July 2004 - Ifeffit - millenia.cars.aps.anl.gov

re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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Athena & Artemis in Windows
by Peter Southon 22 Dec '04

22 Dec '04

Hello Windows people A few days ago Shelly suggested that Athena and Artemis don't work when installed in the directory "C:/program files/ifeffit/". This has always worked for me using XP, though I wouldn't be surprised if it caused problems in some earlier versions of Windows. Regarding Poorani's question about TRAP files, I have found it useful to put a shortcut to "C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP" on my desktop or wherever for easy access. Cheers, Peter >Date: Fri, 11 Jun 2004 08:36:32 -0500 >From: "Kelly, Shelly D." <SKelly(a)anl.gov> >Subject: RE: [Ifeffit] Running FEFF >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A1B6D(a)ANLMAIL.anl.gov> >Content-Type: text/plain; charset="us-ascii" > >Hi Poorani, > >I believe that Athena and Artemis do not work properly when installed in >the C:/program files/ifeffit directory. The installation proceedures >say to specify C:/ifeffit instead. To fix if, but all of C:/program >files/ifeffit into the trash and then re-install. > >Shelly Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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RE: [Ifeffit] Using more than one E0
by Kelly, Shelly D. 14 Dec '04

14 Dec '04

Hi Guys, I wanted to add another comment about using multiple E0's. One of the best formulas that I have found involves assigning different atom types different E0's. This method seems to work well for M.S. paths. Here is an example of how it goes. I think that Daniel Haskel was the first to publish this type of E0 stuff. "Single and multiple scattering XAFS in BaZrO3: a comparison between theory and experiment" D. Haskel, B. Ravel, M. Newville and E. A. Stern Physica B 208&209 (1995) 151 Lets pretend that we have a copper oxide that we want to model. First shell Oxygen called O1, Second shell Cu called Cu1, Third shell Oxygen called O2. This method would use three E0's. One for the first shell oxygen atoms, Eo1. One for all the Cu atoms Ecu. and one for all other oxygen atoms Eo2. The Cu-O1 path has E0=Eo1. The Cu-Cu1 path has E0=Ecu. The Cu-O2 path has E0=Eo2. The Cu-O1-Cu-O1 path has E0=Eo1, (only scattering from O1 atom). The Cu-O1-Cu1-Cu path has E0=0.5*Eo1+0.5*Ecu. (scattering once from O1 and once from Cu1) ... And so forth and so on. Now if you set something like this up. You need to look at the results carefully and see if it works. Generally, scattering from an atom that has lost an electron due to an ionic bond will have a positive deltaE, and scattering from an atom that has gained an electron will have a negative deltaE. Of course this negative/positive deltaE is added to the alignment deltaE. If the values for Eo2 and Ecu are the same within the uncertainties of the measurement then you need to make them the same variable, so then you will only have two energy shifts, but you can still use it. This is most often the case as Matt mentioned but I always like to test it out. In addition, one electron transfer is about a shift by 6 eV, so if these values differ by more than say 10 eV something is not right. Since the shift is generally smallish, say 2 eV, your fit has to be really accurate to "see" these shifts. In particular they seem to be most important when you have all the deltaR values constrained in some way so that the error in deltaR is really really small. For example all deltaR values are related to unit cell parameters and atomic positions or and overall expansion term. HTH Shelly -----Original Message----- From: Wojciech Gawelda [mailto:wojciech.gawelda@epfl.ch] Sent: Thursday, May 27, 2004 1:18 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Using more than one E0 Hi everybody, I would like to address a couple of questions which are partially related to my recent struggles in fitting some EXAFS data. I'm trying to fit my data using several shells of different neighbors including a few single scattering paths and also so multiple scattering contributions (mainly collinear multiple scattering paths) all calculated with the help of FEFF 8.20. Now, I found once in the FEFFIT manual the following suggestion: one might consider using several different E0's for different paths in order to improve the fit. Ok, the explanation was based on some approximations coming from FEFF code which include incomplete core-hole shielding, lack of angular variations of the valence charge distribution and charge transfer between atoms in polar materials. My question is the following: does anyone of you have some experience with such procedure? And if yes, shall than distinguish between the first shell of nearest neighbors and the rest of the atoms in terms of their E0 corrections (using 2 parameters)? Or perhaps one can use separate E0's for each path? That's one thing... The second question concerns the background correction in Artemis: I was trying to find an easy explanation of what this procedure does during the fit but I guess I'm still somewhat confused...how one can judge whether the spline co-refinement does the right job? Some people on this mailing list underline that one should avoid high correlations between fitting parameters and background parameters in order to make sure that the fit is correct. But is it the only criterion? In some of my fits background line looks kind of constant over the entire R-range which was taken into the fit. Sometimes it becomes like a modulation peaking underneath some scattering paths...even if the background parameters don't correlate significantly with fitting parameters I have my doubts whether the result is trustful. Any hints about this procedure? Well, I'll greatly appreciate any comments and feedback from all you guys. I hope I'll be able to share some of my own soon :-) Cheers, Wojciech ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: <mailto:wojciech.gawelda@epfl.ch> wojciech.gawelda(a)epfl.ch WWW: <http://lsu.epfl.ch> http://lsu.epfl.ch *********************************************************************

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EXAFS analysis of homonuclear metal clusters
by m.bondin＠pgrad.unimelb.edu.au 30 Jul '04

30 Jul '04

Dear mailing list - This is a general EXAFS question I decided to post in regards to your collective thoughts and/or experience with this EXAFS analysis approach. I am currently attempting to model a number of Fe-S clusters with nuclearities of 2, 3, 4, 5, and 6. In some cases (where all the Fe atoms are chemically equivalent i.e. same oxidation state and coordination geometry) it is easy to approach this by assuming a single Fe absorber model. When the Fe atoms become inequivalent (oxidation states which may be a mixture of I, II or III, and different coordination geometry) I can average the environments (by including all interactions and ajusting coordination numbers for the different iron atoms accordingly) again into a single Fe absorber model. The fits go well, giving realiable bond lengths (when compared to available crystallographic data), DW's, and statistics (I am also keeping in mind the number of refined parameters to ensure a well over-determined fit for each of the models). My only hesitation, and main reason I am posting this question, is that I am not completely sure this is a reasonable assumption as the Fe atoms are in different oxidation states and will have different E0's. What I do know is there is a shift of roughly 2 to 3 eV in E0 to higher energy for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)). Is there any way of determining if this small difference in energy, and hence E0, between the Fe atoms in the clusters can or cannot be neglected in modelling the EXAFS? Regards, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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one more thing about atoms error
by Carlo U. Segre 29 Jul '04

29 Jul '04

Bruce: One more thing I noticed. If I try FEFF7 there is an error at the same spot, however, FEFF8 and FEFF8-exafs do work. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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EXAFS analysis of homonuclear metal clusters
by m.bondin＠pgrad.unimelb.edu.au 29 Jul '04

29 Jul '04

Dear mailing list, This question relates to an EXAFS analysis approach I am currently investigating in respect to a number of iron-sulfur clusters with nuclearities of 2, 3, 4, 5 and 6. The analysis is easy enough to perform when the Fe atoms in the clusters are chemically equivalent (i.e. same oxidation states and coordination environments) and can be simplified to a single Fe absorber model. The analysis gets a little tricky when the oxidation states of the Fe atoms, and also coordination environments are different hence the sites become chemically inequivalent. The approach that I use takes into account these different environments and resulting populations for each of the iron atoms, again collapsing into a single Fe absorber model and I am able to obtain nice fits of the data with bond distances in close agreement with compounds in which these distances have been obtained through crystallography. The DWs, visual fit and statistics are also well behaved and I have taken into consideration the number of refined parameters to ensure a well over-determined fit to the models (i.e. the data is not simply fitting to anything with lots of fitting variables). The main hesitation I have, and reason for me posting this question, is for the compounds in which the Fe atoms are in different oxidation states we would expect there to be differences in the E0 of these atoms. I know that for every increase, by one, in oxidation state (i.e. Fe(I) to Fe(II)) there is a shift in E0 to higher energy by roughly 2 to 3 eV (as can be observed in the XANES from studies conducted on mononuclear Fe compounds). I am really not sure as to what extent this effect may alter the EXAFS signal for a cluster. From what I observe in the fitting I would say not much, but I would like to know if this has been encountered, or thought about before by anyone else (i.e. maybe in reference to EXAFS studies on other homonuclear metal cluster systems in catalysis). Regards, Mark -- Mark Bondin PhD student School of Chemistry, University of Melbourne (03) 8344 7015 (Tower lab) 0409 252 983 (mobile)

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problems with atoms and tkatoms
by Carlo U. Segre 29 Jul '04

29 Jul '04

Bruce: I have been trying to generate a feff input file with atoms and tkatoms. Here is what happens when I work within artemis I import an atoms.inp that I wrote out previously (attached). This file written out previously when I used it with tkatoms to make a *.xyz file. I notice that it does not properly read the angles but I fill them in anyway. When I run atoms to get the FEFF input file I get the following error: Tk::Error: Illegal division by zero at /usr/share/perl5/Xray/ATP.pm line 634. Xray::ATP::ATP_corrections at /usr/share/perl5/Xray/ATP.pm line 634 Xray::ATP::parse_atp at /usr/share/perl5/Xray/ATP.pm line 387 main::run_atoms at /usr/bin/artemis line 5565 [\&main::run_atoms] Tk callback for .frame3.canvas2.frame.notebook.atoms.frame2.button1 Tk::__ANON__ at /usr/lib/perl5/Tk.pm line 225 Tk::Button::butUp at /usr/lib/perl5/Tk/Button.pm line 111 (command bound to event) main::__ANON__('Tk::Error: Illegal division by zero at /usr/share/perl5/Xray/...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 409 Tk::Error('MainWindow=HASH(0x96d864c)', 'Illegal division by zero at /usr/share/perl5/Xray/ATP.pm line...', 'Xray::ATP::ATP_corrections at /usr/share/perl5/Xray/ATP.pm li...', 'Xray::ATP::parse_atp at /usr/share/perl5/Xray/ATP.pm line 387', 'main::run_atoms at /usr/bin/artemis line 5565', '[\&main::run_atoms]', 'Tk callback for ..frame3.canvas2.frame.notebook.atoms.frame2.b...', 'Tk::__ANON__ at /usr/lib/perl5/Tk.pm line 225', 'Tk::Button::butUp at /usr/lib/perl5/Tk/Button.pm line 111', ...) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1792 If I run the same input file in tkatoms, I get a popup saying there is a divide by zero in ATP.pm line 634. If I try to generate an *.xyz file it works fine. I am using the latest version of horae. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Importing in Athena
by Dave Baker 29 Jul '04

29 Jul '04

I have recently been looking at some standards and I came across some Cu foil data in a two-column .dat format; "energy" and "xmu". (Incidentally, it is standard data taken in '92 by none other than Bruce R. and Matt. N.) Anyway, the data seems to load just fine using either the "xmu.dat" or the "Mu(E)" import profile, and I can remove backgrounds, do both forward and backward FT's and generally manipulate the data normally. Everything is fine until I try to save the chi(k) data. The program displays that it's saving the file, but does not report success. The file is indeed written, but with a file size of zero. Following this attempt, the graph may or may not be stuck in the last plot, and if it is stuck, no amount of frantic clicking on my part changes it. The Ifeffit buffer is empty, and there are no error trap files. -Dave Baker ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ --

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RE: [Ifeffit] artemis development in the near future
by SCHLEGEL Michel 177447 29 Jul '04

29 Jul '04

Bruce, > * Windows users who would like to be involved with the development > branch should consider installing ActiveState's perl distribution > on their computers as that would allow you to test the source code > as it becomes available. If anyone is interested in this, I can > help get you started. But I would encourage only the enthusiastic > to consider this. Most users will prefer to use the executables > that I will build for the stable version. Well, to paraphrase some recent declaration, sometimes you have Activestate, sometimes, you haven't, there's this little third category... Yes, I have installed ActiveState a long time ago, but that was just to run some script, and it is unclear to me if you plan to run the development versions of Athena and Artemis as script, or if you will ask each and every Windows user to compile his/her own little executable. In the later case, You'll have to explain me. Othervise, the new version runs fabulously great, apart from a minor point: I can't fit simultaneously several spectra (polarization data) in q-space. TApparently Artemis traps some kind of error message. but the software keeps on running. Otherwise, there's a little practical point which bothers me: when it comes to publishingand citing, we know how to shower praise on Matt, but we are still yearning for some sound reference for the Ravelware. Is there any chance that this 'bug' will get fixed in the near future? Best regards, Michel Schlegel

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RE: [Ifeffit] artemis development in the near future
by SCHLEGEL Michel 177447 29 Jul '04

29 Jul '04

Bruce, > On Wednesday 28 July 2004 12:47 pm, SCHLEGEL Michel 177447 wrote: > > versions of Athena and Artemis as script, or if you will ask each and > > every Windows user to compile his/her own little executable. In the > > later case, You'll have to explain me. > > Well, the point I was trying to make was that building and testing > windows executables adds considerably to my work. I would like to be > able to release the development version frequently -- the > early-and-often approach to software development. If I have to build > windows exes everytime, that will slow me down, wear me out, and make > it not worth my time to bother with the whole idea of a fork. Yes, I now, we Windows user recriminate a lot, demand even more, and offer little in return.. ;-) > > Othervise, the new version runs fabulously great, apart from a minor point: > > I can't fit simultaneously several spectra (polarization data) in q-space. > > TApparently Artemis traps some kind of error message. but the software > > keeps on running. > > OK, thanks for the report. I'll look into it. q-space fitting is not > one of the well-tested corners of the code since I never do > that myself. I am aware of Matt's recommandation - that fitting in R-space should be preferred. However, there are sometimes informations in the q-space on the nature of backscatterers from, e.g., the shape of the amplitude enveloppe of the Fourier-filtered contribution. Plus, it is always interesting to compare fitting results in both spaces. I ran a test fit in q-space with four spectra and Artemis 0.7.008. It seems that the fitting stage is performed well, and the fitting results in the q-space are even displayed in the Graphics windows. Trouble seems to arise when Artemis tries to write the log file. The 'Artemis palettes' windows doesn't appear on the screen. I then tried to fit into R-space (worked well), and again into q-space: the same error message appeared. I copied the message displayed on the console into the attached file. Best regards, Michel Schlegel

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