to be over-rode in simulation codes.
3. However, the name "dose_entities" may imply organisms or populations.
4. To prevent confusion, we should rename it as "dose_functions" or "simulation_functions".

[clarencecastillo]

1. dose_entities renamed into simulation_functions.
2. Named dose_entities in the simulate function as dose_functions in order to avoid local referencing.