Hi Anouk, I am not sure what is happening with that CIF file. When I try to read that with pymatgen, I get
>>> from pymatgen.io.cif import CifParser >>> structs = CifParser('VOXZAJ.cif') >>> structs.get_structures() .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species occupancies sum to more than 1!. warnings.warn(f"Error is {str(exc)}.") .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0 Species occupancies sum to more than 1! warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings)) Traceback (most recent call last): File "<stdin>", line 1, in <module> .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures raise ValueError("Invalid cif file with no structures!") ValueError: Invalid cif file with no structures! If you remove all the atomic sites that have a "B" in their name, that gets resolved, but I do not know if that is still the correct structure - or what the "B" means. CIF is complicated, but just from a practical point of view, I think we are going to take `pymatgen` as the arbitrator of "valid CIF". On Wed, May 24, 2023 at 11:30 AM Volker, Anouk <a.vol...@student.rug.nl> wrote: > Dear all, > > I hope this email finds you well. I have encountered a problem that I have > not been able to fix on my own. I have a specific CIF file (from the CCDC > database) that is attached to the e-mail. After removing the duplicate > atoms in the file, the ATOMS window seems fine. The FEFF calculation will > run without any errors and within the FEFF window the paths are displayed > and can be plotted. The problem arises when I try to take some of the paths > from the FEFF window and drag them into the Path window. Now the paths can > no longer be plotted and when trying to use them to fit, it seems like the > paths are non-existent as well. > > Is there something wrong with the CIF file that causes this to happen and > if so, what can be done to fix it? I have already tried to make a feff.inp > file from the xyz data (after opening the CIF file in any viewer), but this > gives the same problem. > > Thank you in advance, > > Kind regards, > Anouk Volker > > Master student, Browne Group > Stratingh Institute, University of Groningen > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit