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

Fe oxide
by Juraj Majzlan 26 Sep '05

26 Sep '05

Hello, I am trying to fit an EXAFS spectrum of an X-ray amorphous Fe precipitate. In a model (goethite), there are Fe atoms at 3.02, 3.29, and 3.45 A. Fitting the two most distant shells of iron gives strange results. Fitting them simultaneously gives very high amplitudes (32, -66) which cancel each other (fig. 1) and produce a beautiful and unreasonable fit (fig. 2). Fitting them separate gives small ('reasonable') amplitudes, but the distance (dr) have very high uncertainties, e.g., dr = 0.12 +- 20.3. Can I expect to resolve these three Fe shells or is it asking too much? I am also attaching the Artemis file, but will appreciate any comments and suggestions. Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de/sites/personen/majzlan.html

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problems on running the windows 1.2.8 ifeffit version
by M Ceolin 23 Sep '05

23 Sep '05

Dear Bruce et al. I just installed the new 1.2.8 for windows version of ifeffit and I am experiencing problems to run any of the programs associated (arthemis, athena, etc.). I installed the programs in a Win98 machine where the previous versions of IFEFFIT were running. I took care of adding the suggested line to the config.sys file and installed the program in c:\ifeffit (as suggested). However, both, starting from the icons in the desktop, from the applications installed at c:\ifeffit\bin or from the menu at the start, the runner program (installed with the pakage) send an error message forcing to abort the run. The message says: (sorry, in spanish) Este programa ha efectuado una operacion no admitida y sera interrumpido (in the datails window says) RUNNER provoco un error de pagina no valida en el modulo MSVCRT.DLL de 017f:7801274b. etc. (registry numbers). Could you comment the point and, perhaps, suggest a solution ?. Yours. Marcelo Ceolin. *************************************** Dr. Marcelo Ceolin Centro Regional de Estudios Genomicos UNLP-AUGM Av. Calchaqui km 23,5 (4to piso) (1888) Florencio Varela Argentina Tel/Fax: +54-11-42758100 e-mail 1: mceolin(a)creg.org.ar e:mail 2: mrceolin(a)yahoo.com.ar WEB: www.creg.org.ar *************************************** PLEASE NOTE THAT THE E-MAIL ADDESSS mceolin(a)gwdg.de IS NO LONGER AVAILABLE. USE ONE OF THE ADDRESSES ABOVE. --------------------------------- 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo Abrí tu cuenta aquí

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RE: [Ifeffit] writing beam time proposals
by Frenkel, Anatoly 23 Sep '05

23 Sep '05

I rate proposals on the merit but it a former XAFS school student is a research group member it makes me happier. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Fri 9/23/2005 12:06 PM To: Carlo Segre; XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] writing beam time proposals In my opinion, it is better for the student or post-doc to write the beamtime proposal and be listed as PI, with the advisor listed somewhere on the proposal Many proposal foms have a checkbox for 'is this work part of a thesis', and that is definitely monitored (at least at the APS, but I'd imagine it to be true at other facilities), even if it is not formalized. There is usually an eagerness for bringing new students (and new post-docs and new faculty members) to the syncrotrons. Also, in my experience reading beamtime proposals now and then, students and post-docs do a better job at writing them <wink>. Even f the professor is listed first (and many groups do this!), I would suggest that the student/post-doc actually write the proposal and have the advisor look it over before submitting. Other advice for writing proposals: - communicate with the beamline scientist to make sure the work is feasible and appropriate. - write it to convince someone in a *different field* why the experiment is important. - include references to previous work to show that you know the field. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Tip of the Week: Constraining parameters between data groups in Athena
by Bruce Ravel 23 Sep '05

23 Sep '05

Hi, This week's tip of the week is "Constraining parameters between data groups in Athena": http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek?action=show B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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/

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Re: [Ifeffit] Ifeffit 1.2.8
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you have Ifeffit 1.2.7 working on Tiger, I'd suggest just doing horae_update. The changes to the Ifeffit library are very small, so you could just wait until an installer for Mac OS X 10.4 is available. If you really want to be using 1.2.8, you could try installing from source. --Matt On 9/18/05, Stefano Ciurli <stefano.ciurli(a)unibo.it> wrote: > Hi Matt, > > >Ifeffit 1.2.8 is now available. There are minor changes to the core > >library and new versions of horae (055: athena 0.8.043, and artemis > >0.8.002) in the Windows and Mac installers. A few version notes are below, > >and I will be putting more information at > >http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ > > Thanks a lot! I am running OSX Tiger on a G4 and I am currently > working with Athena 0.8.039 and Artemis 0.7.015 > > What should I do ot update my environment to Ifeffit 1.2.8? > Thanks > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high". > _______________________________________________ > 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] Fit in R and k space
by Frenkel, Anatoly 20 Sep '05

20 Sep '05

I personally like this argument in favor of r-space fitting over k-space fitting. I am pretty sure it was made by Ed Stern: R-space allows to think of EXAFS in terms of radial distribution of atomic positions relative to the central atom. Peaks in r-space usually correspond to atomic positions and the regions between the peaks - to the interstitial regions in the structure (of course, there are 1000 counter-examples, but we are talking about some 'average, well behaving' system where a peak is NOT an atomic AXAFS, nor it is caused by a Ramsauer-Townsend resonance, etc., and a valley is NOT a destructive interference between neighboring shells' - AF). We know, on another hand, that FEFF approximation electron charge density as spherical and the potential as muffin tin. This approximation is not as accurate in the interstitial region between the atoms (where potential profile in real systems may be anything but flat) as it is near the atoms. Thus, intuitively, FEFF should do better job fitting 'peaks' in r-space rather than fitting the interstitial. However, the r-factor and chi square do not really care. Technically, if two models give similar r-factors and chi-square, the one that has better fit in the peak region, the other - in the interstitial, one will examine the r-space fit and choose the one that fits peaks better over the one that fits interstititial region better. However, this information, localized in r-space, is distributed in k-space. Thus, if you look at the graph where data and fit are shown together, either in raw unfiltered k-space or in q-space, the misfit is difficult to interpret. It is, however, possible to interpret the misfit in r-space, and that what often helps to refine the model or choose the better one. Anatoly Anatoly Frenkel Department of Physics Yeshiva University -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Michel Schlegel Sent: Tuesday, September 20, 2005 9:07 AM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fit in R and k space Hello Bruce, >Although I prefer to think about the EXAFS problem in R space, I don't think >this is the reason to do the fit in R space. Regardless of which fitting >space you use, you are relying on Feff to supply some fraction of all the >Fourier components in the data. We could also used reference-derived phase and amplitude function, as in the good ol'time ;) > The first-shell feff path only has Fourier >components (or frequencies, if you prefer) corresponding to the first-shell >portion of chi(R). Thus that feff path can only fit those frequencies. >That's true in k-space as well as in R-space True in R-space, and that's why Athena-Ifeffit are doing such a wonderful job at providing windows to fit only selected area of the fourier transform. Almost true also in q-space. In k-space... hmmm, well, I would love to see the mathematical demonstration of it for a limited k-range and a Feff(k) (eventhoug I agree that many people have performed tha fit in k- and R-spaces, and found about the same paramters, so it must be verified somehow). >What's more, I think the problem of non-modelled shells affecting the >modelled >portion of the data exists in R-space just as much as in k-space. Because of >sigma^2 and the finite data range, peaks have width. In R-space, a given >path is centered at a particular R-value (or, in other words, its >contribution to the spectrum is dominated by a particular frequency). >However, the peak has width (it contains frequencies below and above the >dominant frequency). Thus longer paths always interfere with shorter paths >to some extent. I think the effect of interfering contributions in the Konigsberger and Prins. What I noticed, though, is that the fit of closer shells can affect that of the furthest shell because of the "spillof" from the first peak. The recciprocal I was not aware of. But I do agree with you on the whole. However, I think that in the FT case, these interences are limited to the nearest shells, whereas in k-space, nothing protects you from shells at, say, 2R and 3R (so to speak. Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/DANS/DPC/SCP/LRSI Bat 391 - Piece 205B F91 191 Gif-sur-Yvette Cedex, France Ph: +33 (0)1 69 08 93 84 Fax: +33 (0)1 69 08 54 11 _______________________________________________ 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] Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Stefano, If you've already done 'sudo horae_update' (and thanks for the correction!!) and have the latest versions of Athena and Artemis installed, I would say that you don't need to use the binary installer. The changes in the binary installer are tiny. --Matt

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Ifeffit installer for Mac 10.4 (Tiger)
by Matt Newville 20 Sep '05

20 Sep '05

Hi Everyone, Paul Fons has generously made a binary package installer for Ifeffit 1.2.8 for Mac 10.4 (Tiger). This is now available from both cars.uchicago.edu and sourceforge.net, from the Ifeffit download page: http://cars9.uchicago.edu/ifeffit/download.html If you try this out, please send positive and/or negative reports to me. Thanks again Paul!! --Matt

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RE: [Ifeffit] R-factor
by Scott Calvin 20 Sep '05

20 Sep '05

Hi Alison, I agree entirely with Victor and Anatoly. In addition, I'd say that in my work an R-factor of above 0.1 is pretty sketchy. How sketchy depends on the complexity of the fit, of course; you're going over a big r-range, so if it takes you only two or three parameters to get an R-factor of 0.11, I guess that's not too bad. But if you have more parameters than that and it's still not fitting so well, I'd be concerned. As a referee, for example, that would be a much larger warning flag to me than the little discrepancy between the R-factors for the k- and q-space fits. Just to echo Victor and Anatoly again: it's quite easy for me to believe that the fitting algorithm just happened to find a somewhat different minimum in the fitting space in the two cases. They both suggested ways to test if that is the case. Although I've never fit in q-space, I've seen something that on the face of it is equally baffling: sometimes I've added an additional fitting parameter, changing nothing else, and seen the R-factor <italic>increase </italic>slightly. In some ideal sense, that shouldn't be--the fitting routine (this one happened to be Ifeffit) "should" at worst get the identical fit as to when the new parameter was constrained. But it is impossible to write a fitting routine that is guaranteed to find the closest possible fit, so all routines will occasionally generate those kinds of results. --Scott Calvin Sarah Lawrence College >-------------- Original message -------------- > >> Bruce, >> >> I've looked, and my R-factors for the back-transformed >> space are not necessarily twice the value of the R-factors >> for the k-space fits. In fact, they are often quite >> close. For example, just recently I had a k-space >> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I >> realize those numbers are very close, but I'm afraid if I >> try to publish this, then I will get criticism for the >> q-space R-factors being larger. If I can explain it, then >> maybe it won't be a problem. >

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RE: [Ifeffit] Fit in R and k space
by Kelly, Shelly D. 20 Sep '05

20 Sep '05

Hi Michel, Michel wrote: Finally, another issue - for which I would not lay out my neck, though - is the noise. In EXAFS, the signal to noise increases with k, and of course fitting in the raw k space is another way of dealing conveniently with the noise -or relative uncertainty, as we may name it. However, the FT is a way of filtering out some of this noise, and so maximise the signal from a shell. Likewise, fitting in filtered q-space may yield more accurate results, because some of the noise is filtered out. However, I concur that somehow the fact that the uncertainty on the high-q part of the filtered contribution os greater than in the low q-part should be implemented somehow. It is true that the signal to noise ratio becomes smaller at high k values. It does seem magical that the Fourier transform can pull a signal out of the high k-range where the noise is large and that this signal seems to be well defined. I find it helpful to remember that each signal in the EXAFS chi(k) spectra is given by ONE frequency. That frequency is well defined at low k were the signal to noise ratio is large. Extending this frequency into the high k-region is trivial as long as that frequency co-exists with all the noise at high k. In fact I don't need data at all to extend a well defined frequency to infinity. The part of the signal that is not so well defined at high k is the amplitude. A lot of noise often masks itself by a large variation in amplitude for a given signal at high k, this effect will result in poor values for CN and 2. But the amplitude of the signal has a well known k-dependence so with enough low k information about the amplitude even the amplitude does not become affected by the noise at high k. The point to remember is that the signals are defined from k=0 to k=something bigger than zero. As long as the signal to noise ratio is reasonable from k=0 to some k~10? Then the signal including frequency and amplitude is well described all the way to k=infinity. It is often helpful to look at the fit and the data in k-space all the way out to 16 1/angstroms even if you are only using the k-range to 12 1/angstroms. If the model continues to follow the data to 16 then it is a good model. Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60440

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