The degeneracy and the coordination number
Zhaomo Tan, I think you have to set the path degeneracy to 1 because the model you used for Cu in Artemis has already found that there are 12 degenerate paths which make up the first scattering distance. By setting it to one, you then create a fitting parameter for the coordination number CN. You also must constrain the amplitude factor SO2 to some value because these parameters, N and SO2, are correlated. SO2(somewhere between 0.8-1.0) * N (=1) * CN(guess parameter) - Chris ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 12/26/2012 6:23 AM, Zhaomo Tian wrote:
Dear all,
I am confused about the degeneracy and the coordination number used in the Artemis program. I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case.
So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N?
Thanks so much.
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Dear Zhaomo Tian, This is an idiosyncrasy of Artemis/Ifeffit. In the EXAFS equation, coordination number only appears multiplied by S02. Therefore it makes no sense to fit both S02 and N for a single path, as they would be 100% correlated. Artemis' solution to this is to only allow you to fit S02, requiring you to interpret whether you are doing that to fit the actual value of S02, or to fit the coordination number. To fit coordination number for the first shell, therefore, you need to know the value of S02. Hopefully, examples will make this clearer. Suppose you know S02 = 0.90 (from, for example, fitting a standard). One way to fit the first-shell coordination number would be to Set a parameter amp = 0.90 and guess a parameter N1 = 12. Then enter amp*N1 in the S02 box for path 1 in Artemis, and 1 in the N box. Another way would be to Set amp = 0.90 and N1 = 12, and then enter amp*N1/12 in the S02 box and 12 in the N box. There are, of course, other strategies that are also mathematically equivalent. The key is that you must never put a variable in the N box, instead allowing the S02 box to do all the work of fitting. --Scott Calvin Sarah Lawrence College On Dec 26, 2012, at 3:23 AM, Zhaomo Tian wrote: Dear all, I am confused about the degeneracy and the coordination number used in the Artemis program. I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case. So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N? Thanks so much. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Zhaomo,
On Wed, Dec 26, 2012 at 5:23 AM, Zhaomo Tian
Dear all,
I am confused about the degeneracy and the coordination number used in the Artemis program. I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case.
So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N?
Thanks so much.
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
I don't know what "N" and "N1" mean in your model. It would be helpful to know what you're setting the Path Parameters to. This topic can be sort of confusing. The way Feff/Ifeffit/Artemis models EXAFS, there are 3 separate values that scale the EXAFS amplitude. These are: degen: the "path degeneracy" built into the Feff.dat file. This is the value for coordination number from the cluster of atoms used in the Feff calculation. S02: the "amplitude reduction factor", a number (generally) slightly less than 1.0 meant to cover over mediocre amplitudes from Feff, and really, imperfect experimental amplitudes. N: The coordination number for the structure. In the EXAFS equation used by Artemis, these are all multiplied together. Amplitude = degen*N*S02 There are few common scenarios: A: "I know the coordination number and want to refine S02". This is useful for well-defined structures and standards, where a single cluster of atoms put into a single Feff calculation models the spectrum well. Here, you generally use the "degen" values from the Feff.dat files, set N to 1, and refine a value for S02. B: "I know S02, and want to refine N". This would be the more common situation for "unknown structures". Here, you ***SET degen to 1***, set S02 to the "known value" ( presumably determined with a standard and scenario A). Then you Guess a value for N and refine it. The "N*S02" entry in Artemis should then contain the expression for the product of the variables holding S02 and N. For example: set S02_Cu = 0.87 guess N_1st_Shell = 12.0 Path 1: 'N*S02' = S02_Cu * N_1st_Shell Hope that helps, --Matt
Go the archives for this mailing list: http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/index.html Enter the words "coordination" and "degeneracy" in the box at the top of the page, then click the button labeled "Search". I suspect the answers from the many times this question has been asked before will be helpful to you. For example, this post from Scott -- http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03435.html -- in response to a thread on this very topic -- is quite helpful. If it's still not clear, then ask again about the part that remains confusing to you. Cheers, B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Zhaomo Tian [zhaomo1989@postech.ac.kr] Sent: Wednesday, December 26, 2012 6:23 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] The degeneracy and the coordination number Dear all, I am confused about the degeneracy and the coordination number used in the Artemis program. I want to get the coordination number of 1st shell of my copper sample, so I set a guess number N1=12(initial guess) as the coordination number which will vary during the fitting iteration, but when I am looking at the 1st path's parameters, there is another N appear which may stand for the degeneracy.The 1st path of copper model is single scattering, so the degeneracy N equals coordination number . But when I set N=12, the guessed N1 will have a value which is closed to 1, only when I set N=1, the guessed N1 will have a value which is closed to 12. It seems that N and N1 are reciprocals. But I think N actually equals N1 in the single scattering case. So I am really confused, If I want to get coordination number of a shell in a fitting, how can I deal with floated coordination number and its path degeneracy N? Thanks so much.
participants (5)
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Christopher Patridge -
Matt Newville -
Ravel, Bruce -
Scott Calvin -
Zhaomo Tian