Improvements to file generation methods, file templates, and a new universal templater function

[ZoeRichter]

Summary of changes

This PR is an improvement to the auto-generated file templates and templating methods used in Ghastly. It also sets up the template directory to be better organized by organizing templates for LAMMPS into a new lammps/ directory inside the templates folder.

I added a _templater() function, which renders a file using the provided dict and template. While updating the functions to use the generic _templater, I found some opportunities to simplify file generation, and as a result, some functions were no longer needed, and have been removed.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• I have read the CONTRIBUTING document.
• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have added tests to cover my changes.
• All new and existing tests passed.

Associated Issues and PRs

• Issue: closes [Feature] Verbosity specification for runs #18, closes [Feature] When a jinja2 template is used, make the file choice an input parameter with a default setting #24, and closes [Bug] Update Tests to account for changed attributes #47

Checklist for Reviewers

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Review Checklist before they begin their review.

[ZoeRichter]

I'm also going to @PeterCannon10 - I think this is a bit much for your first PR, but since you'll be working with Ghastly, I'm pinging you so you can take a look, if you would like.

Peter wants to re-review -- accidental approve button mash.

[ZoeRichter]

No worries - I'm also going to tag Megan, once I figure out her username. I'll require an approval from a more senior ARFC member before merging, so don't stress too much about having your review be perfect. If you end up only asking questions about how things work, that's fine by me. You can also always come in and ask questions in person, or in the undergrad slack.