Fixed typos, missing docstrings, format issues, and minor mistakes of the whole documentation

[wehs7661]

Description

This pull request is meant to address issue #49. Reading through the whole documentation thoroughly, I've fixed some typos, missing docstrings, format issues, and minor mistakes in the newly created branch improve-documentation. Overall, the documentation is very clear and beginner-friendly. Below are some notes/discussion points, some of which are minor but I'll just share all my thoughts.

• User guide
  • There are a lot of output messages shown in the example in the section Kinetic energy validation (full system), but I think it is not clear enough which output message corresponds to which parts of ana_water.py. I think it might be easier for the beginner to check the output (including the figures, which are not shown on the documentation page now) step by step if we set up the example in a jupyter notebook. Or if setting up jupyter notebooks is too tedious, we could just make clear which parts of the code did a certain part of the outputs came from. (We could put some of the important figures, which I think help the user to understand.)
  • Also, the output on the documentation page seems kind of different from the output messages from executing ana_water.py. We might want to fix this.
  • Not sure if it is better to include the key equations in each example in the user guide, e.g. the pdf of the kinetic energy showing that the gamma distribution.
  • Update: I've added links to the documentation of the relevant functions, some of which had notes elaborating the related theory (e.g. the notes about the strict test checking the gamma distribution using K-S test). I think this sort of solves the problem.
  • We need an example for section Kinetic energy validation (equipartition). I can help set that up in the near future if that's wanted.
  • The output messages of ana_argon.py are kind of different from the ones shown in the documentation (in the section of integrator validation). Do we want to make them consistent?
• Data format and parsers
  • In the example of using the flat file parser, I think it might be useful to provide example files kinetic.dat, potential.dat, and total.dat.
  • Later found that the docstring of physical_validation.data.flatfile_parser.FlatfileParser did actually mention the format of the input files clearly, so attaching example files might not be needed. I'll just leave the comment here in case there is room for discussion.
  • Some paragraphs mentioned units without using latex (e.g. nm^3). Do we want to use latex and make the format of all the units consistent?
  • Also, the Boltzmann constant was written as kB instead of $k_{B}$ (e.g. the docstring of physical_validation.data.unit_data.)
  • Does the todos in the section "System: SimulationData.system of type SystemData" correspond to any issue? It might not be of high priority though.
• Package reference
  • The documentation of the argument verbose of physical_validation.integrator.convergence was missing (fixed).

Todos

Update: The todos as follows will be addressed in other issues/PRs.

• [x] An example for the section Kinetic energy validation (equipartition) (#102 )
• [x] Update the example outputs on the documentation to make sure they are consistent with the real outputs from ana_water.py and ana_argon.py (if there is a need to do so).

Questions (Discussion points)

• [x] Whether we want to set up jupyter notebooks for the example or just improve the ones on the documentation (e.g. attaching the important figures).
• [x] Whether we want to provide example files like kinetic.dat, potential.dat, and total.dat for the example of using the flat file parser.
• [x] Whether there is a need to fix the font (latex or not) for units (and the Boltzmann constant).

Status

• [x] Ready to go