ValueError: Negative values in data passed to `pairwise_distances` about matid

[lauri-codes]

Hi @xiaoboy185!

Thank you for bringing up this issue. Indeed there was a small problem in the code. I have now fixed this problem and released a new version of the package (0.5.5) both in GitHub and PyPI.

The issue was that if the distance between two atoms was smaller than the sum of their covalent radiis, the cluster detection would fail. This happens rarely but is possible with heavier elements, such as uranium in your case. To deal with this I have clipped the distances that enter the cluster detection to be equal or bigger than the sum of the two radii.

Hope this helps,
Lauri

[xiaoboy185]

Dear Lauri Himanen Thank you very much for your message. Now, the problem is fixed. Best regards Bo Xiao Lauri Himanen <[email protected]> 于2019年12月19日周四 下午11:05写道：

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