Refactor calculations into functions and modules

[Frank-Duffy]

Refactoring the calculations into functions and .py modules will improve the project in multiple ways:

1. The notebook will be easier to read since there will be functions in place of all the large code blocks.
2. The modularized code will be easier to test and debug.
3. The modularized code will enable users to build scripts that can be automated more easily than a notebook alone will allow.
4. Parallel computing is more straightforward with python scripts than it is with Jupyter Notebooks.