September 2005 - Ifeffit - millenia.cars.aps.anl.gov

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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Ifeffit 1.2.8 installer for WinXP
by Leandro Langie Araujo 19 Sep '05

19 Sep '05

Greetings everybody, I'm another newcomer to the EXAFS world whose life was made much easier thanks to this wonderful software package. My sincere thanks to Matt, Bruce and everyone else involved in the "Ifeffit family" project. But, although the software is very nice, I'm having some trouble installing the newest version (1.2.8). I've been trying to install the Ifeffit 1.2.8 package on my WinXP, but there seems to be a problem with the files. I've downloaded the installers from both sourceforge and cars.uchicago.edu, but whenever I try to run any of them I get the following message: "The setup files are corrupted. Please obtain a new copy of the program." So, I'd like to ask if anyone from the mailing list managed to install Ifeffit 1.2.8 on WinXP or if anyone got the same kind of error message when trying to install. Thanks, Leandro

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Ifeffit 1.2.8
by Matt Newville 18 Sep '05

18 Sep '05

Hi Folks, 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/ == Windows == For Windows, there is a new installer, but no update. The new installer has the latest versions of the programs and also has dramatic changes to how the programs are organized and run. The batch files and the old automatic updater are gone, replaced by a single program 'runner' that checks for updates and runs all of the applications. There is also a completely new layout of C:\Program Files\Ifeffit. Bruce and I have been working on this for a while, and we believe it will be a lot easier for us to maintain. We expect that the changes will be mostly invisible to users, except when you install it. A result of the new layout is that *** *** *** you must uninstall any previous version of *** *** Ifeffit before installing the new version. *** *** *** Really, we're not kidding. There is a potential problem with this, as you may have your own projects under C:\Program Files\Ifeffit, say in \horae\ or in \examples\. You probably don't want to delete these!!! We recommend that you either move C:\Program Files\Ifeffit\horae and any other folders you may have file in to somewhere safe *before* you remove Ifeffit, or simply rename C:\Program Files\Ifeffit to Ifeffit_OLD and leave it there for a few weeks. And of course, we recommend that you save your data somewhere outside of C:\Program Files and make regular backups ("Gee, thanks, Mom!"). Then use the Control Panel 'add/remove programs' to remove Ifeffit. This will try to delete everything that originally got installed (and so *should* leave your data, but I wouldn't bet on it!!), including the shortcuts in the Start Menu. Once the C:\Program Files\Ifeffit folder is gone or cleaned out, you can then safely install the new Windows installer. The older Windows version (1.2.7) will see one more update, which will simply remind you to install the new version of the full installer. All further updates will be available only to the new version. == Mac OS X == For Mac OS X (10.3), the binary installer includes the codes from horae-055. The previous attempt to support Aquaterm is now dropped -- plotting is done with the X Windows plotting terminal. Since Athena/Artemis require X, and since X11 now comes from Apple, the Aquaterm support was more trouble than it was worth. == Unix == For Linux/Unix users using the source kit, the 'where is termcap?' problems should be gone. In addition, building on 64-bit linux machines should be much easier. PGPLOT_install now has a '--with-64bit' option which is needed for 64bit linux. Ifeffit's normal './configure' should then work fine. It now warns if the termcap library cannot be found. Let us know if there are any questions or troubles with these new versions. --Matt

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Athena Bug in Peak Fitting
by Barton, David (DG) 16 Sep '05

16 Sep '05

Bruce, FYI: I recently installed Ifeffit v1.2.8 using the new Windows installer and it worked perfectly on a couple Win XP machines. After using the latest version of Athena 0.8.043 I noticed a bug in the Peak Fitting Routine and also have a couple of other minor suggestions. Description of Peak Fitting Bug: --The centroids that are reported on the screen and in the results file are not updating after a peak-fit is done. When the checkbox is marked to fit the centroid the fit appears to be changing the centroid because the resulting plot looks like a better fit, however the value of the centroid on the screen is not updating and the results file does not reflect any changes in centroid. Then if you push the "Plot Lineshapes" button it uses the centroid on the screen and the fit changes dramatically using the original value of the centroid. This bug can be reproduced by pulling up any spectra, setting the centroid of the arctan to something that results in a poor initial fit, check the box to fit centroid, run the fit....you should see that the fit moves the centroid however the value on the screen does not update and then if you "Plot Lineshapes" you will see the fit change to value of the original centroid. Other Suggestions for minor improvements to Athena: --In Compute Difference window it would be nice to have a checkbox that allows the user invert the difference (do spectra-ref instead of ref-spectra). This would be helpful for doing the difference of Marked spectra where we would like to do the spectra-ref. --in Compute Difference window it would be nice to have a checkbox to plot the components of the difference along with difference (similar to LCF window). Helpful for diagnostic checks of difference. --in your new Plot Style functionality it would be nice if Athena would automatically replot the last plot choice after a new Plot Style is chosen. This would save a few clicks as I click back and forth between two different plot ranges. --the link to the Plot Style POD documentation is broken. Let me know if you need any further clarification. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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