October 2009 - Ifeffit - millenia.cars.aps.anl.gov

Athena User Guide—FCFS
by Julie Olmsted Cross 09 Nov '09

09 Nov '09

I have ten copies of the Athena User Guide leftover from the 2009 APS XAFS School. If you want one, send me your mailing address. First come, first served. ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

14 17

Got Athena data plotted
by abhijeet gaur 28 Oct '09

28 Oct '09

Thanks a lot kicaj, I followed the procedure step by step and I got the data plotted in Excel. Thanks again Kicaj. Abhijeet

3 2

Re: [Ifeffit] Normalization in Athena
by Gudrun Lisa Bovenkamp 27 Oct '09

27 Oct '09

Hi everybody, I am sure that Athena was tested a lot, but as Jeremy pointed out, which I think now is the answer: If the background is substracted before the fitting of the post edge. That is actually how we are normalizing XANES data in our group and that is what I tried in Athena. It is actually working much better with 2. order norm and flattening. Since I do not want to do it by hand for all spectra and import them back into Athena for LCF. This time I attached a the example Athena project file. But with this approach I rarely get the spectrum oscillating around one. I will think about it. Thanks for the hint, Matt, about "no points" in the range. But Athena is acutally complaining, if there are no points to fit the line. Of course, I read the chapter on Normalization in Athena. And what is giving me trouble, why I try the "1-point" approach, is that the small differences in the first post-edge normalization point make a great deal of difference in the normalization of the spectra respective to each other and thus LCF. Finally, I believe it is a very interesting question of taste how to determine the edge step for XANES data or when to substract the background. Or is there any specific reason for a special approach? Thank you all for your help!! Greetings, Lisa > Hi Lisa, > > Be sure that Athena has been rigorously tested and she does know how >to > normalize data. It is much more likely that the default values are >not > the "best" ones for your data. > > My book chapter goes over how Athena normalizes data in detail. If >you > send me your email address I'll send you a copy. In particular see > figure 14-16. > > Cheers, > Shelly > > Shelly, > > I agree that Athena applies its (her) algorithm correctly. Whether >that > algorithm is correct may be a matter of opinion. The apparent > discrepency Lisa sees is due to Athena's algorithm: > > i.e., fit preedge line, fit postedge function to normalization >range, > extrapolate both functions to edge energy to find edge step. > > Another option would be to fit predge line and subtract it. After >that, > fit the post edge normalization range. > > With Athena, if there is a non-zero slope to the preedge line and >you > choose norm order 1, you get Lisa's result. With normalization >order 2 > or 3, the results should either be the same, or at least, much >closer. > > Jeremy > > > > It is a little hard to evaluate your results, Lisa, without an > example. It may help to attach a small project file which > demonstrates your question. > > Without an actual example, I would have to guess that the bottom >line > is an odd choice of parameters. This page from the document might >be > helpful: > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html > > B > > > > Lisa, > > I think the issue you're seeing is most likely due to telling athena > to fit the data between E0+199 and E0+200 with a constant. I'd > recommend expanding that range some to give Athena a chance -- if > there isn't any data between E=E0+199 and E0+200, Athena won't be >able > to figure out what the edge step should be. If you really want >the > edge step to be the value of pre-edge subtracted mu(E) at >E=E0+200eV, > you'll have to do that by hand. > > > --Matt > >

2 1

SrSO4 (Celestite) and SrCO3
by Peter Nico 27 Oct '09

27 Oct '09

Hello All, Would anyone out there have a SrSO4 or SrCO3 standard XANES spectra they would be willing to share? There aren't any in the databases of which I am aware, namely "Lytle, GSECARS, and NSLS X18b." There is a SrCO3 but its really an EXAFS standard (the edge consists of ~3 points.) I am sorry that I can't necessarily promise a publication acknowledgment because I am not sure if the work will ever be published. However, if it is, I'll definitely acknowledge the help. Thanks. --Peter

3 2

Cu oxide fitting
by abhijeet gaur 27 Oct '09

27 Oct '09

Hi all, I had posted a problem related to fitting results of Cu2O. But there are some problems related to the fitting procedure . So now I have used a different fitting procedure, still there are problems with fitting results. like 1. The value of SO2 is coming low. 2. Value of E0 is coming high though I have calibrated the experimental data. 3. The ss (Debye Waller factor) for some of the paths are coming very high. I am not able to understand the value of ss for multiple scattering path. One more problem is that if I try to align the data with theory by adjusting E0 , the data get distorted. The Artemis file is attached herewith. This time I had made fitted the whole data in one fit by taking all parameter as guessed. With thanks Abhijeet Gaur

1 0

atom.inp file for Zr50Cu50
by S. Gautam 27 Oct '09

27 Oct '09

Dear All, Can anyone help me with the atom.inp file for ZrCu bulk metallic glass samples? I am studying the Ag doping effects over the inter-atomic distance and co-ordination number through Artemis. thanking you, sincerely sanjeev --------------- Dr S. Gautam Nano Materials Analysis Center Korea Institue of Science and Technology Republic of Korea -790 784 Phone : +82-54-279-1503 (Off) 1599 (Fax) : +82-10-8061-5767 (Mob) Email : sgautam71(a)kist.re.kr

1 0

suppressing the stdout of FEFF
by Jochen Brendt 26 Oct '09

26 Oct '09

Hello everybody, I want to use FEFF8 in a program loop and redirect the stdout of this programm in a textfile. When I run the loop several times this textfile becomes very large. Does anybody know, if there is a way to suppress the stdout of FEFF8 ? Regards, Jochen

3 3

Rbkg value
by Chris Patridge 26 Oct '09

26 Oct '09

Hello everyone, In removing background, most literature suggests Rbkg value of 1.0 because below this represents mostly noise and low freq components not part of the scattering effect. In using Feff and viewing the individual paths calculated a number of them have paths near 1.5 A, therefore meaning that they have some contributions very close to 1.0 A and below in R space due to phase shift. Has anyone modeled materials which contain these rather short Reff and how did you decide what was scattering and noise? Thank you all, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

4 3

Normalization in Athena
by Gudrun Bovenkamp 26 Oct '09

26 Oct '09

Hey everybody, while I try to figure what effect normalization has on Linear combination fitting in my lead L3 edge XANES system, I came accross this problem: Athena does not normalize correctly: Normalization in Athena (post-edge): using 1.order normalization, no flattening (which in this case is irrelevant anyway), points +199 eV and +200 eV above E0. Normalization in Origin (post-edge): using point 13235 eV (+200 eV above E0); dividing the spectrum column by that value. See the two examples in the attachment. In both examples the normalized spectrum imported from Athena does not have the norm value of 1 at 13235 eV. Why is that? The offset is also not the same for every spectrum. That undoes the normalization routine. Greetings, Lisa

5 4

Xanes with Athena?
by Annette Pietzsch 26 Oct '09

26 Oct '09

Hi, I tried to use the self absorption function of the Athena package (FLUO) with my Xanes data (Fe3O4 at the Fe L3 edge). The program identifies the edge correctly, but gives only a zero line for the correction. I think it might be due to the energy value of the Fe L3 edge emission in the database which is prompted to be zero by Athena. Could this be the reason? If yes, is there a possibility to change the energy database to the correct value? \ Annette

2 1