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Code cleanup/enhancement suggestions #20

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kavanase opened this issue Aug 10, 2024 · 2 comments
Open

Code cleanup/enhancement suggestions #20

kavanase opened this issue Aug 10, 2024 · 2 comments

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@kavanase
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Some small suggestions:

  • The anharmonic example notebook is 32 Mb which is too large to display on GitHub, whereas the next largest notebook is the updated workflow one which is only 2 Mb and has as many plots in it. I'm not sure what the issue is here, but I think just re-running this notebook and saving might fix this (I think we added some plotting updates before to fix this? Otherwise using whatever options are used in the CarrierCapture_workflow notebook to reduce these unnecessarily large plot sizes)
image
  • It would be good to give an example notebook for generating the input structures for the carrier capture calculation. Currently this is only shown using the gen_cc_struct.py script here, which also assumes that the two structures are correctly symmetry-matched. I think I sent you some example notebooks for this before @xw-w (symmetry-matching the structures and generating the selected path structures)? Would you mind uploading one to the example/notebook folder? I've attached an example of doing this for NEB calculations in case needed (same steps just changing the selection of Q coordinates)
    Example_NEB_Path_Generation.ipynb.zip

  • Less urgent but good housekeeping; currently the readme points to some of the old (deprecated) notebooks as example usages. Would be good to update this to point to the new recommended workflow (i.e. the CarrierCapture_workflow notebook)

@kavanase
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I tried tackling the first of these myself but I don't have julia installed on my laptop currently so it's a pain. Should hopefully only take a minute or two to re-run that notebook if you already have julia up and running!

@kavanase
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Slightly updated path generation notebook here!
Example_CC_Path_Generation.ipynb.zip

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