About error:No Voronoi neighbors found for site - try increasing cutoff

When i use this featurizer : SiteStatsFingerprint.from_preset(“CoordinationNumber_ward-prb-2017”),there will be error like:No Voronoi neighbors found for site - try increasing cutoff.
how should i increase the cutoff? where should i modify?
please any help will be appreciated

It looks like we did not allow passing options from the Featurizer to the part of the code (VoronoiNN) which computes the neighbors. Do you want help fixing that?

oh! thank you so much sir. I am appreciate for the replying. Now i almost settled the issue and I’ve found the source code to increase the cut off.
By the way, me and my group have read your paper, it solved us many problems. Thanks for your work.
Wish you good luck,

sir, i have a question .I use matminer try to featurize my dataset, but I met the error: “ValueError: No Voronoi neighbours found for site - try increasing cutof”. I increase the cutoff to 100 angstroms, it still show this error, how should I fix this?

Interesting about the error. Some structures are just problematic to compute a tesselation for. I’ve got around that by perturbing atomic positions as a small amount before doing so.

What structure are you computing the tesselation for?

Could you please tell me how and where to modify the code for perturbing atomic position ? what should i do exactly.
Appreciate for your helping.

I don’t have specific code, but the idea is to modify your structure file before calling the featurizer.

A displacement of less than 0.1 should be enough to break the symmetries (which cause problems in the tessellation) and not enough to affect your features. See this method: pymatgen.core package — pymatgen 2023.10.4 documentation

I modified the structure file like this but i still can’t featurize my data.
It just freeze like this.

I am not sure if i operate the solution in wrong way.