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

Basic question in normalization and background removal
by Bajamundi Cyril 08 Feb '13

08 Feb '13

Hello, I have here a very basic XANES data processing. I am but a novice in this XANES analysis. In Bruce's lecture "Athena: Data processing I<mms://diamstream02.diamond.ac.uk/xafs-2011-2>" posted in the Diamond Light Source website, he used the Fe_lepidocrocite.000 example to show how background removal and normalization is done. For the normalization range he used the range 150 - 742.610 because his original photon energy scan range is quite long [ Emin: -200 and Emax: 800]. However, say that your original scan range is only short e.g. within the range Emin : -30 to Emax: 80, such that you don't see the non-wiggly range and you only see the a short portion of the post edge range, how does one set the normalization range for this data? Since I'm very new to XANES analysis, I keep second-guessing my choice of normalization range. Your patience for answering this simple question will definitely help me in moving to the actual fingerprinting analysis that I need to do with my sample. Many thanks. Warm regards, Cyril [cid:image004.jpg@01CE05DE.B8F89320] [cid:image007.jpg@01CE05DE.B8F89320]

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XAS position in Industry
by Shelly Kelly 06 Feb '13

06 Feb '13

Dear XAS Community, We have a position open at UOP LLC, A Honeywell Company to support our XAS/tomography group. The position description can be found under Req number 00213183 at http://www.careersathoneywell.com/en/home. Please apply through the web site. Thank-you, Shelly Kelly

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Open post-doc position in Korea
by Deok-Yong Cho 04 Feb '13

04 Feb '13

Dear Ifeffit users: To whom interested in post-doc position in Korea: A two-year contract post-doc position is open in the Center for Functional Interfaces of Correlated Electron Systems (CFI-CES), Institute for Basic Science (IBS), located in Seoul National University, Seoul, Korea. We expect he/she will perform spectroscopic analysis including IR spectroscopy (Spectroscopic ellipsometry and FT-IR) at the institute and synchrotron experiments such as soft/hard x-ray absorption spectroscopy and XAFS analysis for new functional oxide materials (mainly strongly-correlated electron system). Please find enclosed document for more details. Best Regards, Deok-Yong Cho Spectroscopy team in CFI-CES, Institute for Basic Science (IBS), Seoul National University

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Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel)
by Raoul-Marie Couture 30 Jan '13

30 Jan '13

Dear Bruce, The patch worked, I was able to configure the plugin and import the binary data. I changed the default columns, otherwise some files were imported scrambled: Energy :1 (that one was ok) I0 : 6 (that one was ok) Narrow (I imported I_Trans instead): column 7 Trans (I imported Total_fluo instead): column 8 Wide (I imported S K-alpha fluo instead): column 9. Thanks for the quick and helpful reply. Raoul ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: January 30, 2013 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 119, Issue 31 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Look for paper about WL (Gudrun Lisa Bovenkamp) 2. Re: Help with importing binary files from NSLS BM X15B in athena (Bruce Ravel) 3. Re: Look for paper about WL (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 30 Jan 2013 04:27:35 +0100 From: "Gudrun Lisa Bovenkamp" <bovenkamp(a)physik.uni-bonn.de> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Look for paper about WL Message-ID: <web-12374983(a)be2.uni-bonn.de> Content-Type: text/plain;charset=iso-8859-1; format="flowed" 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 ------------------------------ Message: 2 Date: Wed, 30 Jan 2013 10:03:49 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Help with importing binary files from NSLS BM X15B in athena Message-ID: <1855179.1CSfgNSBKa(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Wednesday, January 30, 2013 02:17:35 AM Raoul-Marie Couture wrote: > 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. The problem seems to be one of column selection. I am suspicious that a detail of how the data are saved to the binary files may have changed since I wrote the X15B plugin many years ago. Attached are two file that you should be able to drop in place on top of your current installation. Put both files in C:\strawberry\perl\site\lib\Demeter\Plugins The file "X15B.pm" wil replace the version of the file that is already there. The file "x15b.demeter_conf" is new. Make sure that you save them with filenames *exactly* as written above. For instance, if you let Outlook save "X15B.pm" as "X15B.pm.txt", it won't be recognized by Athena and everything I say below won't work. The new file will allow you configure the X15B plugin. In the Plugin Registry page, rightt click on the X15B entry. See: http://bruceravel.github.com/demeter/aug/other/plugin.html#athena%27splugin… The variables set using that configuration file, tell Athena which columns from the original data file (also which columns from the text conversion using the beamlilne tool) should be preserved when Athena converts the binary blob to an ascii column file. Most of the columns are filled with zeros, which is why the plugin wants to discard those columns. Side note: Athena deals very pooly with ascii data file that don't have the energy in the first column, which is why it has trouble reading the text file from the beamline tool. I would like to hear back from you about how this works out. If it works well for you, then it will be included in the next release of the software. If there are still problems -- then I need to know. B PS: It is possible that the "x15b.demeter_conf" file has the columns for narrow and wide backwards. Let me know if you think that's the case. I am writing this email without wandering down to X15B to ask Paul the details. -- Bruce Ravel ------------------------------------ bravel(a)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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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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