Atoms and Feff for CuFe2O4 structure
Dear all, I am using Atoms to calculate a Feff input file for CuFe2O4 spinel. However running Atoms/Feff results in program crash owing to 'two atoms very close together'. I modified the .cif file before importing (owing to partial occupancy issue) as following: Deleted: Fe2 Fe3+ 8 d 0.5 0.25 0.125 . 0.5 0 Modified: Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 0.5 0 to Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 1 0 After importing the file in Atoms, I also used different shift vectors (e.g. -0.125 -0.125 -0.125) but the issue is not resolved. Can someone help me please to solve this problem? Thanks. Best Regards Qasim
The first hit for spinel MgAl2O4 at crystallography.net gives these coordinates: Mg1 Mg2+ 8 a 0. 0. 0. 1. 0 d Al1 Al3+ 16 d 0.625 0.625 0.625 1. 0 d O1 O2- 32 e 0.375 0.375 0.375 1. 0 d That's completely different from what's in the CIF file you sent. Your cif file does not have Cu or O at symmetry positions associated with a spinel. I suppose that makes sense given that your CIF file does not use the spinel space group. It is true that Feff crashes, taking Artemis with it, when you try to run it on a list of atoms which has atoms that are 0.09 Angstroms apart. I suppose that Artemis should recognize that situation and ask whether you really want to run Feff with such ridiculous input. I'll put that on my to do list. None of that answers your question of what to do. You have some crazy structure that comes from who-knows-where, that is not a spinel, but which you think is a spinel. I don't know what advice you are looking for, but you need to figure out your structure and make sure it runs to sensible completion in Atoms. B On 04/30/2014 01:55 PM, Qasim Imtiaz wrote:
Dear all,
I am using Atoms to calculate a Feff input file for CuFe2O4 spinel. However running Atoms/Feff results in program crash owing to 'two atoms very close together'. I modified the .cif file before importing (owing to partial occupancy issue) as following:
Deleted: Fe2 Fe3+ 8 d 0.5 0.25 0.125 . 0.5 0 Modified: Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 0.5 0 to Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 1 0
After importing the file in Atoms, I also used different shift vectors (e.g. -0.125 -0.125 -0.125) but the issue is not resolved. Can someone help me please to solve this problem? Thanks. Best Regards
Qasim
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
We used to say that FEFF will run on any input, but we've been proven wrong
several times :p.
Kevin Jorissen
On Sun, May 4, 2014 at 2:41 PM, Bruce Ravel
The first hit for spinel MgAl2O4 at crystallography.net gives these coordinates:
Mg1 Mg2+ 8 a 0. 0. 0. 1. 0 d Al1 Al3+ 16 d 0.625 0.625 0.625 1. 0 d O1 O2- 32 e 0.375 0.375 0.375 1. 0 d
That's completely different from what's in the CIF file you sent. Your cif file does not have Cu or O at symmetry positions associated with a spinel. I suppose that makes sense given that your CIF file does not use the spinel space group.
It is true that Feff crashes, taking Artemis with it, when you try to run it on a list of atoms which has atoms that are 0.09 Angstroms apart. I suppose that Artemis should recognize that situation and ask whether you really want to run Feff with such ridiculous input. I'll put that on my to do list.
None of that answers your question of what to do. You have some crazy structure that comes from who-knows-where, that is not a spinel, but which you think is a spinel. I don't know what advice you are looking for, but you need to figure out your structure and make sure it runs to sensible completion in Atoms.
B
On 04/30/2014 01:55 PM, Qasim Imtiaz wrote:
Dear all,
I am using Atoms to calculate a Feff input file for CuFe2O4 spinel. However running Atoms/Feff results in program crash owing to 'two atoms very close together'. I modified the .cif file before importing (owing to partial occupancy issue) as following:
Deleted: Fe2 Fe3+ 8 d 0.5 0.25 0.125 . 0.5 0 Modified: Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 0.5 0 to Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 1 0
After importing the file in Atoms, I also used different shift vectors (e.g. -0.125 -0.125 -0.125) but the issue is not resolved. Can someone help me please to solve this problem? Thanks. Best Regards
Qasim
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
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Bruce Ravel -
Kevin Jorissen -
Qasim Imtiaz