Query regarding inequivalent sites in the EXAFS fitting
Dear Bruce, Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites. For example, In Ca3Co2O6 compound, the Co ion occupies two inequivalent crystallographic sites with the Co1-O bond distance at 1.960 and Co2-O at 2.09 Ang. How does one invoke the contribution of both the bond distances in the first shell fitting? Best regards Bindu Dr.Bindu R. Visiting Fellow DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.
Hi Bindu: On Fri, 29 Feb 2008, Bindu R. wrote:
Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites.
The simplest way to do this is to prepare 2 distinct FEFF calculations, each with the central atom being a different site. You will then be able to import the first path of each calculation into the model. You will have to make sure that the parameters you use for the two different paths are set up consistently. Also remember that if the two sites have different multiplicities, this will have to be reflected in the amplitude factors of the two paths. Hope this helps, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Hi, does your proceeding make sense for XANES calculations, too? For example for an atom-cluster with some sulfur absorber? best regards, Eckhard
Hi Bindu:
On Fri, 29 Feb 2008, Bindu R. wrote:
Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites.
The simplest way to do this is to prepare 2 distinct FEFF calculations, each with the central atom being a different site. You will then be able to import the first path of each calculation into the model. You will have to make sure that the parameters you use for the two different paths are set up consistently. Also remember that if the two sites have different multiplicities, this will have to be reflected in the amplitude factors of the two paths.
Hope this helps,
Carlo
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--------------------------------- Eckhard Bosman e.bosman@stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany
Hi Eckhard: On Fri, 29 Feb 2008, s440697@stud.uni-goettingen.de wrote:
Hi,
does your proceeding make sense for XANES calculations, too? For example for an atom-cluster with some sulfur absorber?
best regards, Eckhard
Yes, you can do this for XANES calculations too. The outputs need to be summed over all the inequivalent positions. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
You will then be able to import the first path of each calculation into
Hi, my normal proceeding is (for example Na_2 SO_4) to calculate with an atom-cluster of this substance with lots of atoms an lots of sulfur. I chose one as the absorber and make one single feff-run. But when i do this for all sulfur atoms consecutively (because in experiment every sulfur absorbs the x-rays of course) i have lots of single results in my several folders. Now the question: How can i combine this results meaningful? You said: the >model. Where can i find the first paths? paths.dat, list.dat or feffNNNN.dat? And what do you mean with "import into the model"? Which model? Sorry, but i worked only with the command-line based FEFF 8.4 and
The outputs need to be summed over all the inequivalent positions.
Carlo
Can you explain it please a little bit more in details? best regards, Eckhard
Hi Eckhard: On Fri, 29 Feb 2008, s440697@stud.uni-goettingen.de wrote:
Hi, my normal proceeding is (for example Na_2 SO_4) to calculate with an atom-cluster of this substance with lots of atoms an lots of sulfur. I chose one as the absorber and make one single feff-run. But when i do this for all sulfur atoms consecutively (because in experiment every sulfur absorbs the x-rays of course) i have lots of single results in my several folders. Now the question:
You will then be able to import the first path of each calculation into
How can i combine this results meaningful? You said: the >model. Where can i find the first paths? paths.dat, list.dat or feffNNNN.dat? And what do you mean with "import into the model"? Which model? Sorry, but i worked only with the command-line based FEFF 8.4
The original answer I gave was for EXAFS fitting using Artemis. There, the individual was asking how to use the first shell paths from the two inequivalent positions in crystal structure to develop a model for EXAFS. My impression from your message was that you are more interested in doing XANES calculations with FEFF (perhaps I misunderstood...). For the XANES calculations, you get output files with density of states and other information. In order to obtain something that will simulate the experimental data that you obtain, you need to add all of these contributions together and then apply a Fermi function to properly simulate an edge. There is probably a lot more that can be done but I am not an expert there. For this kind of calculation, Artemis doesn't really help, command line invocation of FEFF8.4 is the only thing to do.
Can you explain it please a little bit more in details?
The bottom line is that I was answering what I percieved to be two different questions, one EXAFS, the other XANES. If I was incorrect, please let me know. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
As is often the case, the FAQ may help. Look at question 14 at http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling B On Friday 29 February 2008 00:06:28 Bindu R. wrote:
Dear Bruce,
Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites.
For example,
In Ca3Co2O6 compound, the Co ion occupies two inequivalent crystallographic sites with the Co1-O bond distance at 1.960 and Co2-O at 2.09 Ang.
How does one invoke the contribution of both the bond distances in the first shell fitting?
Best regards Bindu
Dr.Bindu R. Visiting Fellow DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830
--------------------------------- 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Bindu, I'm sorry. I misread your question. Carlo's answer is much more to the point than mine was. B On Friday 29 February 2008 00:06:28 Bindu R. wrote:
Dear Bruce,
Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites.
For example,
In Ca3Co2O6 compound, the Co ion occupies two inequivalent crystallographic sites with the Co1-O bond distance at 1.960 and Co2-O at 2.09 Ang.
How does one invoke the contribution of both the bond distances in the first shell fitting?
Best regards Bindu
Dr.Bindu R. Visiting Fellow DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830
--------------------------------- 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
participants (4)
-
Bindu R. -
Bruce Ravel -
Carlo Segre -
s440697＠stud.uni-goettingen.de