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

Reading in mu(E) data
by Carlo U. Segre 25 Apr '03

25 Apr '03

Bruce: i have been using our rebinning program to combine data before loading into Athena. The data produced is a two column file, E and mu(E). When I try to read it into Athena, the edge is not properly detected and I have to set it by hand before the background can be subtracted properly. I haven't seen any way to avoid this problem. Is there something funny about this kind of data which would cause this problem? 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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artemis updated (again!)
by Bruce Ravel 24 Apr '03

24 Apr '03

Hi folks! Well, it didn't take me very long to find several very serious bugs in the multiple-data-set version of artemis that I released the other day. I was able to fix most of them and have posted new tarballs and windows executables. One problem had to do with the first path in a fit sometimes being neglected by Artemis. Yikes! The other problem had to do with sving and rereading project files multiple data sets. Both of these and a few smaller problems are fixed in version 0.6.002. One problem which remains is in the brand new Project Assistant. Suppose that you want to fit several scans of the same material measured at different temparatures. In that case you would want to import several data files and then import the same feff calculation(s) for each data file. If you attempt to import the same feff calculation more than once with the Project Assistant, it will not do the right thing. Other uses of the Project Assistant, including single data set fits and multiple data set fits with *different* feff calculations, *will* work as intended. Also, if you import your data and feff calculations outside the Project Assistant (i.e. by using the appropriate entries in the File menu), then you can set up a multiple-temperature fit. So, if you want to do a fit with many data sets and a single feff calculation which is used repeatedly, you must set it up by hand and not by using the Project Assistant. This will be fixed in 0.6.003. Regards, B -- 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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artemis 0.6.001 and athena 0.8.016
by Bruce Ravel 21 Apr '03

21 Apr '03

Hi folks! Today I am pleased to announce the first version of Artemis that supports multiple data set fitting. That is, you can import 1 or more data sets along with all the relevant feff calculations and use parameters which impose constraints between the data sets. The second huge new feature in Artemis is something I call the Artemis Project Assistant. This is a wizard-like feature of the program which helps you walk through the steps necessary to import one or more data sets and one or more feff calculations and to set up fitting parameters. This will, I hope, reduce the difficulty and complexity of getting started with Artemis. I threw together a web page explaining the Project Assistant: http://feff.phys.washington.edu/~ravel/software/exafs/apa.html There are lots of pictures on that page as well as a step-by-step recipe using the copper example that comes with the distribution. The third big change has to do with how k-weighting is done for fitting and plotting. It is now possible to do a multiple k-weight fit, that is to simultaneously fit data using, for example, both k=1 and k=3 weighting. This is often helpful for distinguishing between correlated variables which have different k dependence, such as sigma^2 and S_0^2. To explain how to use the various k-weighting options in fits and in plots, see this web page: http://feff.phys.washington.edu/~ravel/software/exafs/kweight.html I am looking forward to getting some feedback on this new version of Artemis, both in terms of bug reports and in terms of suggestion for user interface improvements. The problem of organizing and presenting a fit with multiple data sets and multiple feff calculations is very difficult. I have tried to present it in a way that is tractable, but I am open to any suggestions any of you might have to make is better and more clear. As for Athena, 0.8.016 represents only a few small changes. The most important is that I fixed a very serious bug in the deglitching interface. As always, new tarballs and Windows executables are available on my web site. Please note that unix, linux, and OSX users must be running at least version 1.0076 of Ifeffit. If you have not updated the Ifeffit core recently, please do so before installing the latest tarball. Thanks this time to Adam Webb for pointing out the deglitching bug in Athena. And a huge pile of thanks to Shelly Kelly for testing Artemis last week and for making many great suggestions for improving the Project Assistant and multiple data set fitting in general. Regards, Bruce -- 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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a pgplot question
by Bruce Ravel 18 Apr '03

18 Apr '03

Hi Matt, The attachement is a screenshot of the PGPLOT window that was left lying around from the last time I fired up athena. My question is about the large white-space gutter around the plot. Is there some way that I don't know about of reducing the size of that gutter? That is, can I expand the bounding box around the plot to be much closer to the size of the window? Also, what exactly does the reset argument to plot() do? And what is the most reliable way to get pgplot to *not* write a legend entry for a plot? Is it plot(a.x, a.y, key="")? Thanks B -- 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: Calculating Phase Corrected Re and Im
by Matt Newville 14 Apr '03

14 Apr '03

Dear Ian, On Thu, 10 Apr 2003, Ian Drake wrote: > ... I would like to calculate and plot the fourier transform > of the phase corrected chi function. Can I do this using > the UWXAFS software suit? If not, can you recommend other > software. I have Mathematica....do you recommend its use in > the analysis. My curiosity on this issue stems from the > work of Lee and Beni in PHYS. REV. B, 15, 1977, pg.2862. Thanks for the question. Yes, phase-corrected Fourier transforms can be done. I hope it's OK if I CC this reply to the Ifeffit mailing list, as this is a fairly common question about XAFS analysis... Also, since you asked about UWXAFS software, I'll point out that Ifeffit is the successor to the UWXAFS programs, and includes those programs and quite a bit more capability, including a few GUIs. See: http://cars.uchicago.edu/ifeffit/ for more details. The longer answer about Phase-corrected FTs: Phase-corrected FTs are not always as good as you might hope. They don't give real radial distribution functions. They do give somewhat cleaner XAFS FTs and put peaks in |chi(R)| closer to the corresponding distance. Of course, to do these, you need to know the phase. Also, since you can do only one phase-shift correction, you can't correct all shells or multiple-scattering contributions. Anyway, lots of people like phase-corrected FTs, especially for making plots to show non-XAFS people, and it usually work fine for the first-shell. With ifeffit, there are a couple ways to do phase-corrections. The simplest way is to name the central atom/edge (eg, 'Cu K') to the fftf() command. In ifeffit commands, this looks like: read_data(file= 'my_chi.dat', type='chi') fftf(my_chi.chi, kmin=2, kmax=15, dk=2, kweight=2, pc_caps = 'Cu K') ^^^^^^^^^^^^^^^^ (pc_caps is for Phase-Correction, Central Atom Phase Shift), This will do only the central-atom portion of the phase-shift, so will be incomplete, but is often most of the correction, will work for the whole spectra, and doesn't require knowing much about the system. Athena (the excellent GUI to ifeffit from Bruce Ravel) can do these central-atom phase-corrections very easily (ie, no typing commands). I think Sam Webb's SixPack doesn't do phase-corrected FTs, but I could be wrong. If you know have a Feff calculation for a scattering path, in the form of a feffNNNN.dat file, you can use this for a more-complete phase-corrected FT, like this: path(1, feffNNNN.dat) fftf(my_chi.chi, kmin=2, kmax=15, dk=2, kweight=2, pc_feff_path = 1) ^^^^^^^^^^^^^^^^ This version includes both central-atom and scattering-atom phase-shifts, which will give a much better phase-correction, but assumes you know quite a bit about the system. I think athena doesn't do this form of phase-correction, and I don't remember if artemis does this (yet??). Feffit will aslo write out phase-corrected FTS (the full kind, using the first feffNNNN.dat file listed in feffit.inp) if the keyword 'pcout=1' in in feffit.inp. Finally, some people use phase-corrected FTs for analysis, especially to pick R_NN at a place where Im[chi(R)] = 0. I'm not sure what the accuracies of this are, but pelase note that Ifeffit (and feffit) swaps real and imaginary parts for its FT, so that it is actually Re[chi(R)] that is ~=0 at R=R_NN for these FTs. Hope that helps, but don't hesitate to ask again if it's not clear enough. --Matt Newville

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Debian packages
by Carlo U. Segre 01 Apr '03

01 Apr '03

Hello All: I have a first version of Debian Linux packages for IFEFFIT, Atoms and Horae. They now install with no conflicts and appear to work on my machines. I believe that all package dependencies are in place as well. Please feel free to test them out and let me know if there are any big errors. Sources are also on the archive. The apt/sources.list lines would be deb http://fermi.phys.iit.edu/debian binary/ deb-src http://fermi.phys.iit.edu/debian source/ The binary packages have been compiled for the stable (woody) distribution but seem to run fine on testing (sarge). 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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athena 0.8.015 and artemis 0.5.008
by Bruce Ravel 27 Mar '03

27 Mar '03

Hi folks, I am releasing a new source tarball for Athena and Artemis today along with windows executables of both programs. They are available in their standard places on my web site. Athena: One small change in how title lines are handled. Other than that, this release is identical to the last. Artemis: Lots of small bug fixes and usability enhancements, including: 1. You can rearrange the order of the parameters on the Guess, Def, Set page. 2. You can rename data, feff calculations, and feff paths. This changes how they are displayed in the list, how paths are reported after a fit, and how legend strings are generated for plots. 3. Control-right-click or middle-click on an item in the Paths list will pop up a contextual menu. 4. A parameter can now be set as a "skip" parameter (as well as guess, def, or set). This means that Athena will ignore that parameter when building an ifeffit script for fitting. 5. You can now save multi-column data files where the columns contain the selected (i.e. highlighted in orange) items from the paths list I am hoping to start work on multiple data set fits in Artemis real soon. The next release will, I hope, have my first stab at that. Yay! Special thanks this time to Simon Bare for pointing out a very strange bug in Athena. Also I should point out that starting work on the Artemis document proved to be a good way to find bugs and other weird behavior in Artemis. Most of the changes this time are a direct result of stuff I found while trying to start the document! Peace, B P.S. The bug in how Athena handled titles is extremely specific. It was triggered by having a title line in a data file which had a percent sign (%), a hash (#), or an exclamation point (!) inside of matching parentheses somewhere on the line. Then, the problem was only triggered on Windows. I could not reproduce it on linux, only on Win2k. I also have not yet been able to reproduce it in a simpler context using the ifeffit command line. My temporary solution is to remove %, #, or ! from a title line if Athena is running on Windows. This is a bad solution because Athena should preserve the contents of the headers unaltered. However, it seems more important that Athena plot and remove backgrounds and do Fourier transforms. Thus, I decided to release this crude hack with a promise to return to the problem later. Also, I think that Athena's removing those three characters is only a small sin. -- 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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Difference File Fits
by Norbert Weiher 19 Mar '03

19 Mar '03

Hi folks, I was just playing a bit around with some data and it sprang to my mind that sometimes the idea of doing difference file spectra fits would be a nice feature (like XDAP has it). This would be great to identify single contributions of certain scatterers that are close to each other or somehow other produce similar paths. How about including a feature which lets you extract a "new" chi.dat file from the original data minus some paths one has selected? This file could then be further processed. Finally something similar for EASE: I'm still one of those old-fashioned EMACS folks and would like to have something like this at my hands in EASE too. Bruce, what do you think about it? Would it be possible? I'm keen on hearing your ideas about this. Norbert -- Dr. rer. nat. Norbert Weiher (norbertweiher(a)yahoo.de) Laboratory for Technical Chemistry - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 2 3123

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RE: [Ifeffit] A question for Windows users
by SCHLEGEL Michel 177447 17 Mar '03

17 Mar '03

Hello Bruce, everybody you wrote: > Athena is not always particularly creative about the names it suggests > for output files. For example, if you use the feature of saving > several marked groups to a single output file, Athena suggests that > the names be "marked.space". That is, if you save marked groups as > chi(k), the suggested file name is "marked.chi". If you save marked > groups as the real part of chi(R), the suggested file name is > "marked.chir_re". > > It is possible to configure Explorer such that it does not display > file extensions (i.e. the bit after the dot). That might make it hard > to tell different marked group output files apart if the suggested > names are used. > > Is this a problem for anyone? Should I change the suggested names > such that the suggestive part is not in the extension? That is, would > "chi.marked" and "chir_re.marked" be better names? Actually, as a Window user (booo! hisss!), my first move is to have all the extensions appearing in Explorer, a basic security move (e.g., to avoid clicking on a "picture.gif" that actually corresponds to a "picture.gif.exe", with all undesirable consequences). I also find it much easier to keep the pre-dot part of the data file for the sample name, and the post-dot part for the data type (and I'm eternally grateful to Ifeffit to provide us miscellaneous and yet distinct extensions; no joke). Therefore, I suggest NOT to change the current feature. Best regards, Michel Schlegel

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Re: Ifeffit Digest, Vol 1, Issue 123
by Grant Bunker 14 Mar '03

14 Mar '03

HI, Irit - well, I'm sure the whole EXAFS community wishes you the best in delivery of your third child! And the whole world hopes the Bush/Saddam war will be short with minimum casualties on both sides. (I'll continue the conversation without the whole world listening) best wishes - grant ps congratulations on your Nature paper On Fri, 14 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: Ifeffit Digest, Vol 1, Issue 121 (Irit Sagi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Mar 2003 21:07:04 +0200 > From: "Irit Sagi" <cssagi(a)wisemail.weizmann.ac.il> > Subject: [Ifeffit] Re: Ifeffit Digest, Vol 1, Issue 121 > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <se70f2fb.035(a)wisemail.weizmann.ac.il> > Content-Type: text/plain; charset=US-ASCII > > Oops, I see that the whole EXAFS community saw this mail.......Oh well, SHALOM from Israel. Irit. > > > > > > > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> cssagi(a)wisemail.weizmann.ac.il 03/13/03 08:56pm >>> > Hi Grant > I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. > We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. > I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. > I hope that everything is OK with you and your family. > All the best, Irit. > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> > Matt - it might be sensible to just add a new function to do the > rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the > edge could be left unchanged). People could call the function ('rebin"?) > only they needed it; subsequent routines could be kept as they > are now. Anyone who doesn't like the rebinning wouldn't be obligated to > use it. > > thanks - grant > > On Thu, 13 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: Rebinning (Kelly, Shelly D.) > > 2. Rebinning (Bruce Ravel) > > 3. Re: Rebinning (Carlo U. Segre) > > 4. Re: Rebinning (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 12 Mar 2003 13:52:45 -0600 > > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > > Subject: RE: [Ifeffit] Rebinning > > To: "'XAFS Analysis using Ifeffit'" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: > > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > > Content-Type: text/plain; charset="us-ascii" > > > > 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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