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usnistgov / alignn

Atomistic Line Graph Neural Network https://scholar.google.com/citations?user=9Q-tNnwAAAAJ&hl=en https://www.youtube.com/watch?v=WYePjZMzx3M
https://jarvis.nist.gov/jalignn/
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'cif2cell' is not recognized as an internal or external command, operable program or batch file. #169

Open Dalabomba opened 2 weeks ago

Dalabomba commented 2 weeks ago

Hi! I was studying Geometric GNN and trying to use your network to predict one paticular property. My dataset was in cif form. However when i added --file_format cif to make the network predict on cif it would present error as in the following screenshots. I have already installed cif2cell and other requisites in my virtual env.

To Reproduce My command line is python -u train_alignn.py --root_dir "./SuperCon3D/order_Tc_split_1" --epochs 3 --batch_size 2 --config "./SuperCon3D/order_Tc_split_1/config_example.json" --output_dir "./SuperCon3D/temp" --file_format cif

Screenshots image the Chinese characters here means " 'cif2cell' is not recognized as an internal or external command, operable program or batch file."

Package information

I would be grateful if you could help me!!!

Dalabomba commented 2 weeks ago

I tried to use cif2cell alone in GitBash, and it worked and successfully created a POSCAR file of a given cif file. But it indeed can't work in cmd. So what's wrong here?

bdecost commented 6 days ago

hi - sorry for taking a bit to get back to you.

the cif2cell functionality is implemented in this call to os.system in jarvis-tools here

to get this working I would recommend checking if cif2cell is in the system path. My guess is that you have cif2cell installed in a location that is not on the paths that python searches.

I'm not totally how this works on windows systems, on unix you would check that cif2cell is in one of the directories listed by os.environ["PATH"].