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).
This is in the same category as Issue #3.
Overall
Specifics
Serpent Inputs
fuel0material 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.ipynbexists 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?calc-inputs.ipynbinto 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.calcproc.py