September 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. 15 Dec '04

15 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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New user to EXAFS
by William Bisson 07 Oct '04

07 Oct '04

Dear all, I am a new user to EXAFS and I am currently experimenting with the anaylsis software available. Does anyone know how to convert raw data collected from Daresbury, UK, station 7.1 to be read by IFEFFIT? I shall be grateful for any help Kind Regards William Bisson

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Re: [Ifeffit] New user to EXAFS
by Bruce Ravel 30 Sep '04

30 Sep '04

On Thursday 30 September 2004 10:16 am, ritika.uppal(a)yale.edu wrote: > Hi Bruce, > Thanks for the reply. I have attached the artemis project file with > this email. Ritika, I'll add this to my list of things to look at today and get back to you when I have some information. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Fitting Problems via Artemis
by hsnuboy＠ksu.edu 27 Sep '04

27 Sep '04

Dear All, Greeting.This is Yu-Chuan. After struggling a long time, I just felt a little bit progress in the fitting program. However, there are still some questions confused me. 1. What's the meaning and purpose of "Fit Background" in Artemis? I know the backgound as "bare atom" in EXAFS theory. So, what kind of situation we need to use this function? 2. Is that possible for the Debye-Waller factor(sigma^2) be negative? Actually, I am not so sure about the physical meaning for that. Just know its a kind of thermal vibration. 3. Sometimes, The results obtained from Artemis seems not the same. Says, the guess parameters and uncertainties may be varied even if you input the same data for different time.Has anyone met this problem before? Sincerely yours, Yu-Chuan Lin Graduate Student and Reseach Assistant Kansas State University

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RE: [Ifeffit] Fitting Problems via Artemis
by hsnuboy＠ksu.edu 24 Sep '04

24 Sep '04

Dear Norbert, Thank you for your reply. About the DW factor, I think the problem may be another scatterer. Due to the self adsoption, I use Dr. Booth's correlation equation to correlate my data. Is that the way I obtain minus DW factor? The other parameters work great, except DW factor for about -0.001(the uncertainties is +/- 0.00094). Do you thinnk is that possible cause by self absorption or other effects? Thank you for your time. Sincerely, Yu-Chuan On Fri, 24 Sep 2004, nobert.weiher(a)chem.ethz.ch wrote: >Concerning the DW factor, you are right that it accounts for >vibrational disorder in the sample (in the ideal case). If, however, >your material has a high structural disorder by itself, DW factors >might become high due to this. The general behaviour is that they >should increase with temperature of the measurement. A negative value >is physically not possible, and usually means that something is wrong >with your fitting path. Possible things to check are >- did you use proper reference paths (i.e. were they correctly >computed by feff) >- is it maybe another scatterer which contributes to the EXAFS at this >part.

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RE: [Ifeffit] Fitting Problems via Artemis
by Weiher, Norbert 24 Sep '04

24 Sep '04

Dear Yu-Chuan, I quickly comment on the last two points you mentioned in your message. Concerning the DW factor, you are right that it accounts for vibrational disorder in the sample (in the ideal case). If, however, your material has a high structural disorder by itself, DW factors might become high due to this. The general behaviour is that they should increase with temperature of the measurement. A negative value is physically not possible, and usually means that something is wrong with your fitting path. Possible things to check are - did you use proper reference paths (i.e. were they correctly computed by feff) - is it maybe another scatterer which contributes to the EXAFS at this part. Concerning fit stabilities: I never encountered the problem you mentioned, i.e. when I use the same starting values for a fit (even for a bad one), the results are the same. A good fit should by definition converge to the same fitting parameters even when starting from slightly different points on the chi2 surface. However, it is possible that you obtain different results from different starting values. Possible things to do if your fit is not stable: - dont fit all parameters at one run (at least not in the first place) - start fitting all parameters independently, then grabbing the values of the former fits and slowly approach a stable point in the fit - if you have a stable result, try freeing all parameters and see if you reach the same point again. This is a quite good indication that you are on a good way. - if you include another shell, fix all first shell parameters and just fit the second one. Afterwards, vary all parameters again. Finally, the background refinement is a feature of ARTEMIS to correct the background spline you are using. Unfortunately, I have not much experience with it, so I leave it to the other IFEFFITers in the world to comment on this... Hope my suggestions help you to have more productive sessions with these great software packages. Cheers, Norbert

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Re: ? about l_scmt etc.
by k-kupiecki＠northwestern.edu 15 Sep '04

15 Sep '04

Matt & IFEFFIT group, This is actually a feff.inp question.... but I'm hoping someone might be able to clarify this for me... I was wondering what appropriate values are for l_scmt, l_fms, and stoichiometry for the feff.inp I'm working with regarding Au on a Ni surface (I'm fitting with feff calculations with either a single Au atom in the first Ni layer or two Au atoms in the first Ni layer)? Should they all be the same for each potential? I just wanted to check if my values were appropriate. I've used some values based off of an example file all along... but I'm not sure if I used them appropriately for my scenerio. I've read the FEFF8.10 manual but I'm still unclear as to the proper values... (i.e. in the past I have used the following for 2 Au's in the surface) POTENTIALS * ipot z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.001 1 28 Ni 2 2 4 2 79 Au2 3 3 4 Oh... one more question... I haven't been using the ellipticity card in the feff.inp file, even though I've been using "POLARIZATION 1 0 0"... is this OK? Thanks, Kristine

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Artemis and atoms.inp/feff.inp files
by Bruce Ravel 15 Sep '04

15 Sep '04

Hi folks, This morning, a user pointed out an interesting problem in any version of Artemis up to and including 0.7.010. I thought I should mention it on the list because I would be surprised if no one else runs into this particular issue. Artemis currently does no error checking to determine if an atoms.inp file is actually an atoms.inp file. Similarly Artemis does no error checking to confirm the feff-ness of a feff.inp file. This is a problem because there are separate menu entries in the File menu for importing atoms.inp and feff.inp file. Different things happen when you select these two items. If you choose the wrong kind of file, Artemis will get confused trying to read one file type as the other file type. This will lead to lots of error messages and may result in project files that cannot be saved and re-read by Artemis. Currently there is no better solution than to be sure that, when you intend to import a feff.inp file. you select a feff.inp file and, when you intend to import an atoms.inp file, you select an atoms.inp file. If you make this mistake, the best solution may be to quit Artemis and try again. Clearly this is an untenable situation. Building enough intelligence into Artemis to distinguish between atoms.inp and feff.inp files is now high on my to-do list. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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