Pouring (Core Filling Functionality)

[ZoeRichter]

Summary of changes

This PR adds the "pour" functionality to ghastly, i.e., the ability to fill a core with pebbles. It uses a combination of OpenMC to pack cylindrical regions, and LAMMPS to both allow the pebbles to fall under gravity, and add any remaining pebbles needed to fill the core to the desired packing fraction.

It does this using a series of jinja2 templates, which automatically create a LAMMPS input file based on the parameters in the input file, which is a JSON file. There are example input files for ghastly both in the tests and examples directories.

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

• closes Add tests and determine testing guideline/standard #2
• closes Update to pytest #4
• closes Get LAMMPS input and results in didymus repo #10

Checklist for Reviewers

Reviewers should use this link to get to the
Review Checklist before they begin their review.

[LukeSeifert]

Overall, looks good! I had a couple comments, mostly on docstrings and some whitespace for pep8 formatting. I think if you run autopep8, it'll probably automatically catch a couple of my comments.

[nsryan2]

Hi Zoe! Lots of good work here, I have some minor consistency comments and questions.

Before I approve, I'd love to see Pep8 run on this PR. I noticed several instances of missing white space around math operations and other things that it won't like.

[ZoeRichter]

It looks like trusty ol' autopep8 changed some lines I didn't anticipate - give me a bit to fix them and push that commit.

[ZoeRichter]

I think I saved it - sorry folks!

[katyhuff]

Minor changes suggested, most can be handled by creating issues to be dealt with in the future. In fact, I'm going to list this as "approve" so that you can merge as soon you feel you have completed the essential tasks (line lengths, etc.) and created the issues recommended. I see no fatal flaws in this PR, just some things you might consider changing.

[ZoeRichter]

I believe I have either made issues for or fixed issues in new comments! (Thanks all)

[ZoeRichter]

Oops - I missed a few comments because I missed some hidden comments when I when through. Let me make a commit for splitting up functions into smaller sections, and THEN I think I actually covered everything.

[nsryan2]

@katyhuff do you have any insight on why Pep8speaks might not have checked this PR? That would have caught some of each of our comments.