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

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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running diffkk and deltaf
by marie-helene.tuilier＠uha.fr 09 Jul '09

09 Jul '09

Hello everyone, First, I would like to pay homage to the authors of that fairly user-friendly software, which is very useful for a diffusion of XAFS technique. Thanks to the detailed explanation found in the various tutorials, I became able to use it almost without any help. Despite every thing, I encounter now some difficulties running DIFFKK and DELTAF in IFEFFIT. I am trying to reduce DAFS data of a metallic nitride film at the Ti K-edge and I need anomalous scattering factors. First I built diffkk.inp and deltaf.inp files following the instructions given by Matt Newville and Julie O. Cross in the Diffkk tutorial. Then, I begin to run diffkk in ifeffit 1.2.11c as follows: ifeffit> run diffkk ifeffit> read diffkk.inp or ifeffit> run deltaf ifeffit> read deltaf.inp I become only a file named userenv.log with such comments: " cannot process autoexec.bat". Perhaps I loaded a wrong version of IFEFFIT. Thank you in advance. Marie-Hélène Diffkk.inp %Anomalous scattering at Ti K-edge% Title=Ti0.5Al0.5N (2microns) XAFS data out = C:\Program Files\Ifeffit\Ti05diffkk.fpp %output file name xmu= C:\Program Files\Ifeffit\L27ACIEReldeg.xmu %xmu data file name isfeff=false %is this a feff xmu.dat ? encol=1 % energy column mucol=2 % mu(E) column iz=22 % z of central atom (Ti) e0=4968.0000 % edge energy egrid= 1.0000 % energy grid ewidth=1.2000 % for broadening Cromer-Liberman f"(E) elow=70.0000 % how far below the data range to go ehigh=500.0000 % how far above the data range to go %------------------------% Deltaf.inp %Bare atom resonant scattering factors at Ti K-edge% Title=Ti0.5Al0.5N (2microns) delta f" out = C:\Program Files\Ifeffit\Ti05deltaf.fpp %output file name iz=22 % z of central atom (Ti) e0=4968.0000 % edge energy ehigh=500 % how far above the data range to go elow=70 % how far below the data range to go egrid= 1 % energy grid ewidth=1.2 % for broadening Cromer-Liberman f"(E) end %------------------------%

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xanes_normalization range
by Arezki, Bahia 06 Jul '09

06 Jul '09

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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new release of my software
by Bruce Ravel 05 Jul '09

05 Jul '09

Hi everyone, Windows users should soon see that an update is available. This is a relatively small thing -- it contains a new build of Athena with fixes for several recently repoted bugs. As always, it should get installed sometime soon when you fire up one of the Ifeffit programs. For those who build from source, I have also uploaded a new tarball to my web site (already there) and to SourceForge (available soon). Along with the bug fixes to Athena, this new tarball (horae-070) is my attempt to address the serious problems many of you have had in recent months trying to get my codes installed from source. The current tarball contains all of horae as well as all of my libperlxray modules. It also includes all the files required to install the Athena User's Guide (which is why the new tarball is so much larger than previous ones). I have writen a general build script and attempted to explain the installation procedures clearly is files fouond at the top of tarball. Let me know how it goes. For those of you who use the SVN server for the source code, that remains a useful alternative to using the tarball. There is no code in the tarball that is not in the SVN repository. Regards, 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 8
by abhijeet gaur 05 Jul '09

05 Jul '09

Hello Sir, I am fitting Cu2O at room temperature. I got the point. So, the negative value of SS parameter is due to the low value of SO2 guessed by artemis. I have done the fitting again by fixing the value of SO2 to 0.7. Now I am gettig positive value of SS parameter which is around 0.007. Please tell me from where I can get the standard value of SO2 calculated theoretically in the literature. with regards Abhijeet Gaur Dear Abhijit, > > > > The parameters So2 and SS are highly correlated. The negative value of SS > does not make any physical significance. It may be due that Artemis is > conveging for lower value of So2. In your case (So2=0.552 or 0.61) it is > very low. Generelly, it should be in the range of 0.7 to 1. It will be > better if you fix So2 for the standard value calulated theoretically in the > literature or you can try to get approximated value of SS for So2 around 0.8 > to 0.9. > > > > regards > > > > Umesh Palikundwar > > Department of Physics > > RTM Nagpur University, > > Nagpur-440033 > > _________________________________________________________________ > Missed any of the IPL matches ? Catch a recap of all the action on MSN > Videos > http://msnvideos.in/iplt20/msnvideoplayer.aspx >

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Re : Cu2O fitting
by abhijeet gaur 04 Jul '09

04 Jul '09

Hi all, Thanks for the response. I am sorry as I should attach the figure in a viewable format. Anyways now I am attaching a the artemis project file in which I had used a set positive value for the SS parameter of first path. I am not able to understand the reason for negative SS value. Thanks again Abhijeet Gaur

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