New site class testing

[JesseSandberg]

Description

This PR implements two classes: Site (Site.py) and Symmetric_Site (Symmetric_Site.py). It also includes all utility functions necessary (utils.py) and plotting functions necessary (plotting.py) to completely replicate the existing machinery for DTA. It also includes a testing notebook, which will create a symmetric site the old way, a Symmetric_Site the new way, and compare all plots and the resulting delta G. The only thing this won't test is the determination of the accessible area.

Usage Changes

This PR does not change the user experience in any way but adds all the functionality we will need to change the user experience in the future.

Todos

Notable points that this PR has either accomplished or will accomplish.

• Adds a new Site class (Site.py)
• Adds a new Symmetric_Site class (Symmetric_Site.py)
• Adds all the utility functions required to make those classes work (utils.py)
• Adds plotting functions to replicate the plots that are currently made in the nb (plotting.py)

Pre-Review checklist (PR maker)

• Do the plots contain the same data?
• Do the plots look similar enough? (they can be improved in future PRs)
• Do you get the same delta G for the same Site both ways?
• New functions are documented

Review checklist (Reviewer)

Site_testing.zip

• Download the Site_testing.zip file
• Checkout the new_Site_class_testing branch locally
• Put the notebook in your DTA/python folder
• Put the rest of the files from the .zip on your Desktop
• Modify the paths in the first cell to point towards your desktop (and not Jesse's)
• Run all cells
• Do the plots contain the same data?
• Do the plots look similar enough? (they can be improved in future PRs)
• Do you get the same delta G for the same Site both ways?
• New functions are documented
• New functions/variables are named appropriately
• No missed "low-hanging fruit" that would substantially aid readability.
• Any "high-hanging" or "rotten" fruit is added to the issues list.
• I understand what the changes are doing and how
• I understand the motivation for this PR (the PR itself is appropriately documented)

Status

• Ready for review