Change sequence of steps in `prepare_simulation`

[arichar6]

Pull Request

Description

This PR changes the order of the steps in prepare_simulation. Now the clock will be created before the physics modules.

This pull request addresses #140

Checklist

The following items have been checked for this PR:

• [x] Conforms to PEP8 style standards (check with pylint, flake8, or similar)
• [ ] Code is documented with docstrings, or docstrings have been updated as appropriate
• [ ] New unit test/integration test have been added to check new code
• [x] All existing tests still pass

[arichar6]

@NRL-Plasma-Physics-Division/intern-admin do you have permission to review/approve this PR? I can merge it myself, but I'd like someone else to also check my changes.