CrystalNNFingerprint: No Voronoi neighbors found for site - try increasing cutoff. Should I treat as NaNs or average the OK sites?

[sgbaird]

An example of a structure that fails (only on site 6):

Structure Summary
Lattice
    abc : 12.350696 14.104949458808422 14.527473876232783
 angles : 63.92566223904422 79.2990282889014 65.62253736027132
 volume : 2070.508763122277
      A : 12.350696 0.0 0.0
      B : 5.821764 12.847438 0.0
      C : 2.697509 5.787997 13.048756
    pbc : True True True
PeriodicSite: Hg (5.8268, 12.8480, 0.0037) [0.0004, 0.9999, 0.0003]
PeriodicSite: H (9.7351, 5.6024, 8.8724) [0.5786, 0.1297, 0.6799]
PeriodicSite: H (13.8559, 6.0049, 4.5341) [0.8994, 0.3109, 0.3475]
PeriodicSite: H (8.0213, 12.4316, 10.1972) [0.1886, 0.6156, 0.7815]
PeriodicSite: I (10.7995, 9.5062, 6.3019) [0.5227, 0.5223, 0.4830]
PeriodicSite: O (14.0980, 9.7276, 9.5889) [0.7801, 0.4261, 0.7349]
PeriodicSite: O (12.7394, 13.2700, 4.1544) [0.5427, 0.8895, 0.3184]
PeriodicSite: O (8.7643, 5.5144, 8.7059) [0.5033, 0.1286, 0.6672]
PeriodicSite: O (7.3719, 8.8273, 3.1464) [0.2716, 0.5785, 0.2411]
PeriodicSite: O (13.4883, 5.9796, 3.6148) [0.8710, 0.3406, 0.2770]
PeriodicSite: O (7.9270, 12.6247, 9.2341) [0.1743, 0.6638, 0.7077]

Wondering if I should treat this one as a row of NaNs or if I should take the average fingerprint of the sites that computed OK.

Happy to switch over to matminer discussion, but figured it was worth asking here due to the use of CrystalNN.

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Hi all! I am facing an issue in using the LocalPropertyDifference featurizer in Matminer. For some structures, I get an error “ValueError: No Voronoi neighbours found for site - try increasing cutoff” Now while LocalPropertyDifference has no cutoff parameter during initialization, it calls pymatgen’s local_env.py module where the default cutoff is 13 angstroms. I had to increase it to nearly 100 angstroms for it to find neighbors but my structure’s unitcell’s dimensions are less then 10 angst…

How to use CrystalNNFingerprint

I’ve seen your code, which has solved many of my problems.But when I used it, there was a problem When I use BondOrientationalParameter and my code is as follows: from matminer.datasets.convenience_loaders import load_elastic_tensor from matminer.featurizers.structure import SiteStatsFingerprint from matminer.featurizers.site import BondOrientationalParameter df = load_elastic_tensor() dfeat= SiteStatsFingerprint(BondOrientationalParameter()) df = dfeat.featurize_dataframe(df, “structure”…

Related to decisions in Consider use of fingerprint distance instead of `StructureMatcher` for comparison between generated and test · Issue #39 · sparks-baird/matbench-genmetrics · GitHub

[Mengfan_Wu]

Hi, have you fixed this? I also met the same problem, woder if should treat as NaN. If you find the better to fix this, would mind tell me? Thanks so much!