This is in the same category as Issue #3.

Overall

• The structure and organization seems clean and well maintained, but it is a bit hard to understand the different directories without documentation (Issue #3). Other than that, I just have some suggestions on things that you can look into @ZoeRichter.

Specifics

Serpent Inputs

• I noticed that the material compositions take up a lot of space in the input files, perhaps using a separate material file would make organization easier? Particularly if you are reusing material compositions, you can have them saved in a directory and loaded in.
• fuel0 material has a different isotopic formatting used compared to the other materials. I know I had some issues with Serpent when I had mixed formatting (though that was with the reprocessing functions), so maybe reformatting that could prevent possible future issues.

Notebooks

• calc-inputs.ipynb exists in multiple locations (i.e. phlox/full-core/.ipynb_checkpoints/calc-inputs-checkpoint.ipynb, phlox/full-core/post-proc/.ipynb_checkpoints/calc-inputs-checkpoint.ipynb, phlox/full-core/calc-inputs.ipynb). I think they may all be slightly different as well. Perhaps rename them or relocate the notebooks to a centralized directory?
• There is a term 10^(2) 4, should be 10^(24)?
• I think splitting up calc-inputs.ipynb into multiple notebooks may be a good idea, it is quite long as is and goes through a lot of data. Splitting it up would make it clearer what each section is doing and how they are different.
• The plots look good, perhaps consider adding plots of homogeneous vs heterogeneous flux profiles?

calcproc.py

• Some docstrings do not contain "Returns:"
• Docstring formatting not fully consistent (i.e. rebin has parameter xz_col: number of... instead of xz_col: float; number of..." used in other docstrings).

Files in the hidden .ipynb_checkpoints folders should not be kept in the repository. Instead, the actual corresponding .ipynb files should be stored in the repo. The checkpoints are duplicative backup copies, replicating the original notebooks. If the notebooks are stored in git already, it's best not to also commit the checkpoints, since git already provides the functionality to go back to an older version.

This issue can be closed when:

• the .ipynb_checkpoints notebook copies are removed from the repo
• all of the corresponding original .ipynb files are confirmed to be present in the repo

It looks like you've got a lot of really cool calculations and modeling ideas going on here, but it's a little hard to parse what things are for. I think your repo could benefit from some additional notes in the following places:

These suggestions are all based off of what is currently on the fix branch in @ZoeRichter's fork, which (from what I can tell) is ahead of the main branch in this repo.

phlox/:

1. Could use information about implementation and requisite software for replication. You mention Serpent 2 in a sub-folder, maybe tossing in our group's guide for getting a serpent license would be useful (though I'm not sure how useful that is for someone not in the group).
2. You employ .ipynb_checkpoints in a couple different places in this directory, and I’m not totally sure what they are for. They seem like a valuable tool, and I think your README could benefit from mentioning what they are and how to use them if someone is trying to replicate your work.
3. There are a couple parts of the repo that use -20 and -200 to differentiate models, it would be useful to describe those differences at the top level so people know how to interpret it when they encounter it later on.

phlox/reactors/:

1. I could easily be mis-understanding the way you structured this, but it seems like you’re combining the design and analysis in the same reactors folder. I’m not sure if you’ve started the analysis (other than some of the plots you have under full-core/post-proc), but it might be nice to have that exist separately from phlox/reactors/.
2. It would also be nice if this README summarized the three different prongs (fuel-fidelity, full-core, and single-pebble) a little bit to aid in navigation.

phlox/reactors/fuel-fidelity/:

1. I’m not the most familiar with serpent, but I just wanted to check to see if there’s any other information someone would need to run these simulations (like a specific library or something). If those exist somewhere else in the repo, or are a public resource, it might be useful to specify what they are.

phlox/reactors/full-core/:

1. This part of the directory could benefit from a README.
2. Something I noticed is that the htgr-20 and htgr-200 folders are very different in their contents. This could easily be that you’re still working on the htgr-200 one, but some of the things (like the tests or slice information) might be useful to have about both.

phlox/reactors/full-core/htgr-20/:

1. This folder could really benefit from a README detailing things like:
   A. What the 7 digit number folders are
   B. What the slice-#-# is (it’s an intuitive way to name them, I’m 95% sure it means the slice of the core from say 0 to 60 degrees right?)
2. It would be a pain, but your repo might benefit from having a folder for tests, one for the 7 digit number folders, the slices, and some of the other categories in this folder.

phlox/reactors/full-core/pbbls/:

1. A README could help clarify this, but are the pbbls#.inp files generic and the pebbles-20-# for the -20 model?
2. Are these pebble input files only useful for the full-core, could they be used for more generic stuff as well? If so, it would be useful to have them higher up in the directory.

phlox/reactors/single-pebble/:

1. This folder could benefit from a README detailing what’s going on, and the goals for each of the burn-# folders.

You've got a lot of cool results, and I can't wait to see the final product.