CGCNN can't run on certain CIF files

[noortitan]

Hello,

Great work with the project. I have been using CGCNN for perovskites, with the CIF files taken from ICSD database. However, I found out that it only works with certain CIF files, but not the others. Does it only take a certain "type" of CIF files? If so, how do I change the CIF files which don't work to the format that can be inputted into CGCNN?

As a reference, here are some of the ICSD collection codes:

• Working: 110630, 243861, 252316, 255885, 255886, 432089
• Not working: 252317, 252318, 252319, 252320, 254340, 254341, 434118, 432090, 254288

The error that comes out:

Traceback (most recent call last):
  File "main.py", line 513, in <module>
    main()
  File "main.py", line 119, in main
    sample_data_list = [dataset[i] for i in range(len(dataset))]
  File "main.py", line 119, in <listcomp>
    sample_data_list = [dataset[i] for i in range(len(dataset))]
  File "/run/user/1000/gvfs/user/cgcnn-ubuntu/cgcnn-master/cgcnn/data.py", line 326, in __getitem__
    print("Specie number: ",crystal[0].specie.number)
  File "/home/user/miniconda3/envs/cgcnn/lib/python3.7/site-packages/pymatgen/core/sites.py", line 79, in __getattr__
    raise AttributeError(a)
AttributeError: specie

Thank you!

[Andrew-S-Rosen]

This is an issue with the Pymatgen CIF parser. I recommend reading in each of your CIFs with ASE and writing them back out again with ASE, which will result in a CIF format that Pymatgen can read.

[noortitan]

I have tried using both Pymatgen CIF parser, as well as reading and rewriting the CIFs with ASE, but it's still not working. The same error still appears.

[txie-93]

Perhaps the CIF file itself has problems. Sometimes I saw CIF files that include invalid elements like Wa. It cannot be parsed by the pymatgen, so you see an error with the specie.

[Amadeus-System]

I have experienced same problem. so I didn't use cif files directly. I have used pymatgen MPRester and directly accessed to a material-project without using cif file and extract it to a 'structure'.