March 2007 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 08 Mar '07

08 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

3 6

Using parameters in Artemis
by David Weedon 08 Mar '07

08 Mar '07

Hi All, I am new to Artemis so these questions are very basic - but never-the-less confusing to me. I learnt a lot by using Scott Calvin's ZnO example but ran into trouble when I got to Fit 3. In the Journal entry we are asked to click "Guess, Def, Set", then click "new" and enter DelScale = 0. After I hit the "Guess" button I cannot find the parameter "dr" on the list. Am I correct in assuming that "dr" is some kind of reserved parameter name that should not be used in equations? Which leads me to ask several questions (probably silly questions)??? QUESTIONS: 1 I presume all the parameters like "amp, deg, delr, ss2 and enot" relate to the obvious parameters in the EXAFS eqn. Assigning numerical values makes sense but what is going on when we create mathematical functions?? Is there a list of functions that we can model here? Is it somewhere in the software? 2 What are we doing when we make our own parameters? Are they a mixture of parameters from the EXAFS equation that we wish to evaluate in the fit, and if so why? 3 The parameter "amp" is defined as the relative importance of the path and is assigned a value eg. 100 or 30, is this some form of percentage of this path to the first (major) path? Thanks, Dave Dr Dave Weedon Research Fellow - ACeSSS, (Applied Centre for Structural and Synchrotron Studies) Division of Information Technology, Engineering and the Environment, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095 Phone: +61 8 8302 3096 Email: david.weedon(a)unisa.edu.au

3 4

Re: [Ifeffit] Ifeffit on Windows Vista
by Bruce Ravel 07 Mar '07

07 Mar '07

On Monday 05 March 2007 12:28, Francesc Sepulcre wrote: > Dear Bruce, > > Is just to know if is possible to install ifeffit (Artemis, Athena,...) on > Windows Vista. If yes, please, let me know how to do this, because Im > trying to install version 1.2.9 but doesnt works. > > Please, excuse me if this is not the correct way to ask about this problem. Hi Francesc, I am forwarding my response to the Ifeffit mailing list (which is the best forum for questions of this sort.) To join, go to: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ I am not in a position to comment. I don't have a Vista machine of my own. Nor does Matt, as far as I know. So we certainly have not yet tested the software on Vista. Is anyone on the list using Vista yet? Any hints for Francesc about getting the installer to work? Francesc, perhaps if you could give us some more information about how it fails -- screenshots, transcriptions of error messages, something that gives a clue as to what the problem is -- someone may be able to make a useful suggestion. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

2 1

EuL3-edge-XANES (from one of Bruce's courses)
by Joel Brugger 05 Mar '07

05 Mar '07

Hi, Looking at the notes from one of Bruce Ravel¹s 2000 EXAFS courses, I noticed that you used EuTiO3 as an example. My understanding is that this is a Eu++ compound; yet the resonance peak in the XANES spectrum occurs spot on where I would expect Eu+++ to be, around 6982 eV. As the table below shows (from Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700), the location of the Eu++ resonance peak does not seem to vary much from compound to compound. I¹m also joining a figure showing the XANES L3 Eu spectra of EuTiO3 together with other compounds. The Std spectra shown for comparison are for mixtures of Eu2O3, W, and WO3 cooked at 1200C in an inert atmosphere, and prepared so that sample StdB has 20% Eu++, and sample stdC 50% Eu++ (the final product is a mixture of EuWO4 and Eu2(WO4)2). The growing peak at 6974 corresponds to Eu++. Any thought about this discrepancy? Where are the data published? Thanks in advance for you help, All the best as ever, JOEL Ps I cc¹d to Bruce Ravel¹s email address as I don¹t think that the list takes attachments or embedded figures... Rakovan, J., Newville, M., and Sutton, S. (2001) Evidence of heterovalent europium in zoned Llallagua apatite using wavelength dispersive XANES. American Mineralogist, 86, 697-700.

2 1

Re: [Ifeffit] Fwd: Re: why ss_2 is negative?
by hw26＠njit.edu 04 Mar '07

04 Mar '07

Dear all, Thanks million for your great advice for my EXAFS modeling! It helps me understand more about EXAFS and I really appreciate it! But I still have some questions to consult you. I took your suggestion and have the amp and e0 the same for each path. In addition, I fixed the number axial U-O as 2. For the equatorial ligand, since the total coordination number is between 4 and 6, I guess the number of U-F as 2(that is n1), and def the number of U-O as (5-n1)(that is n2). Then I did the fit. The result showed the ss_2 is still negative. So I set the ss_2 as 0.003, did the fitting again. I don't know if it is ok to fix the ss_2=0.003. It seems the dr_1 change a lot. In addition, I tried to do fitting in Kw=2 in stead of Kw=3. At this time, the ss_2 is positive, and from my understanding, it seems the modeling is more resonable for dr_1 and dr_2, but the R-factor is 0.023, a little bit larger than 0.02. How can I decide which one I should use, the Kw=3 or Kw=2? Is there anything I can do to improve the modeling? The attached is my modeling. I am sorry to put attachment in the email that my bother you. Best regards! Hao > Hao, > > A few more comments: > > 1. It is well advised for anyone starting to look at uranyl compounds > with XAS to read Shelly's various publications on that topic. > Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly > useful. Google scholar can help you locate more of her papers. > > 2. I am the first to admit that Artemis and Ifeffit are difficult > tools for the beginning exafs practitioner. These tools try to > provide a usable face to a difficult problem. Ifeffit was written > with enough flexibility and power to allow the so-called experts > to do the analysis they want to do. That means that Artemis has > enough freedom to allow the unsuspecting user to do ill-advised > things. > > You really need to think about what each of the parameters means. > For example, just because Artemis allows you to float e0 freely > for each path does not mean that doing so is a good idea. There > are situations where it is a very good idea to have more than one > e0 parameter in your fit, but I suspect that yours is not one of > them. Consequently, you should consider constraining all your > paths to have the same e0. > > What do I mean by "constrain"? Well, on the Guess,Def,Set page, > you can define a single e0 parameter as a guess parameter, then > use that parameter on each of the path pages. In that way, you > will have one floating parameter in your fit that is used to > describe the e0 of all your parameters. > > Similarly, you should think hard about the numbers of each kind of > path. A uranyl moiety is unlikely to have more or less than 2 > uranyl ligands. The uranyl bond is very strong, consequently it > is energetically unfavorable in a uranyl for those two bonds to be > over- or under-filled. Consequently, you can consider setting the > number of yl oxygens to 2. Furthermore, the equatorial plane is > likely to have between 4 and 6 oxygens, so you should think of > ways to constrain the total number of equatorial oxygens to be > something reasonable. Since the coordination number is highly > correlated with sigma^2 in a statistical sense, thinking well > about coordination number should help address your original > question. > > 3. Scott has made a very nice Artemis tutorial which can be found at > http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib > It comes in the form of a series of Artemis projects. Newcomers > benefit by working through his tutorial before trying to analyse > their own data with Artemis. > > 4. The Ifeffit web site, my home page, and especialy http://xafs.org > are all filled with useful information for the XAS novice. If you > haven't already looked through the resources on those sites, you > really should budget some time to do so. > > > HTH, > B > > > -- > Bruce Ravel ---------------------------------------------- > bravel(a)anl.gov > > Molecular Environmental Science Group, Building 203, Room E-165 > MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 > > Argonne National Laboratory phone and voice mail: (1) 630 252 > 5033 > Argonne IL 60439, USA fax: (1) 630 252 > 9793 > > My homepage: http://cars9.uchicago.edu/~ravel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

3 2