Some script usage issues

[bailinyu]

Hello Mr.
When I downloaded the script I found that the POSCAR atoms were superimposed, as shown in Figure 1.

When I first applied the BDM-ase.py script to my system, I got the situation in Figure 2.

This also happened when I used the BDM-polaron-vasp-python3.py script.

I executed the script by installing PYTHon3 BDM-polaron-vasp-python3.py POSCAR 2 30 8. But the results were strange. Could you tell me how to use it? Thank you very much.

[bailinyu]

Dear Mr. Deskins;
This may seem strange, but so does the POSCAR you provide. I mean does that allow you to go straight to the structure optimization and then look at the structure.
Looking forward to your reply .
Bai

[aarondesk]

Can you post the original POSCAR file that you used with the scripts?

[bailinyu]

OK. This is the POSCAR before I used the script.
POSCAR-LGS.txt
And this is the POSCAR after I used it.
BDM-polaron-POSCAR-LGS.txt

[aarondesk]

Ok, thank you for bringing this up. It looks like there was an error in reading non-orthorhombic cells. I updated the code (BDM-polaron-vasp-python3.py) and it should fix this. I tested on your POSCAR-LGS.txt and it seems to be working now.

[bailinyu]

I have downloaded the new code. Thank you very much for your help!

[bailinyu]

Dear Mr. Deskins;
After I downloaded the new script and used it, the POSCAR structure still looked strange. The first image is POSCAR before I used the script, and the second image is after I used it.

Best Regard!
Bai

[aarondesk]

Are you using BDM-polaron-vasp-python3.py?
Here is the structure before using the code.

Here is the structure after using the code.

It looks fine for me.

[bailinyu]

Thank you for your answer. The problem appeared in my VESTA version and has now been fixed.

[bailinyu]

Dear Mr. Deskins;

Although the structure looks more reasonable than before, after executing the script, the Ga and Si atoms overlap, which is clearly not structurally optimized.

This is the POSCAR after executing the script, the first marked with Ga and the second marked with Si.
Thanks for your help!

Bai

[aarondesk]

Could you try the latest version? I think this corrects that error.

[bailinyu]

Thank you for your constant help. It worked this time.