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

Proper data processing in Athena with large pre-edge features
by Chris Patridge 22 Jul '09

22 Jul '09

Hi everyone, I am working on Vanadium K-edge EXAFS with various VxOx oxides. My question concerns deciding E0 and background spline in Athena. The K edge at 5465eV has a large peak before the edge jump and when subtracting the background and moving to K-space using the default settings, the Bkgd looks incorrect. Any suggestions on how to set the background for further processing? Thank you everyone as this is my firstpost and first EXAFS analysis, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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Re: [Ifeffit] Ifeffit Digest, Vol 77, Issue 19
by abhijeet gaur 21 Jul '09

21 Jul '09

Re :inquire (Makoto Matsuura) Dear Makoto, I also encountered the same problem you are facing now. The basic problem is that when you save k chik or k2 chik in Athena and then get it imported in Artemis then the data is already k weighted and when you again try to weight it in Artemis, the data gets disturb. So, you have to save simply chik of your data in Athena and then import it into Artemis.Then in Artemis you can weight your data as you have done in Athena and it will look same as Athena plot. Also from Artemis you can select the groups of which you which you need chi k or chir and then you can go for option save selected groups in Artemis. You will get all the data in one file . then you cam import it in Origin or any other software by import single ascii option. In your case you save chir data the real part, imaginary part also got saved with magnitude, so if you need your fourier transform as seen in Athena, you just plot the magnitude column with data. I think this will work Abhijeet Gaur School of Studies in Physics Vikram University Ujjain ( India) On 7/21/09, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > 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. inquire (Makoto Matsuura) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 21 Jul 2009 15:28:34 +0900 > From: "Makoto Matsuura" <m_matsuura(a)imr.tohoku.ac.jp> > Subject: [Ifeffit] inquire > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <000601ca09cc$790f3aa0$6b2dafe0$(a)tohoku.ac.jp> > Content-Type: text/plain; charset="us-ascii" > > Hi! > > I'm annoyed with the mismach of Fourier transform between Athena and > Arthemis. The k-weighting (k^1), k-window( Kaiser Bessel) and k-range are > kept same for both. The input chi-data and resultant Fourier transforms are > attached. > > One more question of Arthemis is that when I try to output data of chi(k) > or chi(r) from menu of File, null data file comes out while right data can > be obtained for the fitted data. How can I get data of chi(k) or chi(r) in > ascii format for Arthemis? Thank you. > ======================================================================== > Makoto Matsuura > > IMR Tohoku Univ. Sendai, Japan > > ========================================================================= > >

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inquire
by Makoto Matsuura 21 Jul '09

21 Jul '09

Hi! I'm annoyed with the mismach of Fourier transform between Athena and Arthemis. The k-weighting (k^1), k-window( Kaiser Bessel) and k-range are kept same for both. The input chi-data and resultant Fourier transforms are attached. One more question of Arthemis is that when I try to output data of chi(k) or chi(r) from menu of File, null data file comes out while right data can be obtained for the fitted data. How can I get data of chi(k) or chi(r) in ascii format for Arthemis? Thank you. ======================================================================== Makoto Matsuura IMR Tohoku Univ. Sendai, Japan =========================================================================

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Re: [Ifeffit] atoms location in feff.inp
by Eugenio Otal 17 Jul '09

17 Jul '09

Yes, that is the point, I need to move the central atom from 0,0,0 to change the symmetry. Now everything gonna be more easy. Thanks, euG I am not sure I quite understand the question, but ... The central atom does not need to be at (0,0,0) in the feff.inp file. Atoms puts it there for the convenience of the human reading the feff.inp file, but that is not a requirement. It also does not need to be the first item in the atoms list. HTH, B

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atoms location in feff.inp
by Eugenio Otal 17 Jul '09

17 Jul '09

Hi, I am performing some XANES simulations of site distortion in ZnO, and found some problems to change atoms position and run atoms. I want to know if is the same to change the atoms position of the ipot0 in the feff.inp file. Thanks, euG

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Re: [Ifeffit] Error in paths with ifeffit
by Bruce Ravel 16 Jul '09

16 Jul '09

On Thursday 16 July 2009 04:42:41 pm you wrote: > When I try to obtain the path with the attached > cif file, I find distance As_O(8) = 2.142 A, this > is uncorrect, because there is no oxygen atom at that distance. > What is going on? Hi Elsa, For some reason, Artemis does the wrong thing with the setting of the space group. According to your CIF file, the proper setting of the space group is P 21/n. For some reason, when Artemis reads that CIF file, it uses P 21/c as the space group symbol. That is strange behavior -- I will have to investigate what is going on. The work-around on the Atoms page in Artemis is to change the space group to "P 21/n" before running feff. If you are using Atoms at the command line, you will have to tell Atoms to write out an atoms.inp file, edit that, then run feff. That's all a bit irritating, but it is at least workable. When I ran your cif file after specifying "P 21/n" on the Atoms page, I got this for the first several neighbors: 0.00000 0.00000 0.00000 0 As1 0.00000 -0.46784 -0.12630 1.58774 4 O3_1 1.66004 -0.88804 -0.96644 -1.02986 4 O1_1 1.66830 1.65544 -0.19677 -0.19615 4 O2_1 1.67859 -0.36279 1.66519 -0.35929 4 O4_1 1.74171 -0.22909 1.88872 -1.29544 1 H1_1 2.30172 2.26346 1.49452 0.40642 1 H13_1 2.74263 2.03956 -2.01248 0.21917 1 H10_1 2.87366 1.14080 -0.11749 2.64281 1 H8_1 2.88092 2.08625 -0.17254 -2.02856 1 H5_1 2.91501 -2.72907 -0.44011 -1.05767 1 H9_1 2.95976 That looks more like what you were expecting.... B PS: The proper address for the mailing list is ifeffit(a)millenia.cars.aps.anl.gov rather than ifeffit-owner@... Mail to ifeffit-owner goes just to Matt and I rather than to the whole list. -- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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post-doc position
by Matt Newville 16 Jul '09

16 Jul '09

Hi Folks, A Post-Doctoral position using XAFS in Earth Sciences is open at St. Francis Xavier University, working with Alan Anderson. More details are at http://xafs.org/Jobs --Matt

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Re: [Ifeffit] Athena XFit report, possible (minor) bug.
by Bruce Ravel 16 Jul '09

16 Jul '09

On Wednesday 15 July 2009 09:33:25 pm you wrote: > Hi Bruce, > > I was looking at some Co data this morning, and having a problem whereby > the XFit program Spline was crashing when trying to read in an XFit report > output from Athena 0.8.059. After some head scratching and fidling, I > figured out it was because the XFit report had used Cobolt as the absorber > instead of Cobalt. I'm not even 100% sure this is directly related to > Athena, although I couldn't find any reference to Cobolt or Cobalt in the > raw ESRF data. Stacey, Wow. The word "Cobalt" is misspelled in the tool that Athena uses to translate between Z number and element name. This is my favorite kind of bug -- one that is not my fault ;-) I'll update that tool on the machine that I use to build windows executables. The next time I build and release a windows executable, this will be fixed. In the meantime, you will need to manually fix that misspelling for all you Co data. B -- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Ifeffit Digest, Vol 77, Issue 11
by Zuzaan, Damdinsuren 10 Jul '09

10 Jul '09

Dear all, It is possible to use in Artemis several paths from 2 different FEFF input files in one fit for the unknow sample? Also could I manipulate directly in the feff input file, I mean change elements and so on. Thanks, Damdin ________________________________________ 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: Monday, July 06, 2009 9:39 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 77, Issue 11 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. xanes_normalization range (Arezki, Bahia) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jul 2009 21:36:42 +0200 From: "Arezki, Bahia" <Bahia.Arezki(a)uni-siegen.de> Subject: [Ifeffit] xanes_normalization range To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7093842D66DA64CB51A0EEC99D6BBA31504137B82(a)MAIL30.uni-siegen.de> Content-Type: text/plain; charset="iso-8859-1" Dear IFEFFIT users, I have some problems/doubts with quite basic questions concerning xanes processing. In particular the normalization range. Can anyone please look at my project and tell me if my data processing is correct ? The xanes are at the Fe K-edge, of a F(II)-complex, taken at different temperatures. In fact my question concerns the choice of the starting value for the normalization range. I obtain reasonable lines with a starting point from more that 100 eV after E0. Is it correct to start so far from the edge?? should one start just after the broad feature (onset of exafs ? ) ? if I start the post-edge normalization before ..I obtain different results when I compare the different xanes.. thanks for your help, best regards, bahia

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What you see is "not" what you get: help
by Ismael Graff 10 Jul '09

10 Jul '09

Hi folks, I´ve been working on Xanes peaks fitting with Athena (last version) and I found a strange behaviour. I get a "good" fit looking to the Graphics Window of Athena and to the minimized parameters (R-factor, etc). However, when I use the data of the fit generated by Athena "write a log file" feature and plot them in Origin, the fit looks bad! In order to get a "good looking" fit in Origin I have to change the parameters ad-hoc in Athena fitting dialog box. When I do this, the fit looks bad in Athena Graphics window and better in Origin. The values that are inserted ad-hoc in Athena are not the optimized ones from the fitting procedure output. I have attached the log file from Athena fit and two figures: a PS figure from Athena and a JPG figure from Origin. It resembles that the generated data from Athena are not exactly these ones that I see in the Graphics window! I´m looking for help from someone out there. Kind regards, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418

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