March 2003 - Ifeffit - millenia.cars.aps.anl.gov

Rebinning
by Carlo U. Segre 12 Mar '03

12 Mar '03

Matt and Bruce: Following our previous discussion of rebinning continuous scan data, I am attaching a python code fragment which we use to perform this function. You are free to use it as you like. It was written by Ken McIvor, a student at IIT as part of a larger project to manipulate and preview MR-CAT XAFS data. We simply pulled out the code and annotated it somewhat. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Rebinning
by Bruce Ravel 12 Mar '03

12 Mar '03

Hey folks, As an interface developer, I have to keep a broad perspective. It seems to me that, when Athena gets a rebinning capability, it should give the user a choice between boxcar and convolution (and whatever other technique someone makes a reasonable case for), thus I would want to implement something like what Ken or Shelly wrote as well as an interface to ifeffit's built-in convolution thingie. To address one of Matt's points, I reckon I'll put a flag in Athena's group object that would get set whenever E0 changes. That way Athena could automagically rebin the data before background removal for any data group for which rebinning has been requested. That combined with some of Athena's other automation features should make handling large amounts of qexafs data a breeze. As for which approach is appropriate, Grant pointed out that preserving resolution at high k is not completely necessary. I agree, but only with the caveat that your measurement is of a single edge. One could imagine using quick measurement techniques to measure two different, nearby edges --- perhaps for a dichroism experiment, perhaps simply to measure two exafs spectra. In that case, Matt's concern about boxcar is quite valid. That's not rocket science, but it would be easy to forget at the beamline at 3 in the morning ;-) Regards, B P.S. I really have to insist that everyone (and _especially_ the digest users) respect netiquette quoting guidelines. In the last few days there have been some egregious examples of poor netiquette on our lovely, little mailing list. Here's a nice explanation of how to quote when responding to another person's posting: http://earlydues.hispeed.com/ieel/netiquette.htm#quote -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Rebinning
by Kelly, Shelly D. 12 Mar '03

12 Mar '03

Hello All, There seems to be a lot of interest in Rebinning data. I have a perl script that I've written to do the same thing. I thought it might be of interest. Shelly > -----Original Message----- > From: Newville, Matthew G. > Sent: Tuesday, March 11, 2003 2:08 PM > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Rebinning > > > Hi Carlo, > > Thanks!! That's wonderful. It seems like this should be an > option in spline() and bkg_cl(), and possibly in pre_edge(). I > admit to being still a little confused by the goal of the > rebinning, especially with respect to loss of resolution. It > seems like to use this script, you need to do two things: > 1. select an E0. The data will be put at energies that > will give an even k-grid with this e0. I think it's > inevitable that if e0 changes, you might want to re-bin. > > 2. assume that the k-grid is small enough that the > measurements at independent energies are within the > acceptable energy resolution that they can be > simply summed. > > Is that right? > > Would it be OK with you (and everyone else) to have a weighted > average replace the boxcar average? For example, at k=12, > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > resolutions, so the boxcar average might wash out the high-k > EXAFS, no? It might be better to convolve the spectra with a > lorenztian reflecting the incident energy resolution (probably > defaulting to 1eV). Does that seem OK or is there something eles > going on? > > Anyway, thanks!! > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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rebinning and sampling
by Grant Bunker 12 Mar '03

12 Mar '03

Hi, Matt - I think the essential point is that sampling at 1 eV at k=12 A^(-1) is greatly oversampled. Suppose you want to sample data out to R=10A (just to make sure you get everything). Then the period of those oscillations in k-space is 2 Pi/(2 10A) ~ .3 A^(-1). Nyquist's theorem says you should sample at least twice per cycle, so you need delta K of 0.15 A^(-1) or smaller (you don't want higher frequency noise to alias down to low frequencies0. The 0.05 grid historically used in the UW programs therefore is pretty conservative. Attempting to preserve a 1 eV resolution at k=12 A^(-1) would imply a sampling of about 0.01 A^(-1), which is quite unnecessary. So I think the box-car average is ok when you are far enough above the edge. I implemented something like in my own mathematica programs a couple of years ago and it works fine, and Nick Dimakis built it into the tcl/tk based APEX package last year. thanks - grant On Wed, 12 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: fourier transforms and k grids (Matt Newville) > 2. Rebinning (Carlo U. Segre) > 3. Re: Rebinning (Bruce Ravel) > 4. Re: Rebinning (Matt Newville) > 5. Re: Rebinning (Carlo U. Segre) > 6. Re: Rebinning (Carlo U. Segre) > 7. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Mar 2003 12:04:57 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] fourier transforms and k grids > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0303111110060.24069-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Peter, > > Thanks for the report. I've verified your findings that feffit() > is doing the wrong thing for the Fourier transforms for data on > grids other than k-grid of 0.05Ang^-1. Here's what is happening: > > feffit() really is interpolating data internally onto the 0.05 > grid for the fit. The fit _should_ procede correctly for data on > any grid. > > Anyway, at the end of feffit() command it sends the data off to > the fftf() command to make the chir_mag, etc arrays. It is at > this point that the k-array in ***NOT*** being sent to the FFT. > I've verified in my own tests that including the k-array in the > FFT works, giving the right FFT. hopefully I will get a fixed > version posted this week. But currently, the r-space data (data > only, not the fits) from feffit() are wrong when a non-0.05 > k-grid is used. Simply doing > fftf(real=data.chi, k = data.k) > > will give the correct r-space data. > > I also noticed another wart and small inconsistency between > feffit() and fftf() from your example, which has the 'data' over > a smaller range than the FFT window. > > Thanks, and sorry for the trouble, > > --Matt > > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Mar 2003 12:16:24 -0600 (CST) > From: "Carlo U. Segre" <segre(a)iit.edu> > Subject: [Ifeffit] Rebinning > To: IFEFFIT Mailing List <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0303111214010.702-200000(a)boride.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > > Matt and Bruce: > > Following our previous discussion of rebinning continuous scan data, I am > attaching a python code fragment which we use to perform this function. > You are free to use it as you like. It was written by Ken McIvor, a > student at IIT as part of a larger project to manipulate and preview > MR-CAT XAFS data. We simply pulled out the code and annotated it > somewhat. > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Research, Armour College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre >

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fourier transforms and k grids
by Peter Pfalzer 11 Mar '03

11 Mar '03

Dear Ifeffit Users, I changed to iFeffit recently and like the improved functionality very much. During my test runs I experienced some strange behaviour of the fft functions when using a non-standard k grid. I take from the Ifeffit documentation: - that all the functions performing fourier transforms should yield the same results (given the same parameters as input, of course). Specifically: I understand that fftf() and feffit() both compute ffts from k to R space for the chi data given with the "real=..." and "chi=..." parameters, respectively. - that these functions all use a k grid starting from 0 and having a grid width of 0.05. - that the non-standard k-grid of my data is automatically interpolated to the required k grid whenever the "k=..." parameter is set. This is especially true for the fftf() function as well as for the feffit() function. If these assumptions are right, I do not understand the results of the forward fft of the data array performed by the feffit() command. The fft by feffit() looks like the fft by fftf() when the k array is NOT defined. Is this behaviour correct? Does it affect the fit? Am I making a silly beginners mistake? Is this a bug? Thanks for your help! Peter PS: I am using Ifeffit 1.0076 with the G.I.feffit GUI 0.9 on a Win98SE system. I have attached a Ifeffit input file that tests these differences. -------------------------------------------------------------- Peter Pfalzer Universitaet Augsburg Tel: +49-821-598-3215 Lehrstuhl fuer Experimentalphysik II Fax: +49-821-598-3411 Universitaetsstr. 1 D-86135 Augsburg Germany Peter.Pfalzer(a)physik.uni-augsburg.de -------------------------------------------------------------- Der folgende Teil dieser Nachricht enthält einen Anhang im sogenannten Internet MIME Nachrichtenformat. Wenn Sie Pegasus Mail oder ein beliebiges anderes MIME-kompatibles Email-System verwenden, sollte Sie den Anhang mit Ihrem Email-System speichern oder anzeigen können. Anderenfalls fragen Sie Ihren Administrator. The following section of this message contains a file attachment prepared for transmission using the Internet MIME message format. If you are using Pegasus Mail, or any another MIME-compliant system, you should be able to save it or view it from within your mailer. If you cannot, please ask your system administrator for assistance. ---- Datei Information/File information ----------- Datei/File: test_fft1.iff Datum/Date: 11 Mar 2003, 10:42 Größe/Size: 1454 bytes. Typ/Type: Text Der folgende Teil dieser Nachricht enthält einen Anhang im sogenannten Internet MIME Nachrichtenformat. Wenn Sie Pegasus Mail oder ein beliebiges anderes MIME-kompatibles Email-System verwenden, sollte Sie den Anhang mit Ihrem Email-System speichern oder anzeigen können. Anderenfalls fragen Sie Ihren Administrator. The following section of this message contains a file attachment prepared for transmission using the Internet MIME message format. If you are using Pegasus Mail, or any another MIME-compliant system, you should be able to save it or view it from within your mailer. If you cannot, please ask your system administrator for assistance. ---- Datei Information/File information ----------- Datei/File: feff0001.dat Datum/Date: 11 Mar 2003, 9:57 Größe/Size: 6211 bytes. Typ/Type: Text

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Re: [Ifeffit] XANES
by John J. Rehr 10 Mar '03

10 Mar '03

Regarding XANES fits, I'm glad to hear Bruce is working on adding a principal component analysis to IFEFFIT. Doing XANES fits ala Benfatto and Della Longa would also be desirable in the long run, i.e., fitting the XAS(x) with x standing for various parameters like interatomic distances. To do that would generally require looping over the FMS module in FEFF and could get time consuming. To avoid this, one needs something like a tensor XANES calculation, which computes d mu/ dx via multiple XAS calculations and hence permits fast linear interpolations. This is not implementable with IFEFFIT/ATHENA at present as far as I know. However, I don't see major difficulties in implementation (?). There are some other ways to go, including using the parallel version of FEFF8 (Bouldin for example has suggested using this approach for XANES fits). Also, one might even consider adding constraints ala Krappe and Rossner's Bayesean-Turchin approach for EXAFS analysis. John Rehr > From B. Ravel ... >My program, Athena, currently has the capability of fitting lineshapes >(i.e. an arctangent and a number of Gaussians or Lorentzians) to >normalized XANES data. In the not-too-distant future, Athena will be >able to fit a linear combination of standards to a XANES spectrum and >be able to do principle component analysis (PCA). >

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Athena 0.8.014
by Bruce Ravel 06 Mar '03

06 Mar '03

Hi folks, I am pleased to announce a new version of Athena today. The source code tarball and windows executable are on my web site. Today's version offers three significant new features: 1. A fairly major user-interface change 2. The ability to fetch data files from web sites 3. An improved merging algorithm Please note that I am making use of a very recent feature of Ifeffit (the "nofx" array function) in the new merging algorithm. Windows users need to update to the version of the big Ifeffit installer from January 22, 2003. Linux, Unix and OSX users should be using Ifeffit version 1.0076 or later. The Windows installer and the ifeffit source code can be found at Matt's web site http://cars9.uchicago.edu/ifeffit/download.html If you are not running Ifeffit 1.0076 or later, then merging WILL NOT WORK in Athena 0.8.014. So, please, upgrade. I'll describe each of those features in detail below. I'd like to specifically thank Matt (who suggested the web thing) and Adam Web (who pointed out a problem with the merging algorithm). I'd also like to mention to all the people who have been asking for PCA in Athena that it's moving closer to the front of my TODO list. The change to the user interface is needed to be able to put PCA into Athena in a sensible manner. Regards B The details about each new feature: 1. Although the user interface change is pretty significant, I think it will be easy for current users to adapt to. Indeed, I think most people will appreciate the added functionality that the change allows. In earlier versions of Athena, data processing and analysis chores such as alignment, calibration, and log-ratio were done by interacting with a special dialog that popped up in a separate window. This separate window performed a grab, which means that you could not interact with the main window until you were done with the dialog and had dismissed it. Now, each of the various chores that previously used a pop-up dialog works by replacing the main part of the main window with the dialog specific to that analysis chore. Thus, when you, say, go to align data, the part of the main window where you specify background removal and Fourier transform parameters gets replaced by various menus and entry boxes relevant to that chore. If that's not clear, check out the new screenshots at http://leonardo.phys.washington.edu/~ravel/software/exafs/screenshots.html#… There are screenshots showing each of the eight alternate views in Athena. Not only does this reduce the number of windows that Athena throws up on the screen, it also allows you to use the groups list and the plotting buttons while one of the alternate views is displayed. For example, you can now view one or more data groups in R-space *while* aligning. Chores like alignment and difference spectra which require specifying a second data data group now work by selecting the second data group from the group list. 2. You can now read data files from web sites using an extremely primitive interface. In the File menu, there is an item which says "Open URL". When you select this, the Echo area at the bottom of the screen gets replaced by a bright orange text entry box. If you type in the fully resolved URL of a data file somewhere on the web, Athena will fetch and import that file. This is not extremely convenient because you have to type in the exact URL (or use cut and paste, of course). I have not (yet) implemented a mouse-driven browser of any sort. I may in the future if this feature proves popular. One helpful feature I did implement is that Athena keeps a history of files downloaded during the current Athena session. If you hit the up or down arrows while the URL text entry box has the focus, you will scroll up and down in the history of fetched data files. If you want to try it, I put some iron foil data on my web site. Enter this URL in the orange box: http://leonardo.phys.washington.edu/~ravel/misc/fe.060 This feature will work for Windows users. It will work for other platforms only if you have the LWP perl modules installed. Because that is a very large and frequently changing package, I am not comfortable distributing it with the horae package. If you are a linux, unix, or OSX user and the "Open URL" thing is greyed out, then you will need to install LWP. You can grab the latest version of the Bundle::LWP package from http://search.cpan.org/author/GAAS/libwww-perl-5.69/ Alternately, you can use perl's CPAN interface. At the command line, type perl -MCPAN -e shell then at the CPAN prompt type install Bundle::LWP 3. The merging algorithm has changed. Before, the marked data groups were merged after interpolating them onto the abscissa grid of the first marked group in the groups list. Now, Athena determines what is the longest abscissa range common to all marked groups. The reason for this change is that the prior algorithm would extrapolate if a marked group had a shorter abscissa range than the first group. Often this isn't a problem, but it can lead to very strange and undesirable results in the merged data. I am modestly confident that I have merging working correctly again in all cases. I encourage anyone using the merging algorithm to send me a project file if they suspect that bugs remain. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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[Ifeffit] ldd /usr/local/bin/ifeffit ldd: /lib/ld-linux.so.2 exited with unknown exit code (139)
by Jacques Roux 04 Mar '03

04 Mar '03

This is a short report of various successful installations of ifeffit (and companion programs athena, artemis etc...) on linux boxes running Mandrake 8.1 8.2 and 9.0. However I would like to report one nagging failure which is summarized in the subject line of the message. On my office DELL under Linux Mandrake 9.0 ifeffit core dump and ldd issues the rather terse error message "unknown exit code (139)". The very same code runs fine and (ldd gives a meaningfull answer!) on other machines running the very same version of linux (including gcc, ld, glib etc...). I checked on google and found other people running into very similar problem (OK on one machine, wrong on the other). I tried to recompile ifeffit.f using --static but I could not get the static version of libX11 so for the time being I gave up. BTW it is not too bad as I can use the software on the same computer booting an older version (mdk 8.1) and at home on a 9.0 ! I hope this information may be useful to someone sometime ? -- J. Roux, CNRS-Institut des Sciences de la Terre 1a rue de la Férollerie, 45071 ORLEANS cedex 2, France

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:)
by Du Yonghua 04 Mar '03

04 Mar '03

Dear adaministrator: I have met some unknow problems that I cannot download the iffefit setup file. So I wonder whether you will be so kind to send me a copy of iffefit. The system of my computer is windows and the limination of my mail box is 100MB. Thank you very much! Du Yonghua Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P.O.Box 918 2-7 Tel: (86)01088235980 19(B) Road Yuquan Beijing China

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XANES
by Ahmed M Shahin 03 Mar '03

03 Mar '03

I have some question. I have mixed oxidation states and I would like to fit XANES, to determine the ratio of the mixed oxidation states I have. I looked at the documentations in the Ifeffit website but I could not find it. I have a license of feff. Would you please help me in how to fit XANES. I appreciate your help Ahmed ***************************************************** Ahmed Shahin Chemistry Department University of Missouri-Rolla 142 Schrenk Hall, Rolla, MO 65409-0010 E-mail: shahin(a)umr.edu Phone (573) 341-4083 "Make yourself a better person and know who you are before you try and know someone else and expect them to know you." *********************************************************

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