Can the degeneracy (N) in Artemis be a variable?
Hi all, When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it? Thanks for your reply, Peng -- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu@uwaterloo.ca
I assume you mean you "can't assign a [variable] to N."
It's a quirk of FEFF that the value of N for a path must be a number
(perhaps even an integer?) but amplitude may be any number or a variable.
For that reason it's typical (or at least common practice in my experience)
to leave N as 1 and define the amplitude as some function of So2,
degeneracy, percent of that phase, or whatever else is appropriate for your
sample.
-Jason
On Sat, Jul 26, 2014 at 12:56 PM, Peng Liu
Hi all,
When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it?
Thanks for your reply,
Peng
-- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu@uwaterloo.ca
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Hi Peng: The answer is yes, you can use a variable called "n" or n_o" but you need to be careful on how you set up the fitting. here is one way to do it: For the path of interest, in the two boxes which are labeled "N" and "S02", you fill them in as "1" and "n_o" (for number of oxygens for example). Then you let "n_o" (note that at least in Artemis, lower case is the same as upper case in variables) vary as a guess parameter. The result will be a number that is of the order of the number of near neighbors but it will be too large by the factor of one over the amplitude reduction factor. If you have a way to estimate the amplitude reduction factor as a set variable called "amp" you can set up the model a bit differently, putting "amp * n_o" in the "S02" box. This might give a better estimate of the coordination number (path degeneracy). Note that numerically there is no difference between the above and taking a guessed value of "amp" and multiplying it by the number in the "N" box. It is simply a matter of convenience and ease of looking at the output. Carlo On Sat, 26 Jul 2014, Peng Liu wrote:
Hi all,
When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it?
Thanks for your reply,
Peng
-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org
Peng's question is so common on our mailing list that I would like to write a section of the Artemis document addressing it. At heart, there are two issues. The more important is that N is very highly correlated with S02 (and other things!). The operational issue is the choice I made about only allowing numbers in the N box in Artemis. I would like some suggestions for literature references on the more important part of this question. Specifically, I'd like to know what references all of you cite on the topics of this high correlation and of solving the problem for real measurements. With this bounty, I'll write up a section of the document which we can use when this question comes up in the future. Thanks, B On 07/26/2014 12:56 PM, Peng Liu wrote:
Hi all,
When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it?
Thanks for your reply,
Peng
-- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
I can't come up with a properly humble non-self-promoting way to say this, but for common fitting issues like this I'd cite my textbook. In my experience, I found it difficult to find good discussions of this kind of thing in the peer-reviewed literature, because they're either considered common knowledge or technical detail.
S. Calvin, XAFS for Everyone (CRC Press, 2013).
The degeneracy S02 correlation issue is most directly discussed in Section 10.1.2.
--Scott Calvin
Sarah Lawrence College
On Jul 28, 2014, at 9:51 AM, Bruce Ravel
Peng's question is so common on our mailing list that I would like to write a section of the Artemis document addressing it.
At heart, there are two issues. The more important is that N is very highly correlated with S02 (and other things!). The operational issue is the choice I made about only allowing numbers in the N box in Artemis.
I would like some suggestions for literature references on the more important part of this question. Specifically, I'd like to know what references all of you cite on the topics of this high correlation and of solving the problem for real measurements.
With this bounty, I'll write up a section of the document which we can use when this question comes up in the future.
Thanks, B
On 07/26/2014 12:56 PM, Peng Liu wrote:
Hi all,
When I model a standard, I know the degeneracy through the other data. But for spectra of unknown material, I would like to set degeneracy as a variable like the amplitude, deltE0, e.g.. However, I can assign a letter to N and define it. Do you have any idea how I should do it?
Thanks for your reply,
Peng
participants (5)
-
Bruce Ravel -
Carlo Segre -
Jason Gaudet -
Peng Liu -
Scott Calvin