April 2015 - Ifeffit - millenia.cars.aps.anl.gov

Evaluation of uncertainty using correlated Debye model + advices for the fitting of an hexagonal Co-foil
by Samy OuldChikh 07 Apr '15

07 Apr '15

Dear all, I would like to go beyond the fitting of the first shell for a cobalt metallic foil acquired at FAME beamlime (ESRF). It's not mandatory for the determination of So in this case, but I just would like to improve myself in EXAFS fitting. The cobalt foil has an hexagonal structure (P 63/mmc, a =b=2.507 A, c= 4.068 A) according to the supplier. The first 49 scattering paths calculated with FEFF were selected to cover the R range up to 5.1 A. This include multiple scattering paths. The parametrization of those scattering paths is as follow (.apj enclosed) : - Distances : 1) a spherical expansion term was used to describe distance variation in [hkl] direction (reff*alpha1) with l considered as "large" when compared to h,k (reff*alpha1) 2) another spherical expansion term was used to describe distance variation in pure [hk0] direction (reff*alpha2) 3) a rough average of two previous expansion terms for [hkl] direction when h,k are comparable to l (reff*(alpha2+alpha1)/2). - For modeling disorder, the correlated Debye model was used with 3 parameters dt, dt2, dt3 (t =293K): 1) [hkl] direction with l considered as "large" : debye(t,dt) 2) pure [hk0] direction: debye(t,dt2) 3) for [hkl] direction with h,k comparable to l : debye(t,(dt+dt2)/2) But does this choice of parametrization is really reasonable? It seems very rough to me but when I look at the fit results it looks ok. - Uncertainty on : 1) Distances : is it simply delta(r) = reff*delta(alpha) ? 2) Debye-Waller : I can't figure out how to relate the uncertainty computed for the Debye temperatures (dt, dt2) to the uncertainties of the debye-waller terms for each scattering paths. Although I spent some times trying to understand this paper, http://journals.aps.org/prb/pdf/10.1103/PhysRevB.20.4908, I can't write a simple relation at the end. Many thanks for your kind help, Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]
by Ravel, Bruce 07 Apr '15

07 Apr '15

Zhaoming, This conversation should be happening on the Ifeffit Mailing List. I did not notice that last night when I replied to your first email. Yet another reason not to answer email late at night! I continue to be sceptical of your claims. I have no problems with the data file you sent on either Windows or Linux once I correctly select the columns in the column selection dialog. Once imported, the default values for normalization are set as I expect and the data is interactive in the normal manner. Here are some hints about how to provide a useful bug report: http://bruceravel.github.io/demeter/pods/bugs.pod.html Please read it carefully. If there is more to this conversation, please use the mailing list. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Thursday, April 02, 2015 1:00 AM To: Ravel, Bruce Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Hi Bruce, Sorry, I did have to specify column 4 as energy, 7 as Io and 8 as It. The new version of Athena does read the .dat file in, but the default values for normalization are way wrong, and it doesn’t work by manually change them either. I’m happy to send you screen shots if necessary. Thanks again for your help. Zhaoming From: Ravel, Bruce [mailto:bravel@bnl.gov] Sent: Thursday, 2 April 2015 12:43 PM To: ZHANG, Zhaoming Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Zhaoming, I'm afraid I am sceptical of your story. I have no trouble reading this file and I don't believe that any change I've made since 0.9.20 would have affected this. Who knows, though. I'll take a lok on a windows machine when I get into work tomorrow morning. It's a rather awkward file. The first column is an index, not energy. That's one of my pet peeves -- just a ridiculous way to present the data and kind of mean-spirited to the user. When something is measured in energy, the first column should be energy. That means you have to explicitly select column 2 as the energy. Column 2 appears to be in keV, so you need to explicitly set that in the column selection dialog. Because column 1 was not the energy, Athena had no way of figuring that out. I have no idea which columns have data in them. 7 and 8 look rather like I0 and It. So you need to explicitly set your data columns, as well. I've attached a screenshot of the column selection dialog with all those settings. When data are presented as obfuscated as they are in this data file, it is not reasonable to expect that Athena will magically know how to disentangle everything without your help. You have to be responsible for knowing which columns to combine to turn your raw data into mu(E). B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov<mailto:bravel@bnl.gov> National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter ________________________________ From: ZHANG, Zhaoming [zzx(a)ansto.gov.au] Sent: Wednesday, April 01, 2015 7:34 PM To: Ravel, Bruce Subject: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED] Dear Bruce, I’ve encountered the same problem as Sander Bruun. My data were obtained from the Australian Synchrotron. In the past, I could read the .dat file (see attached example) directly into Athena. But it doesn’t work with the new version (0.9.20), and the beamline scientist doesn’t know why either. I would really appreciate if you could let me know what ‘fix’ we need! Thanks so much. Warm regards, Zhaoming

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Possible Error on 0.9.21
by Clark, Adam 01 Apr '15

01 Apr '15

Hi I have recently encountered an error in displaying the path geometry in the latest version of artemis, 0.9.21. When running feff and then selecting a path and viewing the geometry of this path an incorrect path is shown. This does not occur when using the same feff.inp file on the older 0.9.20 version. The problem is limited to the numbering and showing of the path geometry in the feff calculation window. Attached is the feff.inp, feff.txt files and a screenshot showing the produced feff.txt ‘show geometry for this path window’ for a selected @ O.1 @ path (instead showing the @ Zn.1 @ path) and ‘atoms and feff’ window showing the discrepancy in path numbering between the feff.txt file and feff window. Thanks Adam

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