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

Sorry
by Chris Patridge 23 Jul '09

23 Jul '09

I forgot to post a bitmap of the spectra of the previous message. Thank you all. -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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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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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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Re: [Ifeffit] Fitting Cu2O
by umesh palikundwar 04 Jul '09

04 Jul '09

> Hi all, > I am fitting Cu2O data. But when I fit the first shell using the > first path, I got the guess value for SS parameter negative which is around > -0.0028 and also the guessed value for SO2 parameter comes out to be around > 0.52. Are these values logically correct as I am getting a nice fit. > Also when I use the same SS parameter but with positive sign for the > first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to > be 0.61. > When I fit the higher shells by using the same SO2 and Enot value for > other paths, the value of SS parameter for these paths is coming very high , > i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher > values of SS parameter correct. The resulting figure is attached. > > with thanks > > Abhijeet Gaur > > School of Studies in Physics > > Vikram University, Ujjain, INDIA. 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: [Ifeffit] orbital configuration (FEFF8)
by joshua jason kas 04 Jul '09

04 Jul '09

Hi Iraida, I believe there are a few issues here that could be addressed/explained. First, the electronic configuration given at the end of the potentials is only the configuration of the valence electrons. For example the absorbing oxygen should be interpreted as 0 0 1.953 ~2s2 0 1 5.159 ~2p5 (The ~1 extra valence electron for the absorbing atom is due to the attractive core hole) 0 2 0.040 0 3 0.000 while for Cd 1 0 0.723 ~5s1 1 1 0.711 ~5p1 1 2 10.149 ~4d10 1 3 0.000 Here, the differences from the atomic configuration of 4d10 5s2 are due to the fact that this is a self-consistent solid state configuration, i.e. the valence electrons were allowed to relax and were effected by the solid state potential. That being said, there are ways to change the initial configuration for the elements, but you would have to change the source code and recompile. I don't think this is what you want to do though. As for improving your results, there may be a variety of things that you can do. Off hand your input file looks pretty good. One thing you might try is using the card UNFREEZEF which allows the d electrons from the Cd to tranfer to f states which can sometimes be important when the d band is full. I hope that my answer helps some, at least in interpreting FEFFs output. Josh Kas > Hi everyone,I > would like to calculate K-edge of oxygen XANES spectrum for CdO film. I > attached my feff.inp file to this e-mail. When I check log1.dat file I > observe next information: > "... > Electronic configuration > iph il N_el > 0 0 1.953 //comment: 0-centr.atom (O) > 0 1 5.159 > 0 2 0.040 > 0 3 0.000 > 1 0 0.723 //comment: 1-Cd > 1 1 0.711 > 1 2 10.149 > 1 3 0.000 > 2 0 1.921 //comment: 2-O > 2 1 4.443 > 2 2 0.052 > 2 3 0.000 > mu_new= -5.168 > Charge transfer: iph charge(iph) > 0 -0.152 > 1 0.417 > 2 -0.417 > Done with module 1: potentials." > > As > is well known, orbital configuration for Cd and O is: 4d10 5s2 and 1s2 > 2s2 2p4, respectively. I think that obtained results for Cd differ much > according to presented orbital configuration (s,p). So, my question is: > do there exist some possibilities to change something in my feff.inp > file to improve the results? > > Best regards, > Iraida. > > > >

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Fitting Cu2O
by abhijeet gaur 03 Jul '09

03 Jul '09

Hi all, I am fitting Cu2O data. But when I fit the first shell using the first path, I got the guess value for SS parameter negative which is around -0.0028 and also the guessed value for SO2 parameter comes out to be around 0.52. Are these values logically correct as I am getting a nice fit. Also when I use the same SS parameter but with positive sign for the first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to be 0.61. When I fit the higher shells by using the same SO2 and Enot value for other paths, the value of SS parameter for these paths is coming very high , i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher values of SS parameter correct. The resulting figure is attached. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain, INDIA.

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Fitting Cu2O
by abhijeet gaur 03 Jul '09

03 Jul '09

Hi all, I am fitting Cu2O data. But when I fit the first shell using the first path, I got the guess value for SS parameter negative which is around -0.0028 and also the guessed value for SO2 parameter comes out to be around 0.52. Are these values logically correct as I am getting a nice fit. Also when I use the same SS parameter but with positive sign for the first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to be 0.61. When I fit the higher shells by using the same SO2 and Enot value for other paths, the value of SS parameter for these paths is coming very high , i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher values of SS parameter correct. The resulting figure is attached. with thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain, INDIA.

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orbital configuration (FEFF8)
by Dream Dream 02 Jul '09

02 Jul '09

Hi everyone,I would like to calculate K-edge of oxygen XANES spectrum for CdO film. I attached my feff.inp file to this e-mail. When I check log1.dat file I observe next information: "... Electronic configuration iph il N_el 0 0 1.953 //comment: 0-centr.atom (O) 0 1 5.159 0 2 0.040 0 3 0.000 1 0 0.723 //comment: 1-Cd 1 1 0.711 1 2 10.149 1 3 0.000 2 0 1.921 //comment: 2-O 2 1 4.443 2 2 0.052 2 3 0.000 mu_new= -5.168 Charge transfer: iph charge(iph) 0 -0.152 1 0.417 2 -0.417 Done with module 1: potentials." As is well known, orbital configuration for Cd and O is: 4d10 5s2 and 1s2 2s2 2p4, respectively. I think that obtained results for Cd differ much according to presented orbital configuration (s,p). So, my question is: do there exist some possibilities to change something in my feff.inp file to improve the results? Best regards, Iraida.

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problem with Athena's E0 !
by Arezki, Bahia 01 Jul '09

01 Jul '09

Hi all, I am using Athena (version: 08.058) to study the changes in the XANES profiles as a function of temperature of an organometallic compound containing Fe. I have a problem with the E0 value suggested by Athena : I noticed that it is not taking the same maximum in the first derivative. I am sending 2 examples of xanes taken at RT ( E0 guessed is 1722.8 eV ) and 10 K (1727.3 eV !), can any one help me please to solve this problem ? should I force athena to take the first maximum at 1722 eV ? I tough that my spectra have been properly calibrated: I first calibrated the iron foil -reference channel (E0=1712 eV) of a sample xanes and then I aligned the rest of the reference channels to that one. I though this was enough to calibrate my data. can you please tell me if my data processing is correct? I need to be sure about the E0 value in order to know the correct shift of the different xanes features as a function of temperature. Also, with a wrong E0 the normalization is not correct...did I miss an important step? I am having hard time with these basic questions...before using linear combination analysis and peak fitting analysis. Of course I have already looked in the IFFEFIT archive, but I did not find such problem. I only found a question about a wrong E0 because taken before the edge which is not my case. Thanks so much for your time, Bahia

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Re: [Ifeffit] plotting anotation
by Bruce Ravel 30 Jun '09

30 Jun '09

Hi Dr. Matsuura, I am answering CCing this email to the Ifeffit Mailing List http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the most appropriate forum for asking questions about the software. If you have not yet joined the mailing list, we encourage you to do so. I have also taken the liberty of converting the image file you attached into a format that everyone will be able to view. On Tuesday 30 June 2009 02:49:51 am you wrote: > Dear Bruce Ravel > > I'm a beginner of IFEFFIT. I'm pleased if you could ask following > questions about plotting in Artemis. > > 1) In a plotted figure as attached, annotation shows "2/path #". What > does it mean letter" 2". Presumably, you have more than one Feff calculation in your Artemis project, one of which still has its default name of "Feff2". To save horizontal space in the legend of the plot, I have Artemis drop the ltters "Feff". So, that legend entry means "Path N from Feff calculation 2". > 2) In the plotted figure attached, the sum of each path constituent is > not equal to fitting data. The reason of why. In Ifeffit, we use a complex Fourier transform to convert chi(k) to chi(R), thus chi(R) is a complex function. When the fit is evaluated, the real part of the theoretical chi(R) is compared to the real part of the data chi(R) and the imaginary part is compared to the imaginary part. You have plotted the magnitude of this complex function. You should not expect the sum of the moduli of the paths to equal the modulus of the sum of the paths. For a complex function, summation and mudulus are not commutative operations. B > > > > *************************************************************************** >* ****************** > > Metallic Glass Inorganic Materials Joinning Technology Development > > Institute for Materials Research, Tohoku University,Sendai, 980-8577,Japan > > Dr. Makoto Matsuura > > e-mail:m_matsuura@imr.tohoku.ac.jp > > *************************************************************************** >* ******************* -- 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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Fwd: Follow-up on your Athena issue
by Bruce Ravel 24 Jun '09

24 Jun '09

Gautier, First off: USE THE MAILING LIST! That's what it's there for. Why ask two people for help when you can ask hundreds? As you say, you are not the first to see this behavior, but I am not among those who have witnessed this. It is, of course, hard for me to troubleshoot a problem that I have never seen and don't know how to reproduce. The only helpful thing that comes to mind is to ask if there are any non-lower-ascii characters in the path either to the folder where Ifeffit is installed or to the folder where your data lives. At some point in the last couple years, I thought I had fixed the issues with nono-lower-ascii characters -- but who knows? Perhaps you keep your data in folder called "données" or "データ". If so, try installing Ifeffit in a place with only lower-ascii characters and do the same with your data. No guarantees, but it is something to try. B ---------- Forwarded Message ---------- Subject: Follow-up on your Athena issue Date: Wednesday 24 June 2009 From: Gautier Landrot <landrot(a)udel.edu> To: n.thammajak(a)gmail.com Dear Dr. Thammajak: I noticed on the Ifeffit email list that you posted last year a message about a problem you had on Athena. I currently do have the same problem with my athena, the symptoms I have are the same than those described in your post: 1) Any single XAFS spectrum, which could be opened with Athena before the problem occurred, cannot be opened anymore. Only a message saying "you have not used any memory yet" appears at the bottom of the Athena Window. Oddly, old saved project files can still be opened. Then, when the data is opened from these old projects, new project cannot be saved (nothing happens when I try to save a project). Data files are not corrupted or have strange format, since the files could be opened before the problem occurred. Also I can open the data with Athena installed on other PCs without any problem. 2) The main Athena window won't close. The only way to close that window is to force quit the program. 3) I checked the command rpompt window, and ran Athena, as Bruce Ravel suggested in his reply. A message says "Ifeffit checked for updates recently. Your version of Ifeffit is up to date". That's it. No error message obviously... 4) I reinstalled both Athena and Windows XP, but the problem still occurs. I don't think anybody from the Ifeffit email list found the source of your issue. Is your Athena working now? If yes, have you figured what was the problem? Thanks a lot, Gautier ----------- Gautier Landrot graduate student University of Delaware Plant and Soil Sc. Dept. Environmental Soil Chemistry Group 152 Townsend Hall Newark, DE 19711 (302)831-1230 http://ag.udel.edu/SoilChem/landrot.html ------------------------------------------------------- -- 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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Artemis multiple edge refinement problem
by alessandro di domenico 24 Jun '09

24 Jun '09

Hello to everyone; I'm a master thesist student in physics and I'mdoing a XAS analysis on bimetallic nanoparticles. my problem is that when I try to do a refinement on two different edges (K-Pd and L3-Au) Artemis changes one of the experimental data-set. Say that I have the data set for the K-edge of Pd and L3-edge of Au (which are plotted correctly); after the fit one of the two data set are plotted different. it seems that experimental data have been modified.... I don't know what to do about it; maybe I'm doing something wrong but unfortunately there isn't a complete guide to artemis . On the internet i have found some pdf which deals with the argument but don't focus on the procedure that one has to do in the program. Has someone ever had this problem, and if not can someone suggest me a "tutorial" on multiple edge refinement with artemis that I can follow step by step? Thank you alessandro

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