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

Ifeffit Wiki
by Matt Newville 02 Sep '05

02 Sep '05

Hi Folks, I've created and started a wiki for Ifeffit and related topics. Currently, this is at http://cars9.uchicago.edu/iffwiki At this point, this should be considered experimental. I'm still ambivalent about the whole thing, but we definitely need *something* to allow outside people to add content. Please feel free to play with this wiki, and let me know what you think. If this is something we decide we want to keep, I'll have this become part of the main set of Ifeffit and XAFS pages. I'd like to give it a trial run first, and hear some feedback. For those who aren't familar with wikis, these are set of web pages that are editable and expandable by users. There are all sorts of features for adding content -- too many to explain here. The basic idea is that you log onto the system, and edit the web pages using a web browser in a simplified structured text -- NOT directly editing HTML. Anyway, it's pretty easy to use, and there's plenty of documentation on how to use it. --Matt

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compilation problem under MacOSX 10.4 - again
by Hugh Harris 02 Sep '05

02 Sep '05

Hi all, I'm new to the list and ifeffit. I've tried to get ifeffit 1.2.7 installed (for the first time) under tiger (on a system upgraded from panther) according to the instructions posted in the FAQ and the following modification on the list; > Thanks Matt - installing g77 and then recompiling perl/Tk and horae > did the > trick! > > Bruce - sorry, I meant Perl/Tk... > > Paul, you may want to upgrade the installation notes to mention > that g77 has > to be installed first. Installion with Fink was a pleasure. > > Thanks again guys! > > JOEL I have Xcode installed, g77 via fink, and ran the ifeffit binary installer. Perl/Tk seemingly builds and installs ok but when I try to build horae 0.5.3 I get the following error; [harris:~/Desktop/horae-053] hugh% perl Makefile.PL === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is Mac OSX. Checking dependencies ... Dependencies ok. Cool! Reading configuration file: Ifeffit/lib/athena/athena.config Wrote Ifeffit/lib/athena/athenarc Ifeffit/lib/athena/athenarcw Ifeffit/lib/athena/athena.ini athena_parts/rc.pl Reading configuration file: Ifeffit/lib/artemis/artemis.config Wrote Ifeffit/lib/artemis/artemisrc Ifeffit/lib/artemis/artemisrcw Ifeffit/lib/artemis/artemis.ini diana_parts/rc.pl Assembled athena.pl from its parts (athena_parts/). Assembled artemis.pl from its parts (diana_parts/). Assembled hephaestus.pl from its parts (hephaestus_parts/). Fixing execution path in the Athena, Artemis, and Hephaestus executables... Changing athena.pl to /usr/bin/perl Changing artemis.pl to /usr/bin/perl Can't process diana.pl: No such file or directory Changing hephaestus.pl to /usr/bin/perl Changing ifeffit_shell.pl to /usr/bin/perl Changing horae_update to /usr/bin/perl Changing rdaj.pl to /usr/bin/perl Changing atoms.pl to /usr/bin/perl Ifeffit's installations directory is (found by capturing `ifeffit -i`) Could not open /config/Config.mak file for reading [harris:~/Desktop/horae-053] hugh% Trying to run athena from the xterm gives; Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/ perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level / System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread- multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/ 5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/ Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread- multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. Any ideas? Am I missing something obvious? Cheers, Hugh -- ------------------------------------------------------------------ Hugh Harris ASRP Postdoctoral Fellow School of Chemistry, Building F11 University of Sydney, NSW, 2006, Australia Office: +612-9351-2745 -------------------------------------------------------------------

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Re: Fitting an Extended R-range
by Michel Jaouen 31 Aug '05

31 Aug '05

>Shelly wrote: > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. Hi Shelly, You can add to Scott's list the following entry: Mutiple-scattering EXAFS and EXELFS of titanium alloys T. Sikora, G. Hug, M. Jaouen, and J.J. Rehr, PRB 32, n°3, 1723 (2000) Best regards, M. Jaouen -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hi Scott, Thank you for the help. Have a good one. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Monday, August 29, 2005 10:10 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Sorry, the first one should have been: > >"Estimating crystallite size in polydispersed samples using EXAFS," S. >Calvin, C. J. Riedel, E. E. Carpenter, S. A. Morrison, R. M. Stroud, & V. >G. Harris, Physica Scripta, T115, 744 (2005). >> --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hello Friends, I was hoping that you could help me put together a list of EXAFS papers that fit the R-space data out to at least 5 Angstroms. Thank you Shelly

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RE: [Ifeffit] Fitting an Extended R-range
by Kelly, Shelly D. 29 Aug '05

29 Aug '05

Hi Michel, Since I'm not getting a huge list of papers from anyone, I will take all that you think might be appropriate. SK -----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: Monday, August 29, 2005 2:24 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hello Shelly, >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. > >Thank you >Shelly Does comparison of fourier transforms count as well ? (or are you just interested in the accuracy/uncertainty on the fitting parameters?) Best regards, Michel -- Michel Schlegel Commissariat à l'énergie atomique CEN de Saclay, DEN/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] Fitting an Extended R-range
by Kelly, Shelly D. 26 Aug '05

26 Aug '05

Hi Scott, Thanks for the help. I'm not picky about how it was done....Well, as long as it is reasonable. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, August 26, 2005 4:27 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Hi Shelly, Does fitting to empirical standards count, or do you want only fits to theoretical standards (e.g. FEFF)? --Scott Calvin Sarah Lawrence College > >Hello Friends, > >I was hoping that you could help me put together a list of EXAFS >papers that fit the R-space data out to at least 5 Angstroms. > _______________________________________________ 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] A basic question about data collection
by Frenkel, Anatoly 26 Aug '05

26 Aug '05

I am probably missing the point, but it is not immediately obvious to me why the following is equivalent in terms of improving the signal to noise: a) constant E-space increment and b) constant k-space increment combined with k-dependent integration time. In a), the data cluster at high E, but each data point in E corresponds to a different final state and thus is unique. Averaging over E-space data in the small interval Delta E, (1/Delta E)*Int [xmu(E) dE] is not equivalent to the time average of xmu(E) collected at a fixed E: (1/T)*Int [xmu(E) dt]. Thus, k^n-weighted integration time, to my mind, is the only proper way of reducing statistical noise. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Carlo Segre Sent: Thu 8/25/2005 5:13 PM To: XAFS Analysis using Ifeffit Cc: Subject: Re: [Ifeffit] A basic question about data collection Matt and Scott: On Thu, 25 Aug 2005, Matt Newville wrote: > This is important for QEXAFS (which typically does sample at a > very fine energy grid). I've been told by people doing QEXAFS > that a simple box-car average is good enough for binnning QEXAFS > data. That's what Ifeffit's rebin() function does. I'd think > that a more sophisticated rolling average (convolution) would > be better (and not screw up energy resolution), but apparantly > it's not an issue. > I have ben playing with the athena smoothing and rebinning funcionalities and I think that I prefer the rebinning because smoothing tends to attenuate sharp peaked structure. A rolling average might be good too but I haven't tried it too much. My guess is that for gentle features such as in the EXAFS region, rebinning, rolling averages and smoothing will all give statistically indistiguishable results. I amy be wrong. 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 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Athena, Artemis, Hephaestus
by Seth Mueller 26 Aug '05

26 Aug '05

Please Help, I just installed, using the windows installer, the latest version of Ifeffit onto my computer (Windows XP). I can run all the programs but not the graphical user interfaces Athena, Artemis, and Hephaestus. When I try to run these programs, I get a DOS with a lot of gibberish that opens and closes in 30 seconds. I have no idea what is going on. Can anyone suggest a fix or workaround? ___________________________ Seth Mueller U.S. Geological Survey Box 25046 MS 973 BLDG 20 Denver Federal Center Denver, CO 80225-0046 phone 303.236.1882 fax 303.236.3200

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RE: [Ifeffit] A basic question about data collection
by Kropf, Arthur Jeremy 25 Aug '05

25 Aug '05

Scott, One often overlooked advantage of scanning in small energy steps is that it is much easier to see if a small interfering absorption edge is contaminating the data. Other than that, I agree with everything Matt wrote. In the end it comes down to what is best for your particular experiment; stepping through a fine energy grid may take prohibitively long, if you must wait for the monochromator to settle for 1 second between data points. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory Argonne, IL 60439 Ph: 630.252.9398 Fx: 630.252.9373 kropf(a)cmt.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Newville, Matthew G. > Sent: Thursday, August 25, 2005 3:34 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] A basic question about data collection > > Hi Scott, > > Yep, collecting with an even energy grid is essentially > k-weighting the collection by k^1. It's not quite that simple > -- see below -- but it's close. Of course, you can also step > evenly in k and increase the count time at each point. A > common approach when usig solid-state fluorescence detectors > and/or dilute samples is to k-weight the collection time by > k, k^2, or k^3, and count for, say, 2sec per point at low-k > and ramp up to 10sec per point at high-k (looking at a random > recent scan). > It does definitely help cut down the total collection time to > get reasonably clean spectra on dilute systems. > > The challenge with using data that's on a fine energy grid is > that the routine converting energy to k has to know to use > all that data and also know *how* to use all that data. > Typically (at least, in ifeffit), data is interpolated from E > to an evenly-spaced k grid with a fairly simple interpolation > scheme. > If the energy data are too finely spaced, some data may > actually get ignored. Collecting out to k=18A^-1 with 0.5 eV > steps might not work at smoothing out the data as well as > you'd hope. > Since k=18 -> E=1234.4 and k=18.05 -> 1241.3, there ~6eV > between adjacent k-points (assuming ifeffit's delta_k = 0.05). > > This is important for QEXAFS (which typically does sample at > a very fine energy grid). I've been told by people doing > QEXAFS that a simple box-car average is good enough for > binnning QEXAFS data. That's what Ifeffit's rebin() function > does. I'd think that a more sophisticated rolling average > (convolution) would be better (and not screw up energy > resolution), but apparantly it's not an issue. > > --Matt > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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