Closed leeaburton closed 8 years ago
For this problem, just add a structure.merge_sites() before determiing symmetry.
The reason why we don't do it by default is that it is a very expensive operatino to check validity of structures. The user should be responsible for checking structure validity when working with such files.
System
Summary
segmentation fault when using SpacegroupAnalyzer on some cif files
Example code
for filename in glob.glob('*.cif'): try: s = Structure.from_file(filename) a = SpacegroupAnalyzer(s) except: pass
Error message
"python quit unexpectedly" or "Segmentation fault: 11"
Suggested solution (if any)
previous version of pymatgen exited with helpful message/warning such as 'site occupation > 1' etc.. but current version kills job mid run and gives no indication. Unfortunately not been able to identify the problem
Files (if any)
Just one of several identified culprit cif files: