XANES-2012 short course at Brookhaven

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Anatoly I Frenkel

10 Aug 2012 10 Aug '12

3:48 p.m.

Dear IFEFFIT subscribers: Please find below the information about the short course on X-ray absorption spectroscopy that will be organized at Brookhaven National Laboratory on Nov. 8-10, 2012 Either follow the link in the bottom of the NSLS web page: http://www.nsls.bnl.gov or go directly to the course web site: http://workshops.ps.bnl.gov/default.aspx?w=XANES2012 The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November 8-10 at the NSLS. To qualify for admission, participants should have prior background in XAS theory and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and hands-on data analysis sessions. The lectures cover the XANES fundamentals, surveys recent developments in theory and data analysis, the commonly used computer codes (FEFF and others), data modeling techniques, and specific applications of XANES to research problems. The course enrollment is limited to 30 participants. Application deadline: September 30, 2012. Best regards, Anatoly Frenkel Yeshiva University

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Huaming Guo

20 Aug 20 Aug

1:02 p.m.

New subject: [Ifeffit] How to fit "N" number of Neigbors in (D)Artemis?

...

Dear IFEFFIT subscribers:

Please find below the information about the short course on X-ray absorption spectroscopy that will be organized at Brookhaven National Laboratory on Nov. 8- 10, 2012

Either follow the link in the bottom of the NSLS web page: http://www.nsls. bnl.gov or go directly to the course web site: http://workshops.ps.bnl.gov/default. aspx?w=XANES2012

The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November 8-10 at the NSLS. To qualify for admission,

Dear Colleague, I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this parameter. How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot. Regards Huaming Guo ------------------------------------------- Prof.Dr. Huaming Guo School of Water Resources & Environment China University of Geosciences Beijing 100083 P.R.China Tel: 0086-10-82321366 Fax: 0086-10-82321081 Email: hmguo@cugb.edu.cn ------------------------------------------- Anatoly I Frenkel 写: participants should have prior background in XAS theory and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and hands-on data analysis sessions. The lectures cover the XANES fundamentals, surveys recent developments in theory and data analysis, the commonly used computer codes (FEFF and others), data modeling techniques, and specific applications of XANES to research problems.

...

The course enrollment is limited to 30 participants. Application deadline: September 30, 2012.

Best regards, Anatoly Frenkel Yeshiva University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Bruce Ravel

1:44 p.m.

New subject: How to fit "N" number of Neigbors in (D)Artemis?

On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:

...

I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this parameter. How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression. In the EXAFS equation, N and S02 are multiplied together. Thus, you might consider parameterizing the amplitude by setting N to 1 and putting all of the parameterization in the math expression for S02. B -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

Huaming Guo

1:24 p.m.

New subject: [Ifeffit] How to fit "N" number of Neigbors in (D)Artemis?

Thanks. In this case, is the number of neibors equal to N * SO2 in the model result? Regards HM Bruce Ravel 写:

...

On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:

...
I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this parameter. How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to 1 and putting all of the parameterization in the math expression for S02.

B

--

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

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

Scott Calvin

2:24 p.m.

New subject: How to fit "N" number of Neigbors in (D)Artemis?

Just to fill out some details about how this somewhat quirky aspect of Ifeffit/Artemis can be used: Suppose you want to find the degeneracy of nearest-neighbors, represented by path 1, and next-nearest neighbors, represented by path 2. To fit the degeneracy of one of the paths, 1. Set "N" to 1 for both paths. 2. Create parameters named, say, "amp," "N1," and "N2." 3. Fill in the N box for both the first and second path with "1" (not "N1" and "N2"!) 4. Fill in the S02 box for path 1 with "amp*N1" and for path 2 with "amp*N2." 5. EXAFS does not contain enough information to guess all three parameters; one of them must be set. Often, that is amp, perhaps because it is obtained from a standard. But maybe it's N1: you might know the near-neighbor coordination, but not the next-nearest neighbors. In any case, you need to set at least one of the three parameters to a known (or suspected) value. 6. All your named parameters now mean what you think they should mean in the log files: e.g., "N2" is the coordination number for the next-nearest neighbors. But the "S02" path parameter in the log files is amp*N1 for the first path and amp*N2 for the second path. That's kind of confusing, but because you've designed your guess/def/set parameters effectively, it's not a problem! Hope that helps... --Scott Calvin Sarah Lawrence College On Aug 20, 2012, at 9:24 AM, Huaming Guo wrote:

...

Thanks. In this case, is the number of neibors equal to N * SO2 in the model result?

Regards

HM

Bruce Ravel 写:

...
On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:

...
I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this parameter. How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to 1 and putting all of the parameterization in the math expression for S02.

B

--

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

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

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Wei Li

1:53 p.m.

New subject: How to fit "N" number of Neigbors in (D)Artemis?

Hi, Bruce, Does that mean each shell has a different S02 value? Wei On Mon, Aug 20, 2012 at 9:44 AM, Bruce Ravel wrote:

...

...
I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to be a constant in the (D)Artemis. We can not set the variable for this

On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote: parameter.

...
How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to 1 and putting all of the parameterization in the math expression for S02.

B

--

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

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

-- Wei Li Postdoc researcher Environmental Soil Chemistry Group Delaware Environmental Institute University of Delaware, Newark,19713 Tel:631-949-0663 http://ag.udel.edu/soilchem/li.html http://ag.udel.edu/soilchem/

Bruce Ravel

2:13 p.m.

New subject: How to fit "N" number of Neigbors in (D)Artemis?

On Monday, August 20, 2012 09:53:13 AM Wei Li wrote:

...

Hi, Bruce,

Does that mean each shell has a different S02 value?

No. It means that S02 must be evaluated for each path. Or, I suppose, I should say that the product of N and S02 must be evaluated for each path. No! No! Actually, I should say that the product of N and S02 must be evaluated correctly for each path where what I mean by "correctly" depends upon the details of your fitting model. That sounds right! If you are fitting your copper foil data, then "correctly" probably means to let N be the path degeneracy found by the path finder and to use a single S02 parameter for all paths. If you are fitting a crystal with different sites for the absorbing atom -- say the super conductor YBa2Cu3O7, which has 1 Cu atom in the Cu1 site and 2 Cu atoms in the Cu2 site -- then your parameterization of S02 must be scaled accordingly depending on which Feff calculation the path comes from. If you are fitting an amorphous solid or a nanoparticle or something else which unknown coordination, then you are probably best off setting N to 1 and parameterizing S02 for each path in some manner that captures the details of the coordination environment that you are trying to measure. Remember, N and S02 are multiplied together in the EXAFS equation. HTH, B

...

Wei

On Mon, Aug 20, 2012 at 9:44 AM, Bruce Ravel wrote:

...
On Monday, August 20, 2012 09:02:28 PM Huaming Guo wrote:

...
I am using the (D)Artemis for EXAFS fitting. However, the "N" is set to

be a

...
constant in the (D)Artemis. We can not set the variable for this

parameter.

...
How can I do that if I model non crystalline samples using (D)Artemis? Thanks a lot.

In Artemis, N is a pure number, but S02 can take a math expression.

In the EXAFS equation, N and S02 are multiplied together.

Thus, you might consider parameterizing the amplitude by setting N to 1 and putting all of the parameterization in the math expression for S02.

B

--

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

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

-- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Anatoly I Frenkel
Bruce Ravel
Huaming Guo
Scott Calvin
Wei Li