Problems with FEFF calculation using CIF file
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
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
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
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Volker, Anouk