How to generate defects (atom exchanges) using pymatgen

pymatgen
1

Hello everybody!

I usually use pymatgen to substitute atoms in a structure for other atoms (i.e. 25% subtitution of Mn by Ni in LiMn2O4 generating the different structures of LiMn1.5Ni0.5O4). This time I would like to exchange atoms in one structure (i.e. In LiMn1.5Ni0.5O4 put a percentage of Ni in tetrahedral position and Li in octahedral position, while normally they are the other way around).

Does anybody know how to do it?

Thanks!

Iciar

2

Is it possible to use the SubstitutionTransformation for this? It seems like you could just feed it a dictionary of the form {“Li": {“Li”: 0.5, “Ni”: 0.5}}, “Ni”: {“Li”: 0.5, “Ni”: 0.5}}. I haven’t tried this myself, but looking at the code I don’t see an obvious reason why it would fail.

1 Like
3

I will try it today and let you know! Thanks!

4

After many trial i get a syntax error using:
subtrans = SubstitutionTransformation({“Li”: {“Li”: 8./8, “Ni”: 8./20}}, “Ni”: {“Li”: 8./8, “Ni”: 8./20}})
or
subtrans = SubstitutionTransformation({“Li”: {“Li”: 0.5, “Ni”: 0.5}}, “Ni”: {“Li”: 0.5, “Ni”: 0.5}})
I also tried to add the charge to the atoms like:
subtrans = SubstitutionTransformation({“Li+”: {“Li”: 8./8, “Ni”: 8./20}}, “Ni3+”: {“Li”: 8./8, “Ni”: 8./20}})

Any idea?

5

What is the syntax error message/traceback?

6

Input In [11]
subtrans = SubstitutionTransformation({“Li”: {“Li”: 8./8, “Ni”: 8./20}}, “Ni”: {“Li”: 8./8, “Ni”: 8./20}})
^
SyntaxError: invalid syntax

Thanks!

7

Ah, the brackets are mismatched in the example I gave you, sorry about that. Try {“Li": {“Li”: 0.5, “Ni”: 0.5}, “Ni”: {“Li”: 0.5, “Ni”: 0.5}}, it might work better.

1 Like
8

It seems to work now! Thank you so much! You helped me to save a lot of time!