The structural check was so strict that machine errors were misjudged as structural errors during large supercells

[Lonya0]

Describe the bug

the structure check here is to strict, when constructing a supercell, an 0.00000000000003 distance error was considered as a out bound atom, which should not.

Expected behavior

No response

To Reproduce

No response

Environment

No response

Additional Context

No response

[AsymmetryChou]

As this has been solved by #50, I close it.