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

Fwd: Re: why ss_2 is negative?
by Bruce Ravel 24 Feb '07

24 Feb '07

On Friday 23 February 2007 21:41, hw26(a)njit.edu wrote: > Yes, I am modeling the uranyl ligand and two equatorial ligands, one of > which is hypothesized as U-F (from BF4 anion), and the other as U-O (from > hydration),because in the uranyl nitrate standard sloution(without > MOEMIMBF4), there is only one peak that represents the U-O equatorial > ligand, but with the MOEMIMBF4, the equatorial peak is split to two peaks. > So I guess the other equatorial U-F formed. 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/

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why ss_2 is negative?
by hw26＠njit.edu 23 Feb '07

23 Feb '07

Dear all, I am doing model fitting using Artemis. My sample is uranium solution with an ionic liquid, 1-methoxyethyl-3-methyl imidazolium tetrafluoroborate (MOEMIMBF4). The Fitting seems ok except that the ss_2 is negative. I don't know how can I fix this problem. Can you get a chance to take a look? My fitting is simple, only three single scattering pathes which were produced by Six Pack. The fitting file is attached. I really appreciate it if you could take a look and give some advice! Best regards! Hao

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Re: [Ifeffit] Hephaestus
by Matt Newville 22 Feb '07

22 Feb '07

Hi Carloine, On 2/21/07, Caroline Peacock <clp(a)noc.soton.ac.uk> wrote: > Have just installed the Ifeffit package > (feffit-1.2.9-Mac10.4_horae64pre_pkg.dmg) on my Intel Mac > (OS X 10.4.8)... Upon double clicking Hephaestus (as instructed in the > readme) i am prompted to choose either X11 graphics or Aquaterm - either way > X11 opens and then nothing...Is this a UNIX based program - from the > screenshots i guessed it wasn't? > > Any ideas why it isn't working? I'm copying this to the Ifeffit mailing list, as I think someone else may have a better answer than I can give. Hephaestus does require X11, but I think the problem is that the Ifeffit-1.2.9 disk installers are all PPC only. That is, I think no one has made an installer for Intel Mac. --Matt

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(no subject)
by Ruwan Wijesundera 15 Feb '07

15 Feb '07

Dear Bruce We have used Athena and Artemis software to analyses the EXAFS. When we do the analysis, we used different S2o for each path for fitting of Cu2O data. I succeeded to obtain good fitting by this way. Documents related to percent EXAFS analysis have been mentioned S2o is one value for all paths. What I want to know is our fittings are correct or not. I am looking forward early response. About 10 years ago we had being using another program made by Tokyo University in Japan. In this program, the refined parameters also included S2oj and Nj to the each cells Thanks Ruwn

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Re: [Ifeffit] question about Eo and simultaneous fitting
by tony vitova 15 Feb '07

15 Feb '07

Hi again to everybody, Thank you for the answers. They are all helpful. Just to specify a little more: all samples are measured at the K edge of the doped metal oxide. I expect relation between the coordination environments of the different samples as the reduced and oxidized samples are mixture of two formal oxidation states. I will try with different Eo and the Shelly's aligning-suggestion. Tony ----- Original Message ---- From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Wednesday, February 14, 2007 9:01:29 PM Subject: Re: [Ifeffit] question about Eo and simultaneous fitting Tony -- > Should I fit EXAFS spectra of a doped material and the same material, but > oxidized and reduced (three spectra) simultaneously? In my opinion: yes, as > I am looking for small differences. Is varying one Eo for the three samples > the right approach? > I am also wondering, should I vary one Eo for samples with different doping > concentrations? > I think you need to be more specific about what your samples are and what you're trying to learn from them. For example, I could read your question as meaning you have samples of Mn K edge for Mn doped into silicon ("a doped material") Si K edge of pure silicon ("same material, reduced") Si K edge of quartz ("same material, oxidized") In which case, I don't see that see much to be gained by fitting the spectra together. In general, one fits multiple spectra together when it is expected that there is a relationship between the different coordination environments, most usually a simple relationship between the g(R)'s for the different samples. E0 is typically different for each sample. There are situations where they can be constrained to be the same, such as spectra are all on the same sample at different temperatures. For more specific answers, please ask more specific questions. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ____________________________________________________________________________________ Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/

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question about Eo and simultaneous fitting
by tony vitova 14 Feb '07

14 Feb '07

Hi, first I would like to thank all experienced people answering in this forum!! I have learned really a lot from you. And now my question: Should I fit EXAFS spectra of a doped material and the same material, but oxidized and reduced (three spectra) simultaneously? In my opinion: yes, as I am looking for small differences. Is varying one Eo for the three samples the right approach? I am also wondering, should I vary one Eo for samples with different doping concentrations? Thank you for any hint! Tony ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/

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Re: [Ifeffit] question about Eo and simultaneous fitting
by Scott Calvin 14 Feb '07

14 Feb '07

Hi Shelly, Interesting--I've never tried that method with samples that I expect to differ in oxidation state. If it's differing in oxidation state, the local environment is probably different too...particularly, nearest-neighbor distances should be changed significantly. So how do you align the chi(k) data with each other, when they oscillate at a different frequency? --Scott Calvin Sarah Lawrence College At 10:38 AM 2/14/2007, you wrote: >The approach that I like to take, is to vary the choice of E0 in the >background subtraction step so that the chi(k) spectra are well aligned >with each other and the theory. Then only one Ezero parameter is >needed. > >Cheers, >Shelly

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Re: [Ifeffit] question about Eo and simultaneous fitting
by Kelly, Shelly D. 14 Feb '07

14 Feb '07

Hi Scott, The change in frequency is a bigger affect at high k than the energy shift parameter. The energy shift parameter affects the data more strongly at low k. So I align the data to each other at low k, and then they become out of phase with each other at high k. A similar effect is seen for pressure dependent data where the oxidation state doesn't change but the bond length changes. I also look at how well the data are both aligned to the theory used to describe the data sets independently. The energy shift values should overlap within the uncertainty to justify using a single parameter for them. I suppose that my method might not work for all systems. But if the data are similar enough so that a multiple data set fit has significant overlap in the models used to describe the spectra, then it has worked. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Wednesday, February 14, 2007 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] question about Eo and simultaneous fitting > > Hi Shelly, > > Interesting--I've never tried that method with samples that I expect > to differ in oxidation state. If it's differing in oxidation state, > the local environment is probably different too...particularly, > nearest-neighbor distances should be changed significantly. So how do > you align the chi(k) data with each other, when they oscillate at a > different frequency? > > --Scott Calvin > Sarah Lawrence College > > At 10:38 AM 2/14/2007, you wrote: > > >The approach that I like to take, is to vary the choice of E0 in the > >background subtraction step so that the chi(k) spectra are well aligned > >with each other and the theory. Then only one Ezero parameter is > >needed. > > > >Cheers, > >Shelly > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] question about Eo and simultaneous fitting
by Kelly, Shelly D. 14 Feb '07

14 Feb '07

Hi Tony, The approach that I like to take, is to vary the choice of E0 in the background subtraction step so that the chi(k) spectra are well aligned with each other and the theory. Then only one Ezero parameter is needed. Cheers, Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Wednesday, February 14, 2007 7:52 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] question about Eo and simultaneous fitting > > Hi Tony, > > A quick answer before I try to fight my way through an ice storm to > get to work. :) > > Fitting the three spectra simultaneously makes sense, but if > oxidation state is expected to be different, then you really need > different E0's. > > As far as doping, it depends on the details. In some cases, it may > require a different E0's, in others, not. Of course, you can try it > both ways, and see what the fits think. > > --Scott Calvin > Sarah Lawrence College > > At 05:04 AM 2/14/2007, you wrote: > >Hi, > > > >first I would like to thank all experienced people answering in > >this forum!! I have learned really a lot from you. > > > >And now my question: > >Should I fit EXAFS spectra of a doped material and the same > >material, but oxidized and reduced (three spectra) simultaneously? > >In my opinion: yes, as I am looking for small differences. Is > >varying one Eo for the three samples the right approach? > >I am also wondering, should I vary one Eo for samples with different > >doping concentrations? > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Debian packages
by Carlo Segre 13 Feb '07

13 Feb '07

Hello All: I have set up a new repository for the Debian packages of IFEFFIT & friends. I have also begun to build Ubuntu packages as well. Of course, whenever possible the packages are in the Debian archive. The following are available to use in your /etc/apt/sources.list # backported packages for sarge (will stop supporting this once etch # releases) deb http://debian-xray.iit.edu sarge main contrib non-free # backported packages for etch (now that etch is in freeze, any new # versions will be placed here) deb http://debian-xray.iit.edu etch main contrib non-free # additional software not yet in Debian (you can see what is there just # for grins!) deb http://debian-xray.iit.edu sid main contrib non-free # packages made for Ubuntu (I will support only the last three releases) deb http://debian-xray.iit.edu dapper main contrib non-free deb http://debian-xray.iit.edu edgy main contrib non-free deb http://debian-xray.iit.edu feisty main contrib non-free The old repositories at fermi.phys.iit.edu/debian are still there but not being updated. I will probably remove them in 2007. Cheers, 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 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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