Add min "thickness" check in CifParser to filter invalid structure which leads to infinite loop
#4133
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@anyangml I hope this looks good to you, with this patch your example would terminate gracefully: /Users/yang/developer/pymatgen/src/pymatgen/io/cif.py:1318: UserWarning: No structure parsed for section 1 in CIF.
lattice.volume=2.2009330203855426e-06 ų below threshold, double check your structure.
warnings.warn(msg)
/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py:1322: UserWarning: Issues encountered while parsing CIF: No structure parsed for section 1 in CIF.
lattice.volume=2.2009330203855426e-06 ų below threshold, double check your structure.
warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
Traceback (most recent call last):
File "/Users/yang/developer/pymatgen/debug/recreate_cif.py", line 15, in <module>
read_file("./example.cif")
File "/Users/yang/developer/pymatgen/debug/recreate_cif.py", line 6, in read_file
structure = cif.parse_structures(primitive=True)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py", line 1325, in parse_structures
raise ValueError("Invalid CIF file with no structures!")
ValueError: Invalid CIF file with no structures! |
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@anyangml May I have your permission to include your cif file as a test file for |
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yes! |
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Cool thanks! |
DanielYang59
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CifParser to filter invalid structure which leads to infinite loopCifParser to filter invalid structure which leads to infinite loop
DanielYang59
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Oct 29, 2024
| @@ -969,8 +969,22 @@ def _get_structure( | |||
| primitive: bool, | |||
| symmetrized: bool, | |||
| check_occu: bool = False, | |||
| min_thickness: float = 0.01, | |||
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I hope this default minimal "thickness" of 0.01 Å would be a good default value (it's already "lower than it should be", but I just want to prevent false positive), is there any case that we might expect valid structure below this threshold?
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Summary
CifParserto filter invalid structure which leads to infinite loop, to fix CifParser taking forever without throwing an error #4028