FEFF calculation for two inequivalent absorbing sites
Hello everybody, I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default) My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation? Thank you in advance! Sincerely, Eugenio
Hi Eugenio,
Quick question: Did you change the tags for the Co atoms so that they are
different?
If I do that, I get 4 and 6 coordinate results. you can import the cif file
twice, run atoms on both
sites (with tags different) and get the two feff inputs for running.
-R.
On Thu, Apr 9, 2015 at 5:01 AM, Eugenio Paris
Hello everybody,
I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default)
My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation?
Thank you in advance! Sincerely, Eugenio
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Regarding the "Aggregate" button, it is important to understand what that button is trying to do. It is a tool that is very easy to misuse, or at least get confused by. You should read this page from the manual: http://bruceravel.github.io/demeter/artug/feff/aggregate.html and this article: http://dx.doi.org/10.1107/S1600577514014982 If it's what you're looking for, cool. B On 04/09/2015 06:01 AM, Eugenio Paris wrote:
Hello everybody,
I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default)
My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation?
Thank you in advance! Sincerely, Eugenio
_______________________________________________ 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-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Thank you for your answers,
I think there were several troubles on my analysis.
First of all i didn't understand well how the fuzzy degeneracy works but
after your suggestion i read the JSR paper and now it is pretty clear.
Also, the fact that i was obtaining twice the same path list in the two
sites was due to the mislabeling of the two Co sites (now it works!).
Thank you !
Eugenio
2015-04-09 22:04 GMT+02:00 Bruce Ravel
Regarding the "Aggregate" button, it is important to understand what that button is trying to do. It is a tool that is very easy to misuse, or at least get confused by.
You should read this page from the manual:
http://bruceravel.github.io/demeter/artug/feff/aggregate.html
and this article:
http://dx.doi.org/10.1107/S1600577514014982
If it's what you're looking for, cool.
B
On 04/09/2015 06:01 AM, Eugenio Paris wrote:
Hello everybody,
I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance. Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4. So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number. Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default)
My question is: Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation?
Thank you in advance! Sincerely, Eugenio
_______________________________________________ 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-II Building 535A Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Bruce Ravel -
Eugenio Paris -
Robert Gordon