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

Look for paper about WL
by Gudrun Lisa Bovenkamp 30 Jan '13

30 Jan '13

Dear all, I need reference (paper) to say that WL refers to anti-bonding orbitals and in the same context that pre-edge refers to bonding orbitals. Is there any paper that can help me? Thanks, Lisa

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Help with importing binary files from NSLS BM X15B in athena
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear all, I'm trying to import binary files generated at BM X15B of NSLS, at the S K-edge. I selected the corresponding plugin, and Athena (Demeter 0.9.14) does not import the columns 7-10 containing the Io, It, IF and S Kalpha-fluo. It only imports the first few columns and they don't contain the information I need. If I ask Athena to import more columns it crashes and exit. When I use the utility at BM X15B to convert the binary files in simple text files, Athena does not recognize the text files as data file. I'm I doing something wrong ? Any idea how to solve this problem ? I have attached a binary file, its text translation (using the utility available at BM X15B), and a screenshot of what happens when I import a binary file. Thanks for the help Regards, Raoul Couture <https://sites.google.com/site/couturerm/>

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Different R-factor values
by Christopher Patridge 25 Jan '13

25 Jan '13

Hello List, I know that Horae is no longer supported but I had quick question about the R-factor. I search the mailing list and found this post from 2006 concerning different R-factors in the fit log I have a question about Artemis log file. I noticed that two r-factors are > reported in the log file. One is in the fifth line and it is called > 'R-factor' and the other one is under the data set fitting conditions and > it is called 'r-factor for this data set'. They have in general different > values. What does it mean? Which is the difference between the two? It probably means that I am calculating something wrongly. Here's the concept. If you do a multiple data set fit and you have some value of R-factor, you would like to know how that misfit is partitioned among the data sets. That is, you'd like to know if one set is contributing to the misfit for significantly than the others. When Ifeffit computes the R-factor, it is for the entire fit. My idea in Artemis was to use the formula for R factor from page 18 of http://cars9.uchicago.edu/~newville/feffit/feffit.ps <http://cars9.uchicago.edu/%7Enewville/feffit/feffit.ps> on each data set in a multiple data set fit and report that in the log file. At some point, I must have convinced myself that I was doing the calulcation in Artemis identically to how it is done in Ifeffit. If you are seeing different values, it would seem I was mistaken. I'll make an entry in my to do list to look into that. I am reviewing some older analysis projects from artemis and just wanted to know which R-factor more accurately describes the misfit? I suspect the average over the k weights values since this was adopted in Demeter? Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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(D)Artemis and (D)Athena crash - perl not responding
by Matthias Filez 24 Jan '13

24 Jan '13

Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: <http://helpdesk.ugent.be/e-maildisclaimer.php> http://helpdesk.UGent.be/e-maildisclaimer.php

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Artemis crash and data set limit
by Christopher Patridge 23 Jan '13

23 Jan '13

Hi List, My project file crash about five minutes and I found the dartemis log file attached before opening the program again which I hope will explain the problem. is there a limit to the number of datasets in Artemis? Thanks, Chris -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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self absorption correction
by sumitk＠barc.gov.in 22 Jan '13

22 Jan '13

Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Sumit -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O).

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Multiple Atom.inp in Feff
by Christopher Patridge 17 Jan '13

17 Jan '13

Hi all, Is there a way to remove data sets, feff.inp, or atoms.inp from the main window list? I know this question was raised at one of Bruce's XAFS seminars at Diamond. I looked at the current Demeter List of Things to Do and did not see specifically removing them, just reorganizing lists. I guess it is not really a bug, just annoying, but for some reason, probably user error and impatience, my artemis file saved several "atoms.inp" windows in the Feff list and now I cannot get rid of them. Thanks, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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S02 question
by Eugenio Otal 15 Jan '13

15 Jan '13

Hi all, I have a question about S02 measurement in samples for CN calculation. By example, If I have an oxynitide, LaTiO2N, Can I use TiO2 as standard for S02 even the Ti in LaTiO2N is coordinated to O and N? In a more extreme case, is possible to use metals? Which are the recommendations and limits? Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Prof. Dr. Eugenio H. Otal UNIDEF - CONICET - CITEDEF San Juan Bautista de La Salle 4397. Villa Martelli (B1603 ALO) Buenos Aires Argentina TEL: +54 11 4709-8158. FAX: +54 11 4709-8241. and UTN - Santa Cruz Regional Faculty Av. Inmigrantes 555 Río Gallegos (9400) Santa Cruz Argentina TEL: +54 2966 429173 FAX: +54 2966 42-9173 E-mail: eugenio.otal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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k-range question & R-factor
by Christopher Patridge 15 Jan '13

15 Jan '13

Hello Users, I was looking for an opinion about the chi(k) signal in a set of data I am analyzing. Brief background, this is a set of in-situ XAS data collected at the Fe K edge from a working electrochemical cell at a range of potentials during charge; I did not collect the data. I suspect the feature at ~ 8 angstroms-1, although present in all the spectra is noise or glitch and wondered if I am being overly cautious? My conservative range ( k = 2-7 and R = 1-2) really constrains the model Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me some flexibility. In a multiple dataset fitting, is the R-factor of the whole set just the average or total mismatch across all the datasets or it calculated another way? Working towards happiness, Chris Patridge -- ******************************** Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501

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Re: [Ifeffit] Ifeffit Digest, Vol 119, Issue 19
by Denis Testemale 15 Jan '13

15 Jan '13

Hello Chris. - I don't have an answer regarding the R-factor. - Noise or glitch: how does I0 look like? Is the glitch you suspect visible in I0 at this energy? If you're refering to the feature that points downwards at 8A-1, it actually shifts with the spectra (I can see two groups of spectra in this k-range) so a glitch seems doubtful to me. Can you tell more about the collection of data (transmission, fluorescence, thickness of the sample, temperature, etc.)? By looking at the data, and if you confirm that I0 is glitch-free, I would be more suspicious about the data in the range 10-14A-1 than this 8A-1 feature. Cheers denis > Today's Topics: > > 1. k-range question & R-factor (Christopher Patridge) > > > > Hello Users, > > I was looking for an opinion about the chi(k) signal in a set of data I > am analyzing. Brief background, this is a set of in-situ XAS data > collected at the Fe K edge from a working electrochemical cell at a > range of potentials during charge; I did not collect the data. I suspect > the feature at ~ 8 angstroms-1, although present in all the spectra is > noise or glitch and wondered if I am being overly cautious? > > My conservative range ( k = 2-7 and R = 1-2) really constrains the model > Nidp = 3.31. Luckily, multiple datasets ( 8 ) to the rescue to give me > some flexibility. In a multiple dataset fitting, is the R-factor of the > whole set just the average or total mismatch across all the datasets or > it calculated another way? > > Working towards happiness, > > Chris Patridge > -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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