Simplify and tweak the functionalities for MT-REXEE

[wehs7661]

Some MT-REXEE functionalities introduced by PR #57 / #58 can probably be simplified or moved to better places. Below are a few scenarios in which we should probably consider making some changes:

• Functions like perform_shift_1D, perform_shift_2D. and perform_shift_3D in coordinate_swap.py are similar to each and can be combined.
• Functions like read_top in coordinate_swwap.py should be probably moved to gmx_parser.
• Functions like compute_angle should probably be converted to internal functions.

Note that it might be better to make these changes after we finish developing unit tests for MT-REXEE functionalities, i.e., after we close PR #59.

[wehs7661]

Closing this since the issue has been addressed in PR #58 by @ajfriedman22.