kavanase
commented
2 months ago 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!
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_workflownotebook to reduce these unnecessarily large plot sizes)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.pyscript 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 theexample/notebookfolder? 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.zipLess 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_workflownotebook)