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

Fwd: problem in executing programs
by Bruce Ravel 05 May '03

05 May '03

Hi folks, I received the email below from a new Ifeffit user. Apparently he is having sporadic problems trying to run the programs on Windows ME. Given that he is able to run Athena but not Artemis, I am confused. And I do not have a machine running ME on which I can try to fin a solution. Do any of you have a suggestion for him? (Although "upgrade to Windows XP" and "run linux instead" are both valid suggestions, I am guessing he is looking for a way to actually run the codes on ME.) Thanks, Bruce ---------- Forwarded Message ---------- Subject: problem in executing programs Date: Mon, 05 May 2003 17:20:20 +0100 From: Yuni Krisnandi <y.krisnandi(a)abdn.ac.uk> To: ravel(a)phys.washington.edu Hi Bruce, I just downloaded IFFEFIT and followed instructions for Windows ME. So far, I couldn't run the programs by clicking the icons in the start up. However, I managed to execute iffefit.bat and athena.bat. I still couldn't run artemis, although I've tried another way by typing the path c:\Iffefit\artemis.bat . it always gave message: bad command or file name. I understand this is such a trivial question for you. But I have no clue at all. Thanks, Yuni "Anyone can become angry - that is easy, but to be angry with the right person, to the right degree, at the right time, for the right purpose, and the right way - that is not easy." Aristotle ------------------------------------------------------- -- 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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athena 0.8.018 and artemis 0.6.003
by Bruce Ravel 04 May '03

04 May '03

Hi Folks, I made new versions of both Athena and Artemis today. There are no new features but I fixed a number of bugs that came to my attention in the last two weeks. You can check the change logs on the web site for the details. As always, the new source code tarball as well as new Windows executables of Athena and Artemis are available on my web site. Much gratitude this time goes to Carlo Segre, Paul Fons, and Markus Janousch for useful bug reports. Thanks, guys! 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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Athena - resetting working directory
by Carlo U. Segre 28 Apr '03

28 Apr '03

Hello Bruce: I am using the latest version of Athena on Linux and I have noticed a strange behavior. I cd to the directory where my data is located and run athena form the command line. When I want to open my first file, the dialog puts me in the same directory with no problem. However, any time I try to do another file operation (reading, writing, etc), the dialog starts at the filesystem root "/". Even if I move back to the initial directory the next time it is back at the root. 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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Re: ifeffit window
by Matt Newville 25 Apr '03

25 Apr '03

Hi Frank, I Hope it's OK that I CC: this to the ifeffit mailing list. On Thu, 24 Apr 2003, Frank Haass wrote: > Hi Matt! > > I have worked on my data with the IFEFFIT for a few days now, and I think it > is quite a very good improvement from the autobk and feffit-Versions I used > bevor. Great! But, I have a question concerning the windows for FT which can > be used in IFEFFIT. > > In the "old" FEFFIT, the keyword ikwindo could be used to change the window > function from Hanning to Gau� etc. > > Using the keyword kwindow (kwindow = 1 etc.) in IFEFFIT, it was not possible > to do this. Have I taken the wrong keyword? Are the numbers uses for the > separate window-functions in IFEFFIT the same like in FEFFIT? The 'ikwindo' flags in Feffit were too hard for most of to remember, so Ifeffit uses character strings for the name of the window function as with fftf(data.chi, kmin=2,kmax=12,dk=1, kwindow='hanning') The feffit() and window() command use this keyword too, or it can set with the string $kwindow: set $kwindow = 'hanning' I'm not sure that's easier than it was in Feffit, but it doesn't seem worse. For back-transforms, use 'rwindow' in place of 'kwindow'. The supported window types are: hanning fhanning kaiser parzen welch sine gaussian Only the first 3 letters of these namew are really needed. The default is 'hanning', but 'kaiser' is often a good choice. Of course, the GUIs have drop-down lists for this. I see that this information is not in the on-line docs. Eeek! I would have sworn it was.... I'll be sure to add this when I post the next version. The good news is that I am actually working on this these days, and even though I keep finding more to add and fix, I'm optimistic that 1.0077 will be ready next week. --Matt

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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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Artemis document
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, I got mail this afternoon asking me about documentation for Artemis. That has, of course, been a long-standing shortcoming of the code. It turns out that I have spent a decent chunk of time in the last couple weeks working on the Artemis doc. It is only about 25% written, but the portions that I have written are introductory material. It should be useful even in its current, sparse form. Here's the URL: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html I am only posting the PDF at this time. I'll be updating it frequently as I work on it, but I probably won't announce updates on this channel until it is a lot closer to finished. So check back often if you are interested. Please be aware that it is nowhere near finished. It is full of gaps, typos, suspicious statements, and dangling trains of thought. It is so far from finished that "documentation" may be too kind of a term. However, it seems that posting the unfinished doc on my web site is well within that open source spirit of "release early, release often" that I have adopted with my codes. If it proves useful to some of you -- super! B P.S. If anyone is interested in helping out with the doc, either by copy editing or by contributing text, let me know -- I'd be jumping- up-and-down happy if that happened. -- 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 question for Windows users
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, 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? If no one pipes up, then I'll assume things are ok as they stand. If even one person makes a compelling argument, I'll probably change the suggested names throughout my programs to avoid this situation. 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: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

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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Re: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

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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Re: Ifeffit Digest, Vol 1, Issue 121
by Grant Bunker 13 Mar '03

13 Mar '03

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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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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feff8
by shahin 26 Feb '03

26 Feb '03

Bruce, I have recieved the liscence to install and use FEFF8. Would you please tell me how to upgrade the FEFF6 tiral version, so that, I can use ifeffit with FEFF8 instead of FEFF6. I appreciate your help. Ahmed

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Fresh installations of linux and ifeffit
by Bruce Ravel 14 Feb '03

14 Feb '03

Hi folks, This message is partly in response to Norbert's post from last week and partly because I noticed some things today that may trip up others in my situation. I wanted to post something here so that the solution to a similar problem might be found in the mailing list's archive. Yesterday and today I have been entertaining myself by updating my desktop computer to SuSE's Office Desktop edition of SuSE 8.1 It's pretty nifty and the installation was a breeze. Installing Ifeffit and my programs was not a breeze, however, because of some issues related to a linux distribution with a name like "Office Desktop". Because this distribution is targeted at people who use office applications, it was pretty weak in terms of software development. I had to go to SuSE's online distribution to get rpms for such obviously necessary things as C and Fortran compilers and make! Once I installed all the obvious development stuff, I made a stab at compiling Ifeffit. I immediately saw the problem that Norbert reported, which was the configure script complaining about not being able to find the "tputs" function in any of the terminal libraries. I solved this problem by downloading and installing the ncurses development package. SuSE and Red Hat give names like "ncurses-devel" to these packages, which contain header files and the like. After that, no problem. Ifeffit compiled up just fine. As did Athena and Artemis. However, trying to start Athena it became obvious that I had forgotten to install PGPLOT. Matt's PGPLOT_install script did it's magic exactly as expected. However, to get the compilation of PGPLOT to finish, I had to install the development packages for the PNG, zlib, and X windows libraries. Again, my "Office Desktop" system was lacking the header files needed to compile software. Once those were installed, PGPLOT compiled fine. I recompiled Ifeffit and my codes and I was happy. To summarize: 1. Don't forget to install PGPLOT. 2. If you have a choice about which linux distribution to choose, go for one of the "professional" distributions and make sure to install development packages up front. 3. If your CDs did not have the development packages on them, go to your vendors website and download them. If you ever want to compiler other stuff from the web, you will want these anyway. 4. To compile Ifeffit and PGPLOT, you need the header files for -- ncurses (or whichever terminal library you have on your system) -- the PNG library -- the zlib library -- the X windows headers Hope that's helpful to someone sometime. 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: Ifeffit digest, Vol 1 #109 - 2 msgs
by Zhan Zhang 12 Feb '03

12 Feb '03

Matt, I tried on my Win98. Installing it into C:\Ifeffit solved this icon not run problem for me. In my case, I believe this make_bats.exe works fine all the time. It generates the right .bat files. I would believe that the two easy steps you listed below works well for me. Hope it is fine for all other Win98 users. Anyway, I am working primarily on Win2K or WinXP now. Thanks for the hard work maintaining this! Zhan >My guess is that make_bats.exe that is supposed to make >the *.bat files at the 'Finish installation' step may >also be choking on the space in 'C:\Program Files'. > >Could one or both of you try installing into 'C:\Ifeffit' >instead of 'C:\Program Files\Ifeffit'. That might get the >start menu and desktop icons to work better -- and >everything else is supposed to work fine. If that doesn't >work, we might have to figure out something better. > >In the end, it would be really nice to have a small list >of steps for getting Ifeffit installed on Win98. If it >was as easy as: > 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys > 2. run the installer, but install to C:\Ifeffit. > -------------------------- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Dept. Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Drive 9700 Cass Ave. Evanston, IL 60208 Argonne, IL 60439 U.S.A U.S.A. Email address: zhanzhang(a)northwestern.edu Office: (630) 252-8629 Fax: (630) 252-5498 --------------------------

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Procedure for Win 98 installation
by krk511＠casbah.it.northwestern.edu 11 Feb '03

11 Feb '03

Matt and Group, It appears that the following two steps should be all that is needed to install on Win 98 and make the desktop icons usuable. (THANKS!) I've tried this today on another computer in our lab, and it even managed to install the xxx.bat files without having to go to the Make bats application. (My guess is that when I originally tried this a couple of days ago I may have done the shell command with a number much smaller than 4096, and that was the difference between then and now.) The procedure below appears to work great, if someone has problems they should immediately look to see if the xxxx.bat files were generated, and if not use the Make bats application. -- Kristine MN> In the end, it would be really nice to have a small list MN> of steps for getting Ifeffit installed on Win98. If it MN> was as easy as: MN> 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys MN> 2. run the installer, but install to C:\Ifeffit. MN> MN> That would be good enough for now. MN> Thanks, MN> MN> --Matt

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Problems compiling ifeffit
by Norbert Weiher 11 Feb '03

11 Feb '03

Hi folks, I just got a new computer and put SuSE Linux 8.1 on it. Now I started compiling ifeffit (which worked fine with the 7.3 version on my old one) and it produced the following error: ./configure worked. When I tried to do "make", it gave me loads of "undefined references" to some commands (mainly: tputs and so on). I examined the output of ./configure and found the following lines: checking for tputs in -lncurses... (cached) no checking for tputs in -lcurses... (cached) no checking for tputs in -ltermcap... (cached) no checking for tputs in -lterminfo... (cached) no checking for tputs in -ltermlib... (cached) no Anyone who can help me with this? Thanks in advance :) Regards, Norbert Weiher

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Win 98 cont....
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group: Sorry about the incomplete message. In regards to getting IFEFFIT to work on Win 98: I changed config.sys per Matt's suggestion: -- that changed the MSDOS error message from "Out of environment space" to "too many parameters" when I hit the desktop icon (this is what I still see when I hit the desktop icons) On Matt's suggestion I then looked at the xxxx.bat files in c:\Program Files\Ifeffit: -- I noticed that they weren't automatically installed, so I ran the "Make bats" application, after which I was able to run all the software if I selected it directly from the c:\Program Files\Ifeffit folder. After reading the last message I added Zhan's command to my autoexec file -- but it hasn't seemed to have made a difference in being able to use the desktop icons on my computer. It does still appear that I can get at the software directly by clicking on it from it's actual folder. I hope this helps. I'm just excited to see that it appears to work! Thanks! Kristine Witkowski Northwestern University

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Re: Ifeffit on Win98 (version 1.0076)
by Zhan Zhang 10 Feb '03

10 Feb '03

Bruce, I tried with the version 1.0076 found on the download site. The results are basically same as for 1.0074 If I had SET IFEFFIT_DIR='C:\Program Files\Ifeffit' --no help. SET IFEFFIT_DIR="C:\Program Files\Ifeffit" --sovle the path problem, but introduce some other 'complaining' message shown below. Athena runs. print() on closed filehandle I at athena line 175. print() on closed filehandle I at athena line 196. Unable to write temp config file "C:\Program Files\Ifeffit"\athena.ini-new: No s uch file or directory at athena line 221 print() on closed filehandle M at athena line 240. SET IFEFFIT_DIR=C:\Progra~1\Ifeffit --Runs ok. Zhan -- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Department Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Dr 9700 Cass Ave Evanston, IL 60208 Argonne, IL 60439 Tel: (630) 252-8629 Fax: (630) 252-5498 zhanzhang(a)northwestern.edu

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Win 98 installation
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group, Currently it appears that I can get the various software running (SixPack, GIFEFFIT, etc.) just not from the desktop icons. I have done/tried the following: I made the changes suggested to the config.sys file -- this changed the error message (when hitting the desktop icon) from "Out of environment space" to "too many parameters" the later message I still see when I currently hit the desktop icons. After the previous step I checked the xxxx.bat files in c:\Program files\Ifeffit

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Win 98 installation
by krk511＠casbah.it.northwestern.edu 10 Feb '03

10 Feb '03

Bruce and Group, Currently it appears that I can get the various software running (SixPack, GIFEFFIT, etc.) just not from the desktop icons. I have done/tried the following: I made the changes suggested to the config.sys file -- this changed the error message (when hitting the desktop icon) from "Out of environment space" to "too many parameters" the later message I still see when I currently hit the desktop icons. After the previous step I checked the xxxx.bat files in c:\Program files\Ifeffit

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Re: Ifeffit digest, Vol 1 #106 - 2 msgs
by Zhan Zhang 09 Feb '03

09 Feb '03

Bruce, My Win98 computer had a hard disk failure last year and I upgraded it to Win2K. However, I have another 98 running at home. But I don't have the lastest Ifeffit there. So I just tried this with 1.0074. I will try a latest version later. I don't recall anything about the 'out of memory' problem when installing on my office 98. But this time I do. After changing config.sys. It was gone. And from my experience here, the answer to the first question below is YES. I click the icon on desktop, a DOS shell window (minimized) showed up and the 'too many parameters' information given. Then, well, nothing happened then. I tired put quote on 'C:\Program Files\Ifeffit' in the .bat file. It did not help. And I tried put double quotes on "C:\Program Files\Ifeffit". It helps sovle the 'too many parameter' problem. But it seems introduced another problem. An error message 'bad side "": must be top, bottom, left, or right at Tk/Widget.pm line 1053' showed and quit. The last thing I did was changing it to C:\Progra~1\Ifeffit. And it worked. Putting single or double (' or ") around it would not work again. And the answer to the second question is YES, if the icons here mean the '.exe' file. NO for '.bat' file. It was also a NO if I tried to run them from 'Start-->Programs-->Ifeffit-->Athena(or anyother)'. I believe this means the icons on the desktop point to the correct files (.bat file). And the only problem is the bat file could not set up the path. This won't be a problem if the path is sort of a normal DOS path, say shorter than 8 characters and contains no space. Zhan > Zhan: I have the exact opposite question. Was changing the path to > have the tilde rather than the space required to get the desktop icons > to work? And do the programs run without editing if you click on the > icons in the C:\Program Files\Ifeffit folder? > > Perhaps someone who is python-savvy and has access to a Win98 machine > can help out by doing some tests and figuring out what the > make_bats.py needs to be in order to work correctly on Win9x *as well > as* the later Windows systems. There are some hints in the README.TXT > file in the build_setup folder for how make_bats and the installer > builder all work. > -- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Department Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Dr 9700 Cass Ave Evanston, IL 60208 Argonne, IL 60439 Tel: (630) 252-8629 Fax: (630) 252-5498 zhanzhang(a)northwestern.edu

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S02
by Dr. Paul Fons 09 Feb '03

09 Feb '03

I was curious to tap the collective wisdom of those on the list regarding the "true meaning" of S02, the passive electron reduction factor, at least with regards to fitting experimental data to feff calculated paths. I understand that S02 is an aggregate "energy losses related to core hole creation parameter", but am curious about experimental data fitting. In particular, I have have started probing both high and low energy ranges for exafs and find that my usual experience from the 10-15 keV range don't seem to apply. In particular, I have been measuring energies around the O edge (540 eV) as well as some rather high energies edges Te (31 keV), Cd (26.7 keV) etc.. I have heard (indirectly via my coworker) from Andrei Rogalev that he considers S02 to be just another parameter. As the correlation between S02 and N is unity, this leads to a fair amount of ambiguity in the determination of coordination to say the least. While we are on the subject, are there any general observations about the transferablility of S02 from standards. How about the expected temperature dependence of S02? I do recall reading from John Rehr's article in RMP that S02 (which feff does calculate by the way) is an path dependent, complex sum that must be phasor summed. What are some realistic approximations/trends regarding to S02 and temperature, energy, and/or structure dependence? Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Optoelectronics Division Umezono 1-1-4 Tsukuba, Ibaraki JAPAN 305-8568

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(no subject)
by Bruce Ravel 07 Feb '03

07 Feb '03

Hi Matt, I'm a little confused by the "resolution" of this Win98 issue. It seems as though the two Northwesterners had slightly different experiences. Kristine said: K> I made the change to the config.sys file (which changed the K> message from 'Out of environment space' to 'Too many parameters'). K> I then went to look at the xxxx.bat files and saw that they K> weren't there. After hitting the make bats application to K> generate them and then clicking on the executable (from the K> C:/Program Files/Ifeffit/ folder) things seem to be OK. So it seems as though re-running the make_bats thing was sufficient, although the "too many parameters" thing seems to indicate that there is still a problem with the space in the folder name. It seems that Zhan, on the other hand, needed to fix the space in the folder name to get things to work. ZZ> What I did was just give the path and file name exactly as shown ZZ> in the DOS shell. Something like: ZZ> SET IFEFFIT_DIR=C:\Progra~1\Ifeffit ZZ> After changing all the .bat files, they worked ok for me. Why would one Win98 user need to do that but another not need to? That doesn't seem outside the realm of possibility with the wonderful Win98, but it does seem odd. So I guess I have a couple of questions. Kristine: Do the desktop icons work? Or can you only run the programs if you click on the .bat icons in the C:\Program Files\Ifeffit folder? Zhan: I have the exact opposite question. Was changing the path to have the tilde rather than the space required to get the desktop icons to work? And do the programs run without editing if you click on the icons in the C:\Program Files\Ifeffit folder? Perhaps someone who is python-savvy and has access to a Win98 machine can help out by doing some tests and figuring out what the make_bats.py needs to be in order to work correctly on Win9x *as well as* the later Windows systems. There are some hints in the README.TXT file in the build_setup folder for how make_bats and the installer builder all work. Regards, B P.S. It would be nice if everyone, and particularly digest users, when quoting a previous post, would edit the quote to show just the bit that is relevant to the conversation. It is much easier to understand the flow of the conversation without dozens or hundreds of lines of extraneous stuff. -- 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] Re: Questions about IFEFFIT and Windows 98
by krk511＠casbah.it.northwestern.edu 07 Feb '03

07 Feb '03

Bruce and Matt, Thank you for your help. Things appear to be working now. I made the change to the config.sys file (which changed the message from 'Out of environment space' to 'Too many parameters'). I then went to look at the xxxx.bat files and saw that they weren't there. After hitting the make bats application to generate them and then clicking on the executable (from the C:/Program Files/Ifeffit/ folder) things seem to be OK. (I didn't need to make changes to the bat files I guess)... though I'm still perplexed that I still get the "Too many parameters" message if I click on the icon on the desktop, while if I actually click on the executable in the folder I have no problem. I'm very glad that it appears to be working now. Thanks, Kristine Bruce Ravel <ravel(a)phys.washington.edu> writes on Fri, 7 Feb 2003 09:53:25 -0500: > > > > On Thu, 6 Feb 2003, Matt Newville <newville(a)cars.uchicago.edu> said: > > MN> I thought the 'Too many parameters - Files\Ifeffit Bad command or > MN> file name' message was somehow related to that, but maybe not. > MN> If not, it may be due to a mistake in the files C:\Program > MN> Files\Ifeffit\xxxx.bat (xxx = athena, artemis, ifeffit, > MN> sixpack,....) which all have this line: > MN> @echo off SET IFEFFIT_DIR=C:\Program Files\Ifeffit > > MN> Could the space in the file name be a problem for Windows98 but > MN> not Win2000??? If so, maybe adding quotes will do it: > MN> SET IFEFFIT_DIR='C:\Program Files\Ifeffit' > > I just wanted to say that if the solution to your problem is, indeed, > adding quotes to the .bat files, please let us know so we can do so in > the next version of the installer package. Of course, if the solution > is something else entirely, let us know that also ;-) > > 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: Questions about IFEFFIT and Windows 98
by Matt Newville 07 Feb '03

07 Feb '03

Hi Kristine, On Thu, 6 Feb 2003 krk511(a)casbah.it.northwestern.edu wrote: > Matt, > > I'm trying to get IFEFFIT to work on a Windows 98 machine and I'm trying to > figure out what my options are. (Currently the three machines I use at > Northwestern, home, and Argonne are all Win 98.) > > I've installed IFEFFIT, and did some original changes to correct the "Out of > environment space" problem, now I have a: "Too many parameters Too many > parameters - Files\Ifeffit Bad command or file name " problem. > > I'm looking for suggestions. Just to be sure, I believe the 'Out of environent space problem' on Windows98 can be solved by putting SHELL=C:\COMMAND.COM /E:4096 /P in the config.sys file. Is that right? I thought the 'Too many parameters - Files\Ifeffit Bad command or file name' message was somehow related to that, but maybe not. If not, it may be due to a mistake in the files C:\Program Files\Ifeffit\xxxx.bat (xxx = athena, artemis, ifeffit, sixpack,....) which all have this line: @echo off SET IFEFFIT_DIR=C:\Program Files\Ifeffit Could the space in the file name be a problem for Windows98 but not Win2000??? If so, maybe adding quotes will do it: SET IFEFFIT_DIR='C:\Program Files\Ifeffit' To be honest, I'm not sure, but it's probably something simple like that. Anyone else know how to do this or have ifeffit/athena working on Windows 98? Thanks, --Matt

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A question ...
by Bruce Ravel 06 Feb '03

06 Feb '03

Hi folks, Matt and I are wondering what everyone's opinion is of the Windows installer package. We are concerned that it's huge size is an impediment to you, the users. The installer file is currently over 23 Mb and the full installation is using up over 56 Mb of your disk-space. A significant amount of that is for things like documentation and example files that could be (and in many cases are) found on the web. We are worried about people who are not in North America (as are Matt and I) or about people who do not have high bandwidth internet connections. So, we want to solicit some opinions from the windows users about the installer package. Should we: 1. Release the full, huge installer once per year or less and release smaller patches to the base installation as needed? 2. Release the huge installer, but allow more control over which components get installed? 3. Continue doing what we have been doing? 4. Try to find volunteers to set up mirrors on other continents? Feel free to offer any suggestions you might have about these distribution issues to this list or to Matt or I privately. 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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new version of Athena and new Windows installer package
by Bruce Ravel 06 Feb '03

06 Feb '03

Hi Folks, There is a new version of Athena (0.8.013) ready for use. Along with several small bug fixes are significant improvements to Athena's (but, sadly, not Artemis's) documentation. Because the new documentation involves lots of external files, there is a new version of the big Windows installer on Matt's web site. Unix and OSX people should grab the latest source code tarball from my web site. Windows people should grab the latest installer package from Matt's web site. Along with some work on the on-line document, I have written a selection of demos for Athena. The demos are project files with data that demonstrates some feature of Athena and Ifeffit and uses the journal space to provide an explanation and suggestions for things to try to better understand the demonstrated feature. You can browse the demo projects by selecting the appropriate item from the Help menu. When you read in a project that way, the journal will automatically open up so you can start reading about the feature being demonstrated. For many of you on this list, the demos probably explain things with which you are already familiar. But check them out -- you may learn about a feature you didn't know about. And, as you introduce new users to Athena, point them in the direction of the demo projects. 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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RE: [Ifeffit] athena 0.9.012 + an updater utility
by Kelly, Shelly D. 30 Jan '03

30 Jan '03

Hi Bruce, I believe that the set edge step button is broken in Athena when the Clnorm background is used. To reproduce this error: 1 read in a xmu data set 2 set the background to clnorm and plot the normalized bkg. 3 push the set step height button and change the value. 4 replot the background and watch the set height value go back to the original value. If you need a project file let me know. Shelly > -----Original Message----- > From: Bruce Ravel [mailto:ravel@phys.washington.edu] > Sent: Thursday, January 30, 2003 10:21 AM > To: ifeffit mailing list > Subject: [Ifeffit] athena 0.9.012 + an updater utility > > > > Hi folks, > > I just release a new version of Athena, a new Windows executable for > Athena, and a new source code tarball. You can find them in the > normal places. There are only two new things, but they are both > pretty important. > > 1. Fixed a serious bug in how Athena handles filenames with long, > similar names. There was a problem in how Athena was translating > long filenames into ifeffit group names that could lead to very > broken behavior. > > 2. For unix and Mac users, I wrote a perl script called > "horae_update" which gets installed upon installation into > /usr/local/bin (or wherever athena and artemis go). The purpose > of this script is to automate updating athena and artemis to the > very latest versions. It fetches the latest source code tarball > from the web, unpacks it, builds it, and (if you run it as root) > installs it. Very handy. > > The updater is only loosely tested, so I am eager for feedback > from people, and particularly from the OSX crowd. It seems to > work ok for me and makes updating the codes a snap. > > I plan to write a similar program for Windows users soon. My plan > is to have a button in the Ifeffit menu on the Start Menu that > says something like "Update Athena and Artemis". Clicking it will > fetch and install the latest Windows executables. I'll make an > announcment here when it is ready. > > 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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athena 0.9.012 + an updater utility
by Bruce Ravel 30 Jan '03

30 Jan '03

Hi folks, I just release a new version of Athena, a new Windows executable for Athena, and a new source code tarball. You can find them in the normal places. There are only two new things, but they are both pretty important. 1. Fixed a serious bug in how Athena handles filenames with long, similar names. There was a problem in how Athena was translating long filenames into ifeffit group names that could lead to very broken behavior. 2. For unix and Mac users, I wrote a perl script called "horae_update" which gets installed upon installation into /usr/local/bin (or wherever athena and artemis go). The purpose of this script is to automate updating athena and artemis to the very latest versions. It fetches the latest source code tarball from the web, unpacks it, builds it, and (if you run it as root) installs it. Very handy. The updater is only loosely tested, so I am eager for feedback from people, and particularly from the OSX crowd. It seems to work ok for me and makes updating the codes a snap. I plan to write a similar program for Windows users soon. My plan is to have a button in the Ifeffit menu on the Start Menu that says something like "Update Athena and Artemis". Clicking it will fetch and install the latest Windows executables. I'll make an announcment here when it is ready. 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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minimize function
by Kelly, Shelly D. 28 Jan '03

28 Jan '03

Hi, I would like to use the minimize function to fit a line to some data points. I could not find documentation on the r-square factor that is referred to as the confidence level for the fit. Thanks Shelly

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Ifeffit 1.0076
by Matt Newville 27 Jan '03

27 Jan '03

Happy New Year Everyone, I've just posted a new release of Ifeffit: 1.0076. This has many small fixes and added features, including: - fixed plotting bug in which all legends were not always shown - added 'unguess' command - added 'window' command (generate an FT window without actually doing the FT) - fixed a bug in reading 1-row data files - allow (consistently) '&', ':', and '?' in variable and group names - added the math functions nofx(), join(), and slice() for array manipulations - further tweaks to configuration procedure. There are a few more details are in the ChangeLog. I hope to get changes to the Reference Manual posted within a week. The Windows installer now includes the current versions of Athena, Artemis, Atoms, SixPack, and GIFEFFIT. I have not tried this version on Mac OS X. The installation using Fink and PGPLOT (not to mention Perl/Tk for Athena and Artemis) on Mac OS 10.2 seems especially fragile. For future work, the changes at the top of my list include: - adding an automated way to have feffit() apply more than 1 k-weight at a time, to help overcome the k-dependent biases due to the high correlations of XAFS parameters. - trying to improve the pre-edge subtraction and normalization algorithms. - getting the docs up-to-date. - working on changing the interface of Feff6 so that it can be included in Ifeffit. The still seem to be unresolved issues with QEXAFS data, and probably other things that should be done. Suggestions for improvements or added features are welcome. In fact, I'd like to ask everyone to think about what features you'd like to see added or changed. Thanks, --Matt Newville

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athena 0.8.010
by Bruce Ravel 15 Jan '03

15 Jan '03

Hi folks, The release I made of my software last week was riddled with problems. While I think the Windows executable was ok, the source code tarball for use on linux and Mac OSX was horribly broken. Thanks to helpful interactions with Paul Fons, Jeff Terry, and Shelly Kelly I think I have ironed out all the problems. This release, therefore, is mostly a bug-fix release. The only new bit of functionality this time involves some changes to how derivative spectra are plotted. There are no changes to artemis in this release. The source code and the new Windows executable for athena 0.8.010 are in their normal locations. If you use the source code, you should be running at least version 1.0072 (which dates all the way back to June 2002) of ifeffit. If you ifeffit is older than that, you should upgrade to the latest from Matt's website before installing athena and artemis. 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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trouble, trouble, trouble
by Bruce Ravel 10 Jan '03

10 Jan '03

Hi folks, The release I made yesterday seems to be the buggiest one I have released in quite some time. I have been getting lots of reports of problems with the latest source code tarball. Sigh. I am working on a new release -- hopefully things will be looking better on Monday. If anyone needs a copy of the previous release, you can grab it at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/horae-00… The entire archive of old versions is at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/ Sorry for the confusion and thanks especially to Jeff Terry, Paul Fons, and Shelly Kelly who have been very generous with their time and their useful bug reports. 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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Athena 0.8.009
by Bruce Ravel 09 Jan '03

09 Jan '03

Hi Folks, Since it has been almost a month since my last release of software and since I expect to be busy for the next couple of week, I decided to release all the stuff I worked on over the holidays. There are no changes to Artemis this time, but lots of changes to Athena. A new tarball and a new Windows executable for Athena are on my website. Lots of bug fixes this time, so I recommend that everyone upgrade. Check out the change log on my web page for all the new stuff. The highlights are 1. Fixed the problem involving long file names. Now the group name used by Ifeffit is constrained to 8 characters and is different from the string displayed in the groups list. This solves a number of recent complaints about mysterious misbehavior. It has the additional benefit of allowing you to change the string displayed in the group list to something that has spaces or non-alphanumeric characters. 2. Implemented a "recent files" feature under the File menu. This remembers the 8 most recent files that you read into Athena and allows you to reread them quickly. It uses an external file, so it "remembers" between sessions with Athena. 3. Added a dialog accessible from the Plot menu which allows you to quickly and easily set the y-offset values for marked groups in a way that is suitable for stacked plots. There are several other bug fixes and small improvements. And the documentation lags ever farther behind -- sigh! Extra thanks this time around to Dale Brewe. He pointed out an alarming number of problems one December afternoon while I was working at his beamline. I think I fixed all of them. Regards, B P.S. I have not yet addressed the problem in Artemis which Michel Schlegel pointed out earlier this week. What's mpre, command line users will notice that Artemis spits up a cryptic warning about an "Un-named file" as it starts up. I believe that warning can be safely ignored. -- 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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athena, OS X, and Apple's new X11
by Jeff Terry 09 Jan '03

09 Jan '03

Hi All, I just wanted to let everyone know that Artemis, Athena, and tkAtoms work with Apple's new implementation of X11. Jeff

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a problem with windows on Windows ...
by Bruce Ravel 07 Jan '03

07 Jan '03

Hi all, Michel Schlegel pointed out that there is a problem in the most recent version of Artemis wherein the Fourier transform window does not get properly displayed. Oddly, I could only reproduce this problem on Windows and not on my linux machine. So, for you Windows users -- you will either have to live without plots of window functions until I can get around to finding and fixing the bug or you may want to consider not upgrading Artemis until the next version. This window problem does *not* seem to be an issue for Athena either on Windows or on linux. When I release a version of Artemis that fixes this problem, I will, as usual, make an announcement here. Happy New Year! 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: Plots of apodization Windows in Athena 0.8.005 and artemis.0. 5.004
by SCHLEGEL Michel 177447 07 Jan '03

07 Jan '03

Hello, > I hope you don't mind that I am sending my responses to your questions > to the Ifeffit mailing list. They seem of sufficiently general > interest that I think the Ifeffit list would be interested. I don't. :) > MS> Another detail which kind of puzzles me: whenewever I use a > MS> Kaiser-Bessel window and increase the weight, the *plotted* > MS> limits of the apodization window shift away from the positions > MS> defined in the command window (e.g., for positions set to 2 and > MS> 13 Å-1 in the command window and a weight dk = 1, the plotted > MS> apodization limits are shifted to 1 and 14 Å-1). > > I am a bit confused by the numbers you give in that they are not > consistent with what I observe when I make a plot displaying a > Kaiser-Bessel window. Here is what I observe: > > For a window defined by kmin=2, kmax=18, and dk=2, the first > non-zero value of the window is at k=1 and the last non-zero value > is at k=19. In general terms, the first non-zero value of the > Kaiser-Bessel window is at kmin-dk/2 and the last is at kmax+dk/2. OK, I wanted to make the distinction between the first and last non-zero values as they *appear* in the graphic window, and the numerical values as stored as internal values in the software. I assumed that these values were not the same. This assumption, but was -partly - justified by the wollowing reason: If I keep kmin and kmax constant and increase dk, I increase the k-range covered by the K.B. window, and this should result in an increase of the number of independent points. What I observe is that the number of independent points calculated by artemis is *not* affected by dk, suggesting that the FT range remains limite to [kmin, kmax]. > The bottom line is that you may want to set kmin a bit higher so that > kmin-dk/2 is at the point where you want the window to start. Note > that setting dk to 0 is probably *not* what you want to do, although > it is probably worth doing so just once to see what happens to the K-B > window. I did: the first and last non-zero values plot exactly at kmin and kmax. > MS> A final 'cosmetic' suggestion: would it be possible in future > MS> versions of artemis, to plot both the amplitude and real part, or > MS> amplitude and imaginary parts of experimental and simulated > MS> chi(R) together? > > > You are not the first person to ask for this, Michel, but the last > time this came up, Artemis was much less far along. Sorry for being late... > So, let me put it up to discussion among the folk on this mailing > list. What should Artemis do? > > 1. Allow the user to select one or more parts of chi(R) (or chi(q) > for that matter) and plot each of those parts for each of the > things selected in the "Paths" list. > 2. Allow the user to somehow specify which parts of chi(R) to plot > for the data, the fit, and each path individually. (This would > make the interface somewhat more complex.) > 3. Continue to work exactly as it works now. > 4. Something else entirely. Basically in a simulation, both the amplitude and the phase of selected paths may be (shoud be?) compared. Therefore, I would select (1) (but let me reiterate that this is not a priority to me). Thanks in advance, and happy new year, Michel Schlegel

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Plots of apodization Windows in Athena 0.8.005 and artemis.0.5.004
by Bruce Ravel 06 Jan '03

06 Jan '03

Michel, I hope you don't mind that I am sending my responses to your questions to the Ifeffit mailing list. They seem of sufficiently general interest that I think the Ifeffit list would be interested. MS> I used artemis.0.5.004 to open a project created with MS> artemis.0.5.002. I noticed that the apodization window didn't MS> plot correctly in the R-space (i.e., it is just a red flat line MS> instead of a cathedral door-like shape), eventhough I checked the MS> 'Window' box as a plotting option. Hmm... that certainly seems like a problem, but I am not certain which problem. Unlike the Athena project files, the Artemis project files do not currently contain the data, they only contain a pointer to the data. It is possible that the data moved, that you are on another computer, or for some other reason the path and file listed in your project file just don't point to the correct thing. If you select "Change data file" from the "Data" menu and refresh the location of the data, does that solve the problem? If not, you should prepare a bug report as described at http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html so I can figure out what is really going on. MS> Another detail which kind of puzzles me: whenewever I use a MS> Kaiser-Bessel window and increase the weight, the *plotted* MS> limits of the apodization window shift away from the positions MS> defined in the command window (e.g., for positions set to 2 and MS> 13 Å-1 in the command window and a weight dk = 1, the plotted MS> apodization limits are shifted to 1 and 14 Å-1). I am a bit confused by the numbers you give in that they are not consistent with what I observe when I make a plot displaying a Kaiser-Bessel window. Here is what I observe: For a window defined by kmin=2, kmax=18, and dk=2, the first non-zero value of the window is at k=1 and the last non-zero value is at k=19. In general terms, the first non-zero value of the Kaiser-Bessel window is at kmin-dk/2 and the last is at kmax+dk/2. The ultimate reference is, I suppose, the source code. In the src/lib/ folder of the ifeffit source directory, you will find the source code file "window.f". The first and last non-zero values for this and several other window types are defined around line 123. (Note that the comments at the top of the file regarding the K-B window are incorrect in that they contradict the code around lines 123.) The exact shape of the window and whether it falls all the way to zero is determined by some parameters computed from kmin, kmax, and dk and by the evaluation of a Bessel's function. This is all around line 167. The comments in window.f suggest this as a reference for the K-B window: 'Digital Filter' by J.F. Kaiser in 'System Analysis by Digital Computers' edited by F.F. Kuo and J.F. Kaiser, (New York; Wiley) 1966 The bottom line is that you may want to set kmin a bit higher so that kmin-dk/2 is at the point where you want the window to start. Note that setting dk to 0 is probably *not* what you want to do, although it is probably worth doing so just once to see what happens to the K-B window. MS> A final 'cosmetic' suggestion: would it be possible in future MS> versions of artemis, to plot both the amplitude and real part, or MS> amplitude and imaginary parts of experimental and simulated MS> chi(R) together? You are not the first person to ask for this, Michel, but the last time this came up, Artemis was much less far along. I suppose that it is time to revisit this issue. The reason that Artemis does not currently let you plot more than one part of chi(R) at a time is because it is so very easy to plot the data, the fit, the background spline, and any number of paths with a single mouse click. Already, that can make for an absurdly busy plot. If Artemis plotted *two* parts of each item, the plot would be twice as busy and twice as much of a mess. I suppose, though, that I should not be worried about that. That is, I shouldn't put too many limitations on what you can plot. If you choose to plot an unreadable number of traces, I should certainly let you do so! However, the situation gets more confusing as you allow more possible combinations of traces. For example, it might be reasonable to plot the amplitude and real part of the data and fit along with just the real parts of some of the paths. And so on... So, let me put it up to discussion among the folk on this mailing list. What should Artemis do? 1. Allow the user to select one or more parts of chi(R) (or chi(q) for that matter) and plot each of those parts for each of the things selected in the "Paths" list. 2. Allow the user to somehow specify which parts of chi(R) to plot for the data, the fit, and each path individually. (This would make the interface somewhat more complex.) 3. Continue to work exactly as it works now. 4. Something else entirely. Let me know! Happy New Year to all! B -- Bruce Ravel ----------------------------------- ravel@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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Athena 0.8.008 and Artemis 0.5.004
by Bruce Ravel 13 Dec '02

13 Dec '02

Hi Folks, I just uploaded new source code tarballs and new windows executables for the two programs to my web site. This release is mostly about bug fixes. You can read about those in the change logs. Athena has two big new features. 1. A dialog for fitting Gaussians/Lorentzians and an arctangent to near-edge peaks. See the "Analysis" menu. It is currently undocumented, but you should be able to figure it out by poking at the buttons. Here's a screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/pea… 2. An option at the bottom of the "Edit" menu for generating reports about the background removal and FT parameters for all the data groups. The options for these reports are plain text, Excel spreadsheet files, or comma-separated-value (csv) spreadsheets. The other new thing, which is relevant to Unix and Mac OSX users is a change to the build scripts. I have modified the Makefile.PL to incorporate a suggestion Matt had for avoiding the problems that several people reported this week regarding difficulties finding the PGPLOT library during the build of the ifeffit wrapper. The new build script works for me. I trust you will let me know if you have any problems. Special thanks this time to Adam Webb and Paul Fons who both found ways to crash Athena this week. Happily, they will both now have to start searching for new ways. 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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Re: [Ifeffit] Max OS X woes -- Solution ?
by Paul Fons 12 Dec '02

12 Dec '02

Some observations. In conjunction with the initialization file from fink there are path variables set that tell where the fink pgplot directory is (presumably on other Unixes as well). In terms of moving away from pgplot, I have been using a crystallographic library that uses blt (written in tcl) that is an extension to tcl/Tk. This is free and has scientific graphics functionality and also is being continually updated. The web site is: http://sourceforge.net/projects/blt/. The advantage here is that this is a write-once use everywhere library. The downside is that it is in tcl/Tk so you would have to interface via some intermediate code from fortran, but I suspect Bruce knows a lot more about Tk than I. The blurb on sourceforge states: The BLT Toolkit is an extension to Tcl and Tk. It adds new commands and widgets to the Tcl interpreter. Included widgets are 2D graph, barchart, stripchart, tab notebook, and tree viewer. Also in looking over the fink list, there is a gnu library called plotlibs (http://www.gnu.org/software/plotutils/) which is a device independent library that outputs in just about every format available. This is callable from fortran or c and also would seem to support a format a windows viewer could use (I think other than a blt/java route windows will always have to be different -- Bill Gates wants it that way) (from the web site) GNU libplot and libplotter support all the output formats mentioned above (X11, SVG, PNG, PNM, pseudo-GIF, WebCGM, Illustrator format, idraw-editable Postscript, PCL 5, Fig format, HP-GL/2, ReGIS, Tektronix, and GNU Metafile). They can produce animated pseudo-GIFs, and smooth, double-buffered animations on any X Window System display. The libplot imaging model is similar to Postscript's. In any output format, they can draw the following. • Graphical objects such as lines, circles and ellipses, points, and marker symbols; also paths. A path is defined as in Postscript as a sequence of line segments, arcs (either circular or elliptic), or Bezier curve segments (either quadratic or cubic). Paths may be open or closed, and they may be dashed. The filling of paths is supported (fill color, as well as pen color, may be set arbitrarily). • Text strings, in many fonts. Text strings may include subscripts and superscripts, and may include characters chosen from more than one font in a typeface. The X11, SVG, WebCGM, Illustrator, Postscript, and xfig drivers support the 35 standard Postscript fonts, and the SVG, Illustrator, PCL 5 and HP-GL/2 drivers support the 45 standard PCL 5 fonts. All drivers support a set of 22 Hershey vector fonts. This includes HersheyCyrillic, a Russian font that uses the KOI8-R encoding, and HersheyEUC, a Japanese font that uses the 8-bit EUC-JP encoding. Japanese text strings may include both syllabic characters (Hiragana and Katakana) and ideographic characters (Kanji). A library of over 600 Kanji is built in. When using libplot or libplotter, a programmer draws vector graphics in a `user frame', rather than in the device frame. As in Postscript, the user frame may be transformed into the device frame by an arbitrary affine map. Scaling, rotation, shearing, and translation are all supported. On Friday, December 13, 2002, at 08:17 AM, Matt Newville wrote: > Bruce, Paul, > >> Solving the problem at the level of ifeffit's build doesn't quite >> address the horae problem. The whole point of putting Ifeffit.pm and >> the wrapper in the horae tarball was one-stop shopping for perl-y >> goodness. However, it may suffice if the ifeffit C program, when >> invoked with a --pgplot_dir command line flag, writes the location of >> pgplot to STDOUT and exits. Then I could use perl's exec command in >> the Makefile.PL to set the compiler's -L flag properly. I normally >> avoid exec because I don't understand how it works on Windows. But I >> don't have Makefile.PL compile the wrapper on Windows, so it should be >> ok. > > See, I think ifeffit's build *should* solve horae's problem on > Unixes (Mac OS X included). Windows is inherently different. On > Unix, the issue of how to link to Ifeffit lib, PGPLOT lib (any > extra libs like X, png, ...) and generic C libs on any particular > machine are all fully determined when Ifeffit's Makefile is run. > > So Ifeffit's build can write all the needed build info without > relying on ExtUtils::F77, OS-specific switches, or any hardwired > values. In fact, an easily parsed Config.mak is built and > installed. In perl, this could be used like this: > > $iff_path = `ifeffit -i`; > chomp $iff_path; > $iff_path =~ s/ $//g; > $file = "$iff_path/config/Config.mak"; > open(F,$file) or die "no file $file .. Ifeffit not installed?\n"; > my @keys = ('LIB_IFF','LIB_PLT','LIB_F77','INC_IFF'); > my %build; > while(<F>){ > chomp; > foreach $i (@keys) { > if (/^$i[ ]*=(.*)/) { $build{$i} = $1;} > } > } > close(F) > foreach $i (@keys){ print "$i: $build{$i}\n";} > > I'm sure it could be done more elegantly... But Ifeffit's build > should be fixed to make sure it finds /sw/lib/pgplot and not > /sw/pgplot for PGPLOT on MacOS X. > >> Actually fink is way better than RPM. (More precisely, debian's >> apt-get is way better than RPM. Fink's cleverness was to use apt-get >> but the credit for an amazing packaging system goes to those clever >> debian folks.) > > I can agree that Fink is clever, and that apt is more clever than > RPM. I may even agree that apt is _better_ than RPM. That's not > high praise. All binary package systems are painful. Like, Fink > can just up and decide to move PGPLOT, and we're screwed. > >> And, yes, pgplot is a thorn in my side. Adam Webb at the U of >> Alberta had the linux equivalent of this problem the other day. > > What was the linux problem? PGPLOT_install should work fine on > all linuxes. Or did Adam do something silly like rely on a > binary package from debian... Oh, wait a second. > > I'd much prefer a plotting lib that could be built with ifeffit, > not relying on a separate library, and worked better on Windows. > I'd be willing to use python/blt myself, but some people still > like perl, so something that works in C/Fortran is needed. > PLPLOT is a possibility, so is using R, or wxWindows. PLPLOT is > the most like PGPLOT, but less stable than PGPLOT (no, really), > but at least they're working on it. R is straight C (GPL'ed), > and probably a LOT of work to use, but makes lovely plots. > > --Matt > > Paul Fons, Ph.D. Senior Staff Researcher Photonics Institute National Institute for Advanced Industrial Science & Technology Tsukuba, JAPAN 305-8568 email: paul-fons(a)aist.go.jp tel. +81-298-61-5636 fax: +81-298-61-5615 The lines below are in Japanese 主任研究官　ポール・フォンス産業技術総合研究所光技術研究部門つくば市茨城県　 305-8568

1 0

more Max OS X woes!
by Matt Newville 12 Dec '02

12 Dec '02

Maurizio, Patrick, everyone, It appears there are some serious problems getting the latest 'Ifeffit/Athena' running on Max OS X -- both 10.1 and 10.2. The sympton is gettting messages like dyld: perl Undefined symbols: _pgarro_ _pgask_ which means the Ifeffit perl module is no longer able to find the PGPLOT library. When this happens, older versions of athena are also broken. My guess is that this is related to the changes in horae's Makefile.PL for horae-007, but I haven't looked into it any further. I believe the workaround is to go back to the Ifeffit source distribution and reinstall the ifeffit perl module from there: cd ...../ifeffit_1.0b/wrappers/perl perl Makefile.PL make make install and then back-tracking to horae-006.tar.gz: http://feff.phys.washington.edu/~ravel/software/exafs/packages/horae-006.ta… At least, this worked on Patrick's laptop last week. It might be enough to simply backtrack to horae-006. Sorry for all the trouble, --Matt On Wed Dec 11, Maurizio Aiello <aiello(a)ge.cnr.it> wrote: > > Dear Matt, > I tried to install ona fresh Mac-osX 10.1.4 athena. I followed all steps > necessary, (it required ten hours of continuous compilation) for installing > everything. I replaced dynamic loader with the patched one, and in fact > now I dont' have multiple definition error. But when i run perl -e "use > ifeffit" or I run from within an xterm in Xdarwin the command athena the > answer is: > > [localhost:~] marzia% perl -e "use ifeffit" > dyld: perl Undefined symbols: > _pgarro_ > _pgask_ > ..... > > > If I substitute dyld with the original one now the error is (of course) > [localhost:~] marzia% athena > dyld: perl multiple definitions of symbol _LangExit > /Library/Perl/darwin/auto/Tk/Event/Event.bundle definition of _LangExit > /Library/Perl/darwin/auto/Tk/Tk.bundle definition of _LangExit > > > If I run ifeffit directly from command line it seems to work correctly. > > Can you help me? > Thanks a lot. > > P.S. I am a Unix-Network programmer, I'm doing this job for my wife, she is > a researcher. I don't have any knowledge on what these programs do, I only > compile and debug and so on :-)))) > > Thanks a lot > > Maurizio Aiello On Wed Dec 11, Patrick Allen <allen42(a)llnl.gov> wrote: > > This is entirely FYI: I couldn't resist and got Jaguar 10.2.2 going now. > I reinstalled nearly every package I could think of and got very close > with Athena and get the message: > > dyld: perl Undefined symbols: > _G77_getenv_0 > _pgarro_ > _pgask_ > _pgband_ > _pgbbuf_ > _pgbox_ > etc..... > Trace/BPT trap > > So for the moment, I chickened out and downloaded the whole darn thing > onto my Virtual PC partition on OSX. It works and I can play with my > PNC-CAT files with the latest programs. I'm looking forward to coming out to > Chicago more now. Seasons greetings!

3 3

occupancy numbers vs stochiometry with TkAtoms
by John J. Rehr 11 Dec '02

11 Dec '02

Hi Bruce, I have an inquiry about the Li XANES of a Li silicate Li4SiO4 with the following atoms.inp input file: ------------------------------------------------- title name: Li4SiO4 monoclinic structure title sites1: Si, O1-3, Li1-6 space = P 21/M a=5.14 b=6.10 c=5.30 beta=90.5 core = Li atoms # elem. x y z tag occ Si 0.6640 0.25 0.3252 Si 1. O 0.7737 0.0303 0.1842 O1 1. O 0.3526 0.25 0.3178 O2 1. O 0.7677 0.25 0.6210 O3 1. Li 0.165 0.009 0.174 Li1 0.667 Li 0.398 0.25 0.711 Li2 0.50 Li 0.164 0.25 0.644 Li 0.50 Li 0.398 0.964 0.150 Li4 0.333 Li 0.048 0.034 0.449 Li5 0.333 Li 0.057 0.25 0.981 Li6 0.334 ------------------------------------------------- The "confusing" thing, to me at least, is how TkAtoms interprets the occupation numbers, since the feff8 template gives the wrong stoichiometry for Li (should be identical to that for O, i.e. 8). POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 3 Li 1 1 0.001 1 14 Si 2 2 2 2 8 O 1 1 8 3 3 Li 1 1 18 Questions: 1) what is the recommended procedure for lattices with non-integer occupation? The Atoms documentation seems not very specific on this point, though it does emphasize the "confusing" aspects of the problem and the fact that it is easy to generate nonsense feff.inp. For example I could edit the feff.inp file that is generated and cut out *arbitrarily* some fraction of the atoms of a given tag, e.g., 2/3 of the Li1s, 1/2 of the Li2s, etc. But I also must edit the stoichiometry so the potentials come out right. But this procedure does seem arbitrary. Also, it appears that the Li atoms in this material are not all distinguishable so one has to take a linear combination FEFF runs for the different input Li sites. 2) can TkAtoms take the occupancy into account in determining the stoichiometry? Thanks much for your comments on this. Cheers, John Rehr The full feff.inp file is attached: * This feff8 input file was generated by TkAtoms 3.0beta7 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: Li4SiO4 monoclinic structure TITLE sites1: Si, O1-3, Li1-6 * Li K edge energy = 54.70 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 4.11922 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 10.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 3 Li 1 1 0.001 1 14 Si 2 2 2 2 8 O 1 1 8 3 3 Li 1 1 18 ATOMS * this list contains 720 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Li6 0.00000 0 0.55510 1.47010 1.01806 3 Li1 1.87237 1 0.55510 -1.47010 1.01806 3 Li1 1.87237 2 0.54996 0.00000 -1.79090 3 Li 1.87344 3 -1.14104 1.57990 -0.81154 3 Li1 2.11108 4 -1.14104 -1.57990 -0.81154 3 Li1 2.11108 5 0.87017 1.70983 -0.88315 2 O1 2.11203 6 0.87017 -1.70983 -0.88315 2 O1 2.11203 7 -1.45611 1.34017 1.08967 2 O1 2.25913 8 -1.45611 -1.34017 1.08967 2 O1 2.25913 9 1.75267 0.00000 -1.44630 3 Li2 2.27236 10 1.51933 0.00000 1.77178 2 O2 2.33400 11 -1.48695 0.00000 -1.89502 2 O3 2.40876 12 1.75267 1.74460 0.88040 3 Li4 2.62500 13 1.75267 -1.74460 0.88040 3 Li4 2.62500 14 -2.01994 0.00000 1.84189 1 Si 2.73363 15 -2.33861 1.30540 -0.67389 3 Li4 2.76176 16 -2.33861 -1.30540 -0.67389 3 Li4 2.76176 17 -0.04626 1.31760 2.48080 3 Li5 2.80938 18 -0.04626 -1.31760 2.48080 3 Li5 2.80938 19 -0.53968 1.73240 -2.27429 3 Li5 2.90944 20 -0.53968 -1.73240 -2.27429 3 Li5 2.90944 21 -0.04626 1.31760 -2.81920 3 Li5 3.11225 22 -0.04626 -1.31760 -2.81920 3 Li5 3.11225 23 -0.58594 3.05000 0.20651 3 Li6 3.11263 24 -0.58594 -3.05000 0.20651 3 Li6 3.11263 25 2.80119 1.30540 -0.71875 3 Li4 3.17291 26 2.80119 -1.30540 -0.71875 3 Li4 3.17291 27 -0.53968 1.73240 3.02571 3 Li5 3.52808 28 -0.53968 -1.73240 3.02571 3 Li5 3.52808 29 0.54996 0.00000 3.50910 3 Li 3.55193 30 3.11986 0.00000 1.79703 1 Si 3.60040 31 -3.38713 0.00000 -1.40144 3 Li2 3.66561 32 -1.48695 0.00000 3.40498 2 O3 3.71549 33 1.43401 3.05000 -1.63537 1 Si 3.74611 34 1.43401 -3.05000 -1.63537 1 Si 3.74611 35 0.90101 3.05000 2.10154 2 O3 3.81193 36 0.90101 -3.05000 2.10154 2 O3 3.81193 37 -1.13590 3.05000 1.99741 3 Li 3.81869 38 -1.13590 -3.05000 1.99741 3 Li 3.81869 39 1.51933 0.00000 -3.52822 2 O2 3.84144 40 -3.38713 1.74460 0.92526 3 Li4 3.92076 41 -3.38713 -1.74460 0.92526 3 Li4 3.92076 42 -2.01994 0.00000 -3.45811 1 Si 4.00484 43 -2.10526 3.05000 -1.56527 2 O2 4.02302 44 -2.10526 -3.05000 -1.56527 2 O2 4.02302 45 -3.62048 0.00000 1.81664 2 O2 4.05068 46 3.68370 1.34017 1.04481 2 O1 4.05676 47 3.68370 -1.34017 1.04481 2 O1 4.05676 48 3.65286 0.00000 -1.93988 2 O3 4.13600 49 -2.33861 3.05000 1.65281 3 Li2 4.18370 50 -2.33861 -3.05000 1.65281 3 Li2 4.18370 51 1.75267 0.00000 3.85370 3 Li2 4.23354 52 3.99877 1.57990 -0.85640 3 Li1 4.38402 53 3.99877 -1.57990 -0.85640 3 Li1 4.38402 54 2.80119 3.05000 1.60795 3 Li2 4.44238 55 2.80119 -3.05000 1.60795 3 Li2 4.44238 56 0.90101 3.05000 -3.19846 2 O3 4.51049 57 0.90101 -3.05000 -3.19846 2 O3 4.51049 58 0.55510 1.47010 -4.28194 3 Li1 4.56118 59 0.55510 -1.47010 -4.28194 3 Li1 4.56118 60 0.87017 4.39017 -0.88315 2 O1 4.56188 61 0.87017 -4.39017 -0.88315 2 O1 4.56188 62 3.03454 3.05000 -1.61012 2 O2 4.59385 63 3.03454 -3.05000 -1.61012 2 O2 4.59385 64 -1.13590 3.05000 -3.30259 3 Li 4.63679 65 -1.13590 -3.05000 -3.30259 3 Li 4.63679 66 -1.45611 1.34017 -4.21033 2 O1 4.65223 67 -1.45611 -1.34017 -4.21033 2 O1 4.65223 68 -4.26964 1.70983 -0.83830 2 O1 4.67505 69 -4.26964 -1.70983 -0.83830 2 O1 4.67505 70 3.11986 0.00000 -3.50297 1 Si 4.69087 71 -1.14104 4.52010 -0.81154 3 Li1 4.73200 72 -1.14104 -4.52010 -0.81154 3 Li1 4.73200 73 0.55510 4.62990 1.01806 3 Li1 4.77290 74 0.55510 -4.62990 1.01806 3 Li1 4.77290 75 1.75267 4.35540 0.88040 3 Li4 4.77666 76 1.75267 -4.35540 0.88040 3 Li4 4.77666 77 0.87017 1.70983 4.41685 2 O1 4.81552 78 0.87017 -1.70983 4.41685 2 O1 4.81552 79 -1.14104 1.57990 4.48846 3 Li1 4.89329 80 -1.14104 -1.57990 4.48846 3 Li1 4.89329 81 -4.58985 0.00000 -1.74605 3 Li 4.91074 82 -4.58471 1.47010 1.06291 3 Li1 4.93057 83 -4.58471 -1.47010 1.06291 3 Li1 4.93057 84 -0.53968 4.36760 -2.27429 3 Li5 4.95374 85 -0.53968 -4.36760 -2.27429 3 Li5 4.95374 86 3.65286 0.00000 3.36012 2 O3 4.96324 87 1.43401 3.05000 3.66463 1 Si 4.97879 88 1.43401 -3.05000 3.66463 1 Si 4.97879 89 -3.62048 0.00000 -3.48336 2 O2 5.02411 90 -3.70580 3.05000 -1.59052 1 Si 5.05620 91 -3.70580 -3.05000 -1.59052 1 Si 5.05620 92 1.75267 1.74460 -4.41960 3 Li4 5.06442 93 1.75267 -1.74460 -4.41960 3 Li4 5.06442 94 -1.45611 4.75983 1.08967 2 O1 5.09545 95 -1.45611 -4.75983 1.08967 2 O1 5.09545 96 -5.13980 0.00000 0.04485 3 Li6 5.14000 97 5.13980 0.00000 -0.04485 3 Li6 5.14000 98 -3.38713 0.00000 3.89856 3 Li2 5.16444 99 -2.10526 3.05000 3.73473 2 O2 5.26145 100 -2.10526 -3.05000 3.73473 2 O2 5.26145 101 -2.33861 3.05000 -3.64719 3 Li2 5.29845 102 -2.33861 -3.05000 -3.64719 3 Li2 5.29845 103 0.00000 0.00000 5.30000 3 Li6 5.30000 104 0.00000 0.00000 -5.30000 3 Li6 5.30000 105 -0.53968 4.36760 3.02571 3 Li5 5.34061 106 -0.53968 -4.36760 3.02571 3 Li5 5.34061 107 -2.33861 1.30540 4.62611 3 Li4 5.34547 108 -2.33861 -1.30540 4.62611 3 Li4 5.34547 109 -2.33861 4.79460 -0.67389 3 Li4 5.37693 110 -2.33861 -4.79460 -0.67389 3 Li4 5.37693 111 -0.04626 4.78240 2.48080 3 Li5 5.38775 112 -0.04626 -4.78240 2.48080 3 Li5 5.38775 113 4.00391 3.05000 1.95256 3 Li 5.39873 114 4.00391 -3.05000 1.95256 3 Li 5.39873 115 4.60012 1.73240 -2.31914 3 Li5 5.43514 116 4.60012 -1.73240 -2.31914 3 Li5 5.43514 117 4.55387 3.05000 0.16166 3 Li6 5.48328 118 4.55387 -3.05000 0.16166 3 Li6 5.48328 119 2.80119 1.30540 4.58125 3 Li4 5.52618 120 2.80119 -1.30540 4.58125 3 Li4 5.52618 121 2.80119 3.05000 -3.69205 3 Li2 5.54801 122 2.80119 -3.05000 -3.69205 3 Li2 5.54801 123 -0.04626 4.78240 -2.81920 3 Li5 5.55170 124 -0.04626 -4.78240 -2.81920 3 Li5 5.55170 125 -3.38713 4.35540 0.92526 3 Li4 5.59449 126 -3.38713 -4.35540 0.92526 3 Li4 5.59449 127 2.80119 4.79460 -0.71875 3 Li4 5.59924 128 2.80119 -4.79460 -0.71875 3 Li4 5.59924 129 -4.23880 3.05000 2.14639 2 O3 5.64596 130 -4.23880 -3.05000 2.14639 2 O3 5.64596 131 3.03454 3.05000 3.68988 2 O2 5.66799 132 3.03454 -3.05000 3.68988 2 O2 5.66799 133 4.60012 1.73240 2.98086 3 Li5 5.74873 134 4.60012 -1.73240 2.98086 3 Li5 5.74873 135 3.68370 1.34017 -4.25519 2 O1 5.78553 136 3.68370 -1.34017 -4.25519 2 O1 5.78553 137 5.09355 1.31760 2.43595 3 Li5 5.79777 138 5.09355 -1.31760 2.43595 3 Li5 5.79777 139 -3.38713 1.74460 -4.37474 3 Li4 5.80126 140 -3.38713 -1.74460 -4.37474 3 Li4 5.80126 141 -4.58985 0.00000 3.55395 3 Li 5.80494 142 -5.18606 1.31760 2.52566 3 Li5 5.91695 143 -5.18606 -1.31760 2.52566 3 Li5 5.91695 144 5.69490 1.47010 0.97320 3 Li1 5.96156 145 5.69490 -1.47010 0.97320 3 Li1 5.96156 146 -0.58594 3.05000 -5.09349 3 Li6 5.96569 147 -0.58594 -3.05000 -5.09349 3 Li6 5.96569 148 5.68976 0.00000 -1.83575 3 Li 5.97858 149 5.09355 1.31760 -2.86405 3 Li5 5.99025 150 5.09355 -1.31760 -2.86405 3 Li5 5.99025 151 -5.18606 1.31760 -2.77434 3 Li5 6.02730 152 -5.18606 -1.31760 -2.77434 3 Li5 6.02730 153 4.00391 3.05000 -3.34744 3 Li 6.04476 154 4.00391 -3.05000 -3.34744 3 Li 6.04476 155 -3.70580 3.05000 3.70948 1 Si 6.06594 156 -3.70580 -3.05000 3.70948 1 Si 6.06594 157 3.99877 4.52010 -0.85640 3 Li1 6.09548 158 3.99877 -4.52010 -0.85640 3 Li1 6.09548 159 0.00000 6.10000 0.00000 3 Li6 6.10000 160 0.00000 -6.10000 0.00000 3 Li6 6.10000 161 -4.23880 3.05000 -3.15361 2 O3 6.10042 162 -4.23880 -3.05000 -3.15361 2 O3 6.10042 163 3.68370 4.75983 1.04481 2 O1 6.10878 164 3.68370 -4.75983 1.04481 2 O1 6.10878 165 -4.26964 4.39017 -0.83830 2 O1 6.18111 166 -4.26964 -4.39017 -0.83830 2 O1 6.18111 167 3.99877 1.57990 4.44360 3 Li1 6.18319 168 3.99877 -1.57990 4.44360 3 Li1 6.18319 169 0.87017 4.39017 4.41685 2 O1 6.28803 170 0.87017 -4.39017 4.41685 2 O1 6.28803 171 6.00997 1.70983 -0.92801 2 O1 6.31700 172 6.00997 -1.70983 -0.92801 2 O1 6.31700 173 -0.58594 3.05000 5.50651 3 Li6 6.32199 174 -0.58594 -3.05000 5.50651 3 Li6 6.32199 175 0.55510 4.62990 -4.28194 3 Li1 6.33081 176 0.55510 -4.62990 -4.28194 3 Li1 6.33081 177 -5.67948 1.73240 -2.22944 3 Li5 6.34256 178 -5.67948 -1.73240 -2.22944 3 Li5 6.34256 179 0.54996 6.10000 -1.79090 3 Li 6.38120 180 0.54996 -6.10000 -1.79090 3 Li 6.38120 181 -4.26964 1.70983 4.46170 2 O1 6.40781 182 -4.26964 -1.70983 4.46170 2 O1 6.40781 183 -4.58471 1.47010 -4.23709 3 Li1 6.41355 184 -4.58471 -1.47010 -4.23709 3 Li1 6.41355 185 -1.14104 1.57990 -6.11154 3 Li1 6.41475 186 -1.14104 -1.57990 -6.11154 3 Li1 6.41475 187 1.75267 4.35540 -4.41960 3 Li4 6.44781 188 1.75267 -4.35540 -4.41960 3 Li4 6.44781 189 -1.14104 4.52010 4.48846 3 Li1 6.47144 190 -1.14104 -4.52010 4.48846 3 Li1 6.47144 191 0.87017 1.70983 -6.18315 2 O1 6.47396 192 0.87017 -1.70983 -6.18315 2 O1 6.47396 193 -5.72574 3.05000 0.25137 3 Li6 6.49229 194 -5.72574 -3.05000 0.25137 3 Li6 6.49229 195 1.75267 6.10000 -1.44630 3 Li2 6.50950 196 1.75267 -6.10000 -1.44630 3 Li2 6.50950 197 0.55510 1.47010 6.31806 3 Li1 6.51054 198 0.55510 -1.47010 6.31806 3 Li1 6.51054 199 -1.45611 4.75983 -4.21033 2 O1 6.51944 200 -1.45611 -4.75983 -4.21033 2 O1 6.51944 201 -6.28084 1.57990 -0.76669 3 Li1 6.52172 202 -6.28084 -1.57990 -0.76669 3 Li1 6.52172 203 1.51933 6.10000 1.77178 2 O2 6.53128 204 1.51933 -6.10000 1.77178 2 O2 6.53128 205 -2.33861 1.30540 -5.97389 3 Li4 6.54680 206 -2.33861 -1.30540 -5.97389 3 Li4 6.54680 207 -1.48695 6.10000 -1.89502 2 O3 6.55836 208 -1.48695 -6.10000 -1.89502 2 O3 6.55836 209 -4.58471 4.62990 1.06291 3 Li1 6.60191 210 -4.58471 -4.62990 1.06291 3 Li1 6.60191 211 1.75267 1.74460 6.18040 3 Li4 6.65679 212 1.75267 -1.74460 6.18040 3 Li4 6.65679 213 5.68976 0.00000 3.46425 3 Li 6.66141 214 -2.01994 6.10000 1.84189 1 Si 6.68451 215 -2.01994 -6.10000 1.84189 1 Si 6.68451 216 -5.67948 1.73240 3.07056 3 Li5 6.68477 217 -5.67948 -1.73240 3.07056 3 Li5 6.68477 218 -1.45611 1.34017 6.38967 2 O1 6.68911 219 -1.45611 -1.34017 6.38967 2 O1 6.68911 220 4.60012 4.36760 -2.31914 3 Li5 6.75393 221 4.60012 -4.36760 -2.31914 3 Li5 6.75393 222 2.80119 1.30540 -6.01875 3 Li4 6.76580 223 2.80119 -1.30540 -6.01875 3 Li4 6.76580 224 -6.59591 1.34017 1.13452 2 O1 6.82563 225 -6.59591 -1.34017 1.13452 2 O1 6.82563 226 6.65913 0.00000 1.72693 2 O2 6.87941 227 -6.62675 0.00000 -1.85017 2 O3 6.88018 228 1.75267 0.00000 -6.74630 3 Li2 6.97025 229 4.60012 4.36760 2.98086 3 Li5 7.00875 230 4.60012 -4.36760 2.98086 3 Li5 7.00875 231 -3.38713 4.35540 -4.37474 3 Li4 7.04134 232 -3.38713 -4.35540 -4.37474 3 Li4 7.04134 233 6.89248 0.00000 -1.49115 3 Li2 7.05193 234 0.54996 6.10000 3.50910 3 Li 7.05877 235 0.54996 -6.10000 3.50910 3 Li 7.05877 236 -2.33861 4.79460 4.62611 3 Li4 7.06103 237 -2.33861 -4.79460 4.62611 3 Li4 7.06103 238 6.04081 3.05000 2.05668 2 O3 7.07275 239 6.04081 -3.05000 2.05668 2 O3 7.07275 240 3.11986 6.10000 1.79703 1 Si 7.08328 241 3.11986 -6.10000 1.79703 1 Si 7.08328 242 0.54996 0.00000 -7.09090 3 Li 7.11219 243 -3.38713 6.10000 -1.40144 3 Li2 7.11665 244 -3.38713 -6.10000 -1.40144 3 Li2 7.11665 245 -1.48695 6.10000 3.40498 2 O3 7.14247 246 -1.48695 -6.10000 3.40498 2 O3 7.14247 247 6.89248 1.74460 0.83555 3 Li4 7.15877 248 6.89248 -1.74460 0.83555 3 Li4 7.15877 249 2.80119 4.79460 4.58125 3 Li4 7.19880 250 2.80119 -4.79460 4.58125 3 Li4 7.19880 251 1.51933 6.10000 -3.52822 2 O2 7.20879 252 1.51933 -6.10000 -3.52822 2 O2 7.20879 253 1.51933 0.00000 7.07178 2 O2 7.23315 254 -6.27570 3.05000 2.04227 3 Li 7.27034 255 -6.27570 -3.05000 2.04227 3 Li 7.27034 256 -2.01994 6.10000 -3.45811 1 Si 7.29717 257 -2.01994 -6.10000 -3.45811 1 Si 7.29717 258 -3.38713 1.74460 6.22526 3 Li4 7.29864 259 -3.38713 -1.74460 6.22526 3 Li4 7.29864 260 5.69490 1.47010 -4.32680 3 Li1 7.30166 261 5.69490 -1.47010 -4.32680 3 Li1 7.30166 262 -3.62048 6.10000 1.81664 2 O2 7.32243 263 -3.62048 -6.10000 1.81664 2 O2 7.32243 264 -1.48695 0.00000 -7.19502 2 O3 7.34707 265 5.13980 0.00000 5.25515 3 Li6 7.35079 266 -5.13980 0.00000 -5.25515 3 Li6 7.35079 267 3.65286 6.10000 -1.93988 2 O3 7.36997 268 3.65286 -6.10000 -1.93988 2 O3 7.36997 269 3.68370 4.75983 -4.25519 2 O1 7.37104 270 3.68370 -4.75983 -4.25519 2 O1 7.37104 271 5.09355 4.78240 2.43595 3 Li5 7.39928 272 5.09355 -4.78240 2.43595 3 Li5 7.39928 273 5.69490 4.62990 0.97320 3 Li1 7.40372 274 5.69490 -4.62990 0.97320 3 Li1 7.40372 275 -7.15975 0.00000 1.88674 1 Si 7.40417 276 -5.13980 0.00000 5.34485 3 Li6 7.41519 277 5.13980 0.00000 -5.34485 3 Li6 7.41519 278 -2.01994 0.00000 7.14189 1 Si 7.42204 279 1.75267 6.10000 3.85370 3 Li2 7.42515 280 1.75267 -6.10000 3.85370 3 Li2 7.42515 281 6.57381 3.05000 -1.68023 1 Si 7.43913 282 6.57381 -3.05000 -1.68023 1 Si 7.43913 283 3.68370 1.34017 6.34481 2 O1 7.45804 284 3.68370 -1.34017 6.34481 2 O1 7.45804 285 -6.62675 0.00000 3.44983 2 O3 7.47095 286 -5.18606 4.78240 2.52566 3 Li5 7.49303 287 -5.18606 -4.78240 2.52566 3 Li5 7.49303 288 3.99877 4.52010 4.44360 3 Li1 7.49447 289 3.99877 -4.52010 4.44360 3 Li1 7.49447 290 6.00997 4.39017 -0.92801 2 O1 7.50030 291 6.00997 -4.39017 -0.92801 2 O1 7.50030 292 -5.67948 4.36760 -2.22944 3 Li5 7.50352 293 -5.67948 -4.36760 -2.22944 3 Li5 7.50352 294 6.04081 3.05000 -3.24332 2 O3 7.50420 295 6.04081 -3.05000 -3.24332 2 O3 7.50420 296 -3.38713 0.00000 -6.70144 3 Li2 7.50879 297 3.99877 1.57990 -6.15640 3 Li1 7.50916 298 3.99877 -1.57990 -6.15640 3 Li1 7.50916 299 4.55387 3.05000 -5.13834 3 Li6 7.51284 300 4.55387 -3.05000 -5.13834 3 Li6 7.51284 301 5.09355 4.78240 -2.86405 3 Li5 7.55105 302 5.09355 -4.78240 -2.86405 3 Li5 7.55105 303 6.65913 0.00000 -3.57307 2 O2 7.55717 304 -4.26964 4.39017 4.46170 2 O1 7.57695 305 -4.26964 -4.39017 4.46170 2 O1 7.57695 306 -5.18606 4.78240 -2.77434 3 Li5 7.58047 307 -5.18606 -4.78240 -2.77434 3 Li5 7.58047 308 -7.47842 1.30540 -0.62904 3 Li4 7.61751 309 -7.47842 -1.30540 -0.62904 3 Li4 7.61751 310 6.00997 1.70983 4.37199 2 O1 7.62611 311 6.00997 -1.70983 4.37199 2 O1 7.62611 312 0.87017 4.39017 -6.18315 2 O1 7.63297 313 0.87017 -4.39017 -6.18315 2 O1 7.63297 314 0.55510 7.57010 1.01806 3 Li1 7.65839 315 0.55510 -7.57010 1.01806 3 Li1 7.65839 316 -1.45611 7.44017 1.08967 2 O1 7.65923 317 -1.45611 -7.44017 1.08967 2 O1 7.65923 318 -4.26964 1.70983 -6.13830 2 O1 7.67020 319 -4.26964 -1.70983 -6.13830 2 O1 7.67020 320 -1.14104 4.52010 -6.11154 3 Li1 7.68663 321 -1.14104 -4.52010 -6.11154 3 Li1 7.68663 322 3.11986 6.10000 -3.50297 1 Si 7.69508 323 3.11986 -6.10000 -3.50297 1 Si 7.69508 324 -6.27570 3.05000 -3.25773 3 Li 7.70063 325 -6.27570 -3.05000 -3.25773 3 Li 7.70063 326 1.43401 3.05000 -6.93537 1 Si 7.71092 327 1.43401 -3.05000 -6.93537 1 Si 7.71092 328 4.55387 3.05000 5.46166 3 Li6 7.73757 329 4.55387 -3.05000 5.46166 3 Li6 7.73757 330 3.11986 0.00000 7.09703 1 Si 7.75251 331 1.75267 4.35540 6.18040 3 Li4 7.76136 332 1.75267 -4.35540 6.18040 3 Li4 7.76136 333 -4.58471 4.62990 -4.23709 3 Li1 7.77229 334 -4.58471 -4.62990 -4.23709 3 Li1 7.77229 335 -6.28084 4.52010 -0.76669 3 Li1 7.77612 336 -6.28084 -4.52010 -0.76669 3 Li1 7.77612 337 -0.53968 1.73240 -7.57429 3 Li5 7.78860 338 -0.53968 -1.73240 -7.57429 3 Li5 7.78860 339 -5.67948 4.36760 3.07056 3 Li5 7.79492 340 -5.67948 -4.36760 3.07056 3 Li5 7.79492 341 -2.33861 7.40540 -0.67389 3 Li4 7.79507 342 -2.33861 -7.40540 -0.67389 3 Li4 7.79507 343 -2.10526 3.05000 -6.86527 2 O2 7.80170 344 -2.10526 -3.05000 -6.86527 2 O2 7.80170 345 -1.14104 7.67990 -0.81154 3 Li1 7.80650 346 -1.14104 -7.67990 -0.81154 3 Li1 7.80650 347 -0.04626 7.41760 2.48080 3 Li5 7.82159 348 -0.04626 -7.41760 2.48080 3 Li5 7.82159 349 -4.58985 6.10000 -1.74605 3 Li 7.83105 350 -4.58985 -6.10000 -1.74605 3 Li 7.83105 351 0.55510 4.62990 6.31806 3 Li1 7.85251 352 0.55510 -4.62990 6.31806 3 Li1 7.85251 353 3.65286 6.10000 3.36012 2 O3 7.86408 354 3.65286 -6.10000 3.36012 2 O3 7.86408 355 6.89248 0.00000 3.80885 3 Li2 7.87487 356 -0.04626 1.31760 7.78080 3 Li5 7.89171 357 -0.04626 -1.31760 7.78080 3 Li5 7.89171 358 -3.62048 6.10000 -3.48336 2 O2 7.90264 359 -3.62048 -6.10000 -3.48336 2 O2 7.90264 360 -6.28084 1.57990 4.53331 3 Li1 7.90544 361 -6.28084 -1.57990 4.53331 3 Li1 7.90544 362 0.87017 7.80983 -0.88315 2 O1 7.90763 363 0.87017 -7.80983 -0.88315 2 O1 7.90763 364 -6.59591 1.34017 -4.16548 2 O1 7.91538 365 -6.59591 -1.34017 -4.16548 2 O1 7.91538 366 -7.15975 0.00000 -3.41326 1 Si 7.93173 367 -0.04626 7.41760 -2.81920 3 Li5 7.93541 368 -0.04626 -7.41760 -2.81920 3 Li5 7.93541 369 -2.33861 3.05000 6.95281 3 Li2 7.94438 370 -2.33861 -3.05000 6.95281 3 Li2 7.94438 371 2.80119 7.40540 -0.71875 3 Li4 7.95005 372 2.80119 -7.40540 -0.71875 3 Li4 7.95005 373 -5.13980 6.10000 0.04485 3 Li6 7.97682 374 -5.13980 -6.10000 0.04485 3 Li6 7.97682 375 5.13980 6.10000 -0.04485 3 Li6 7.97682 376 5.13980 -6.10000 -0.04485 3 Li6 7.97682 377 -4.58471 1.47010 6.36291 3 Li1 7.97918 378 -4.58471 -1.47010 6.36291 3 Li1 7.97918 379 -3.62048 0.00000 7.11664 2 O2 7.98463 380 -1.13590 3.05000 7.29741 3 Li 7.99031 381 -1.13590 -3.05000 7.29741 3 Li 7.99031 382 -3.38713 6.10000 3.89856 3 Li2 7.99259 383 -3.38713 -6.10000 3.89856 3 Li2 7.99259 384 -7.24507 3.05000 -1.52041 2 O2 8.00657 385 -7.24507 -3.05000 -1.52041 2 O2 8.00657 386 -2.33861 4.79460 -5.97389 3 Li4 8.00904 387 -2.33861 -4.79460 -5.97389 3 Li4 8.00904 388 2.80119 3.05000 6.90795 3 Li2 8.05413 389 2.80119 -3.05000 6.90795 3 Li2 8.05413 390 0.90101 3.05000 7.40154 2 O3 8.05587 391 0.90101 -3.05000 7.40154 2 O3 8.05587 392 0.00000 6.10000 5.30000 3 Li6 8.08084 393 0.00000 -6.10000 5.30000 3 Li6 8.08084 394 0.00000 6.10000 -5.30000 3 Li6 8.08084 395 0.00000 -6.10000 -5.30000 3 Li6 8.08084 396 7.94100 1.30540 -0.76360 3 Li4 8.08372 397 7.94100 -1.30540 -0.76360 3 Li4 8.08372 398 1.75267 7.84460 0.88040 3 Li4 8.08608 399 1.75267 -7.84460 0.88040 3 Li4 8.08608 400 -1.45611 4.75983 6.38967 2 O1 8.09963 401 -1.45611 -4.75983 6.38967 2 O1 8.09963 402 6.57381 3.05000 3.61977 1 Si 8.10063 403 6.57381 -3.05000 3.61977 1 Si 8.10063 404 3.65286 0.00000 -7.23988 2 O3 8.10921 405 3.03454 3.05000 -6.91012 2 O2 8.14007 406 3.03454 -3.05000 -6.91012 2 O2 8.14007 407 -0.53968 7.83240 -2.27429 3 Li5 8.17375 408 -0.53968 -7.83240 -2.27429 3 Li5 8.17375 409 2.80119 4.79460 -6.01875 3 Li4 8.18903 410 2.80119 -4.79460 -6.01875 3 Li4 8.18903 411 6.89248 4.35540 0.83555 3 Li4 8.19597 412 6.89248 -4.35540 0.83555 3 Li4 8.19597 413 -6.59591 4.75983 1.13452 2 O1 8.21274 414 -6.59591 -4.75983 1.13452 2 O1 8.21274 415 -5.72574 3.05000 -5.04863 3 Li6 8.22042 416 -5.72574 -3.05000 -5.04863 3 Li6 8.22042 417 -0.04626 1.31760 -8.11920 3 Li5 8.22554 418 -0.04626 -1.31760 -8.11920 3 Li5 8.22554 419 -7.47842 3.05000 1.69766 3 Li2 8.25295 420 -7.47842 -3.05000 1.69766 3 Li2 8.25295 421 -3.38713 4.35540 6.22526 3 Li4 8.31841 422 -3.38713 -4.35540 6.22526 3 Li4 8.31841 423 3.68370 7.44017 1.04481 2 O1 8.36764 424 3.68370 -7.44017 1.04481 2 O1 8.36764 425 6.89248 1.74460 -4.46445 3 Li4 8.39531 426 6.89248 -1.74460 -4.46445 3 Li4 8.39531 427 -3.70580 3.05000 -6.89052 1 Si 8.39730 428 -3.70580 -3.05000 -6.89052 1 Si 8.39730 429 -4.58985 0.00000 -7.04605 3 Li 8.40913 430 -0.53968 7.83240 3.02571 3 Li5 8.41384 431 -0.53968 -7.83240 3.02571 3 Li5 8.41384 432 -4.58985 6.10000 3.55395 3 Li 8.42065 433 -4.58985 -6.10000 3.55395 3 Li 8.42065 434 8.25967 0.00000 1.75218 1 Si 8.44347 435 5.69490 4.62990 -4.32680 3 Li1 8.51992 436 5.69490 -4.62990 -4.32680 3 Li1 8.51992 437 -0.53968 1.73240 8.32571 3 Li5 8.52114 438 -0.53968 -1.73240 8.32571 3 Li5 8.52114 439 -5.72574 3.05000 5.55137 3 Li6 8.53840 440 -5.72574 -3.05000 5.55137 3 Li6 8.53840 441 5.68976 6.10000 -1.83575 3 Li 8.54128 442 5.68976 -6.10000 -1.83575 3 Li 8.54128 443 -3.38713 7.84460 0.92526 3 Li4 8.59456 444 -3.38713 -7.84460 0.92526 3 Li4 8.59456 445 5.69490 1.47010 6.27320 3 Li1 8.59920 446 5.69490 -1.47010 6.27320 3 Li1 8.59920 447 3.99877 4.52010 -6.15640 3 Li1 8.62106 448 3.99877 -4.52010 -6.15640 3 Li1 8.62106 449 6.00997 4.39017 4.37199 2 O1 8.63178 450 6.00997 -4.39017 4.37199 2 O1 8.63178 451 -8.52694 0.00000 -1.35659 3 Li2 8.63417 452 7.94100 3.05000 1.56310 3 Li2 8.64900 453 7.94100 -3.05000 1.56310 3 Li2 8.64900 454 -4.26964 4.39017 -6.13830 2 O1 8.67076 455 -4.26964 -4.39017 -6.13830 2 O1 8.67076 456 -1.45611 7.44017 -4.21033 2 O1 8.67198 457 -1.45611 -7.44017 -4.21033 2 O1 8.67198 458 3.99877 7.67990 -0.85640 3 Li1 8.70083 459 3.99877 -7.67990 -0.85640 3 Li1 8.70083 460 0.55510 7.57010 -4.28194 3 Li1 8.71491 461 0.55510 -7.57010 -4.28194 3 Li1 8.71491 462 -7.24507 3.05000 3.77959 2 O2 8.72232 463 -7.24507 -3.05000 3.77959 2 O2 8.72232 464 3.68370 4.75983 6.34481 2 O1 8.74541 465 3.68370 -4.75983 6.34481 2 O1 8.74541 466 -8.52694 1.74460 0.97011 3 Li4 8.75748 467 -8.52694 -1.74460 0.97011 3 Li4 8.75748 468 -0.53968 4.36760 -7.57429 3 Li5 8.75997 469 -0.53968 -4.36760 -7.57429 3 Li5 8.75997 470 6.00997 1.70983 -6.22801 2 O1 8.82221 471 6.00997 -1.70983 -6.22801 2 O1 8.82221 472 0.54996 0.00000 8.80910 3 Li 8.82625 473 4.00391 3.05000 7.25256 3 Li 8.82799 474 4.00391 -3.05000 7.25256 3 Li 8.82799 475 -1.48695 0.00000 8.70498 2 O3 8.83106 476 -7.47842 3.05000 -3.60234 3 Li2 8.84342 477 -7.47842 -3.05000 -3.60234 3 Li2 8.84342 478 -6.28084 1.57990 -6.06669 3 Li1 8.87411 479 -6.28084 -1.57990 -6.06669 3 Li1 8.87411 480 8.17434 3.05000 -1.65498 2 O2 8.88039 481 8.17434 -3.05000 -1.65498 2 O2 8.88039 482 -7.47842 4.79460 -0.62904 3 Li4 8.90565 483 -7.47842 -4.79460 -0.62904 3 Li4 8.90565 484 -7.47842 1.30540 4.67096 3 Li4 8.91340 485 -7.47842 -1.30540 4.67096 3 Li4 8.91340 486 -4.58471 7.57010 1.06291 3 Li1 8.91379 487 -4.58471 -7.57010 1.06291 3 Li1 8.91379 488 -4.26964 7.80983 -0.83830 2 O1 8.94013 489 -4.26964 -7.80983 -0.83830 2 O1 8.94013 490 -8.76028 0.00000 1.86149 2 O2 8.95587 491 1.51933 0.00000 -8.82822 2 O2 8.95800 492 -1.14104 7.67990 4.48846 3 Li1 8.96823 493 -1.14104 -7.67990 4.48846 3 Li1 8.96823 494 -6.28084 4.52010 4.53331 3 Li1 8.96834 495 -6.28084 -4.52010 4.53331 3 Li1 8.96834 496 8.82350 1.34017 0.99996 2 O1 8.98054 497 8.82350 -1.34017 0.99996 2 O1 8.98054 498 -2.01994 0.00000 -8.75811 1 Si 8.98803 499 8.25967 0.00000 -3.54782 1 Si 8.98939 500 8.79266 0.00000 -1.98473 2 O3 9.01388 501 0.87017 7.80983 4.41685 2 O1 9.01439 502 0.87017 -7.80983 4.41685 2 O1 9.01439 503 5.68976 6.10000 3.46425 3 Li 9.03241 504 5.68976 -6.10000 3.46425 3 Li 9.03241 505 -2.33861 7.40540 4.62611 3 Li4 9.03935 506 -2.33861 -7.40540 4.62611 3 Li4 9.03935 507 4.60012 1.73240 -7.61914 3 Li5 9.06718 508 4.60012 -1.73240 -7.61914 3 Li5 9.06718 509 0.90101 3.05000 -8.49846 2 O3 9.07404 510 0.90101 -3.05000 -8.49846 2 O3 9.07404 511 -4.23880 3.05000 7.44639 2 O3 9.09498 512 -4.23880 -3.05000 7.44639 2 O3 9.09498 513 -4.58471 4.62990 6.36291 3 Li1 9.10726 514 -4.58471 -4.62990 6.36291 3 Li1 9.10726 515 5.68976 0.00000 -7.13575 3 Li 9.12647 516 -0.04626 4.78240 7.78080 3 Li5 9.13315 517 -0.04626 -4.78240 7.78080 3 Li5 9.13315 518 -6.59591 4.75983 -4.16548 2 O1 9.13856 519 -6.59591 -4.75983 -4.16548 2 O1 9.13856 520 2.80119 7.40540 4.58125 3 Li4 9.14738 521 2.80119 -7.40540 4.58125 3 Li4 9.14738 522 -0.58594 9.15000 0.20651 3 Li6 9.17107 523 -0.58594 -9.15000 0.20651 3 Li6 9.17107 524 1.75267 7.84460 -4.41960 3 Li4 9.17292 525 1.75267 -7.84460 -4.41960 3 Li4 9.17292 526 6.65913 6.10000 1.72693 2 O2 9.19436 527 6.65913 -6.10000 1.72693 2 O2 9.19436 528 -6.62675 6.10000 -1.85017 2 O3 9.19494 529 -6.62675 -6.10000 -1.85017 2 O3 9.19494 530 -1.13590 3.05000 -8.60259 3 Li 9.19768 531 -1.13590 -3.05000 -8.60259 3 Li 9.19768 532 7.94100 1.30540 4.53640 3 Li4 9.23810 533 7.94100 -1.30540 4.53640 3 Li4 9.23810 534 1.75267 6.10000 -6.74630 3 Li2 9.26252 535 1.75267 -6.10000 -6.74630 3 Li2 9.26252 536 7.94100 3.05000 -3.73690 3 Li2 9.29120 537 7.94100 -3.05000 -3.73690 3 Li2 9.29120 538 6.89248 4.35540 -4.46445 3 Li4 9.29554 539 6.89248 -4.35540 -4.46445 3 Li4 9.29554 540 7.94100 4.79460 -0.76360 3 Li4 9.30756 541 7.94100 -4.79460 -0.76360 3 Li4 9.30756 542 -6.59591 1.34017 6.43452 2 O1 9.31156 543 -6.59591 -1.34017 6.43452 2 O1 9.31156 544 9.13857 1.57990 -0.90125 3 Li1 9.31782 545 9.13857 -1.57990 -0.90125 3 Li1 9.31782 546 1.75267 0.00000 9.15370 3 Li2 9.31999 547 5.09355 7.41760 2.43595 3 Li5 9.32196 548 5.09355 -7.41760 2.43595 3 Li5 9.32196 549 6.89248 6.10000 -1.49115 3 Li2 9.32415 550 6.89248 -6.10000 -1.49115 3 Li2 9.32415 551 3.68370 7.44017 -4.25519 2 O1 9.32911 552 3.68370 -7.44017 -4.25519 2 O1 9.32911 553 3.11986 0.00000 -8.80297 1 Si 9.33947 554 5.09355 1.31760 7.73595 3 Li5 9.35549 555 5.09355 -1.31760 7.73595 3 Li5 9.35549 556 0.54996 6.10000 -7.09090 3 Li 9.36981 557 0.54996 -6.10000 -7.09090 3 Li 9.36981 558 4.60012 7.83240 -2.31914 3 Li5 9.37476 559 4.60012 -7.83240 -2.31914 3 Li5 9.37476 560 6.89248 1.74460 6.13555 3 Li4 9.39121 561 6.89248 -1.74460 6.13555 3 Li4 9.39121 562 -8.52694 0.00000 3.94341 3 Li2 9.39463 563 -5.18606 7.41760 2.52566 3 Li5 9.39654 564 -5.18606 -7.41760 2.52566 3 Li5 9.39654 565 8.79266 0.00000 3.31527 2 O3 9.39691 566 3.65286 0.00000 8.66012 2 O3 9.39899 567 1.43401 9.15000 -1.63537 1 Si 9.40496 568 1.43401 -9.15000 -1.63537 1 Si 9.40496 569 -8.76028 0.00000 -3.43851 2 O2 9.41095 570 -0.53968 4.36760 8.32571 3 Li5 9.41725 571 -0.53968 -4.36760 8.32571 3 Li5 9.41725 572 -0.04626 4.78240 -8.11920 3 Li5 9.42310 573 -0.04626 -4.78240 -8.11920 3 Li5 9.42310 574 0.90101 9.15000 2.10154 2 O3 9.43137 575 0.90101 -9.15000 2.10154 2 O3 9.43137 576 -1.13590 9.15000 1.99741 3 Li 9.43411 577 -1.13590 -9.15000 1.99741 3 Li 9.43411 578 5.09355 7.41760 -2.86405 3 Li5 9.44287 579 5.09355 -7.41760 -2.86405 3 Li5 9.44287 580 8.17434 3.05000 3.64502 2 O2 9.45561 581 8.17434 -3.05000 3.64502 2 O2 9.45561 582 1.51933 6.10000 7.07178 2 O2 9.46195 583 1.51933 -6.10000 7.07178 2 O2 9.46195 584 -5.18606 7.41760 -2.77434 3 Li5 9.46641 585 -5.18606 -7.41760 -2.77434 3 Li5 9.46641 586 -5.18606 1.31760 7.82566 3 Li5 9.48010 587 -5.18606 -1.31760 7.82566 3 Li5 9.48010 588 -8.84560 3.05000 -1.54567 1 Si 9.48347 589 -8.84560 -3.05000 -1.54567 1 Si 9.48347 590 -3.62048 0.00000 -8.78336 2 O2 9.50028 591 -2.10526 9.15000 -1.56527 2 O2 9.51865 592 -2.10526 -9.15000 -1.56527 2 O2 9.51865 593 5.69490 7.57010 0.97320 3 Li1 9.52289 594 5.69490 -7.57010 0.97320 3 Li1 9.52289 595 -1.48695 6.10000 -7.19502 2 O3 9.54931 596 -1.48695 -6.10000 -7.19502 2 O3 9.54931 597 5.13980 6.10000 5.25515 3 Li6 9.55218 598 5.13980 -6.10000 5.25515 3 Li6 9.55218 599 -5.13980 6.10000 -5.25515 3 Li6 9.55218 600 -5.13980 -6.10000 -5.25515 3 Li6 9.55218 601 4.60012 7.83240 2.98086 3 Li5 9.55998 602 4.60012 -7.83240 2.98086 3 Li5 9.55998 603 1.43401 3.05000 8.96463 1 Si 9.57723 604 1.43401 -3.05000 8.96463 1 Si 9.57723 605 -2.33861 9.15000 1.65281 3 Li2 9.58767 606 -2.33861 -9.15000 1.65281 3 Li2 9.58767 607 -5.67948 1.73240 -7.52944 3 Li5 9.58906 608 -5.67948 -1.73240 -7.52944 3 Li5 9.58906 609 -7.15975 6.10000 1.88674 1 Si 9.59332 610 -7.15975 -6.10000 1.88674 1 Si 9.59332 611 -9.40944 1.70983 -0.79345 2 O1 9.59639 612 -9.40944 -1.70983 -0.79345 2 O1 9.59639 613 -3.38713 7.84460 -4.37474 3 Li4 9.59941 614 -3.38713 -7.84460 -4.37474 3 Li4 9.59941 615 -5.13980 6.10000 5.34485 3 Li6 9.60183 616 -5.13980 -6.10000 5.34485 3 Li6 9.60183 617 5.13980 6.10000 -5.34485 3 Li6 9.60183 618 5.13980 -6.10000 -5.34485 3 Li6 9.60183 619 -2.01994 6.10000 7.14189 1 Si 9.60712 620 -2.01994 -6.10000 7.14189 1 Si 9.60712 621 -8.52694 4.35540 0.97011 3 Li4 9.62389 622 -8.52694 -4.35540 0.97011 3 Li4 9.62389 623 4.60012 1.73240 8.28086 3 Li5 9.62990 624 4.60012 -1.73240 8.28086 3 Li5 9.62990 625 -7.47842 1.30540 -5.92904 3 Li4 9.63246 626 -7.47842 -1.30540 -5.92904 3 Li4 9.63246 627 -6.62675 6.10000 3.44983 2 O3 9.64495 628 -6.62675 -6.10000 3.44983 2 O3 9.64495 629 5.69490 4.62990 6.27320 3 Li1 9.65510 630 5.69490 -4.62990 6.27320 3 Li1 9.65510 631 -3.38713 6.10000 -6.70144 3 Li2 9.67429 632 -3.38713 -6.10000 -6.70144 3 Li2 9.67429 633 6.89248 0.00000 -6.79115 3 Li2 9.67605 634 6.65913 0.00000 7.02693 2 O2 9.68100 635 -5.18606 1.31760 -8.07434 3 Li5 9.68640 636 -5.18606 -1.31760 -8.07434 3 Li5 9.68640 637 2.80119 9.15000 1.60795 3 Li2 9.70333 638 2.80119 -9.15000 1.60795 3 Li2 9.70333 639 6.00997 4.39017 -6.22801 2 O1 9.70471 640 6.00997 -4.39017 -6.22801 2 O1 9.70471 641 0.55510 1.47010 -9.58194 3 Li1 9.70994 642 0.55510 -1.47010 -9.58194 3 Li1 9.70994 643 6.65913 6.10000 -3.57307 2 O2 9.71189 644 6.65913 -6.10000 -3.57307 2 O2 9.71189 645 5.09355 1.31760 -8.16405 3 Li5 9.71247 646 5.09355 -1.31760 -8.16405 3 Li5 9.71247 647 -1.45611 1.34017 -9.51033 2 O1 9.71405 648 -1.45611 -1.34017 -9.51033 2 O1 9.71405 649 -8.52694 1.74460 -4.32989 3 Li4 9.72112 650 -8.52694 -1.74460 -4.32989 3 Li4 9.72112 651 3.99877 7.67990 4.44360 3 Li1 9.73225 652 3.99877 -7.67990 4.44360 3 Li1 9.73225 653 0.90101 9.15000 -3.19846 2 O3 9.73470 654 0.90101 -9.15000 -3.19846 2 O3 9.73470 655 -2.33861 3.05000 -8.94719 3 Li2 9.73775 656 -2.33861 -3.05000 -8.94719 3 Li2 9.73775 657 -6.62675 0.00000 -7.15017 2 O3 9.74878 658 -2.10526 3.05000 9.03473 2 O2 9.76530 659 -2.10526 -3.05000 9.03473 2 O2 9.76530 660 3.03454 9.15000 -1.61012 2 O2 9.77361 661 3.03454 -9.15000 -1.61012 2 O2 9.77361 662 -1.13590 9.15000 -3.30259 3 Li 9.79387 663 -1.13590 -9.15000 -3.30259 3 Li 9.79387 664 -2.33861 7.40540 -5.97389 3 Li4 9.79778 665 -2.33861 -7.40540 -5.97389 3 Li4 9.79778 666 -3.38713 0.00000 9.19856 3 Li2 9.80235 667 -4.58471 7.57010 -4.23709 3 Li1 9.81218 668 -4.58471 -7.57010 -4.23709 3 Li1 9.81218 669 9.14371 3.05000 1.90770 3 Li 9.82595 670 9.14371 -3.05000 1.90770 3 Li 9.82595 671 -6.28084 4.52010 -6.06669 3 Li1 9.83285 672 -6.28084 -4.52010 -6.06669 3 Li1 9.83285 673 3.11986 6.10000 7.09703 1 Si 9.86465 674 3.11986 -6.10000 7.09703 1 Si 9.86465 675 0.55510 7.57010 6.31806 3 Li1 9.87585 676 0.55510 -7.57010 6.31806 3 Li1 9.87585 677 -9.72965 0.00000 -1.70119 3 Li 9.87725 678 -1.14104 7.67990 -6.11154 3 Li1 9.88098 679 -1.14104 -7.67990 -6.11154 3 Li1 9.88098 680 -9.72451 1.47010 1.10776 3 Li1 9.89719 681 -9.72451 -1.47010 1.10776 3 Li1 9.89719 682 6.00997 7.80983 -0.92801 2 O1 9.89820 683 6.00997 -7.80983 -0.92801 2 O1 9.89820 684 2.80119 3.05000 -8.99205 3 Li2 9.89980 685 2.80119 -3.05000 -8.99205 3 Li2 9.89980 686 0.87017 1.70983 9.71685 2 O1 9.90443 687 0.87017 -1.70983 9.71685 2 O1 9.90443 688 8.82350 1.34017 -4.30004 2 O1 9.90659 689 8.82350 -1.34017 -4.30004 2 O1 9.90659 690 4.60012 4.36760 -7.61914 3 Li5 9.91405 691 4.60012 -4.36760 -7.61914 3 Li5 9.91405 692 -1.45611 7.44017 6.38967 2 O1 9.91485 693 -1.45611 -7.44017 6.38967 2 O1 9.91485 694 -5.67948 7.83240 -2.22944 3 Li5 9.92841 695 -5.67948 -7.83240 -2.22944 3 Li5 9.92841 696 -4.23880 3.05000 -8.45361 2 O3 9.93647 697 -4.23880 -3.05000 -8.45361 2 O3 9.93647 698 2.80119 7.40540 -6.01875 3 Li4 9.94545 699 2.80119 -7.40540 -6.01875 3 Li4 9.94545 700 -6.28084 7.67990 -0.76669 3 Li1 9.95076 701 -6.28084 -7.67990 -0.76669 3 Li1 9.95076 702 -4.26964 7.80983 4.46170 2 O1 9.95641 703 -4.26964 -7.80983 4.46170 2 O1 9.95641 704 1.43401 9.15000 3.66463 1 Si 9.96034 705 1.43401 -9.15000 3.66463 1 Si 9.96034 706 6.89248 6.10000 3.80885 3 Li2 9.96110 707 6.89248 -6.10000 3.80885 3 Li2 9.96110 708 3.03454 3.05000 8.98988 2 O2 9.96639 709 3.03454 -3.05000 8.98988 2 O2 9.96639 710 -4.58985 0.00000 8.85395 3 Li 9.97292 711 -1.14104 1.57990 9.78846 3 Li1 9.98058 712 -1.14104 -1.57990 9.78846 3 Li1 9.98058 713 6.04081 3.05000 7.35668 2 O3 9.99573 714 6.04081 -3.05000 7.35668 2 O3 9.99573 715 0.87017 7.80983 -6.18315 2 O1 9.99910 716 0.87017 -7.80983 -6.18315 2 O1 9.99910 717 -3.70580 9.15000 -1.59052 1 Si 9.99926 718 -3.70580 -9.15000 -1.59052 1 Si 9.99926 719 END ----- End of forwarded message from John J. Rehr -----

2 1

Re: ifeffit windowfunctions
by Matt Newville 11 Dec '02

11 Dec '02

Hi Daniel, On Wed, 11 Dec 2002, Daniel Grolimund wrote: > In case I am using non-regularly spaced k-chi data, the plot of the > chosen Fourier Transform Window is not represented correctly using the > command plot(group.k, group.win)]. > > Is there a way to get around that (except using interpolated and > therefore regularly spaced) data? Funny you mention this, I just noticed the same problem myself over the weekend. Currently, fftf() writes out the window function assuming the 0.05 Ang-1 grid, regardless of the input k-array. I believe this is fixed (that is, the group.win array corresponds to the group.k array!) in my latest test version. I still need to test other fixes in this version, but hopefully I'll get it out early next week. > Further, in a earlier version one had to use ikwindo = n to specify the > Fourier Transform Window type. In ifeffit the termology kwindow = aaaaa > is used. In addition to 'kaiser' and 'hanning' are there any other > options for kwindow ? Oh right. This is one place where Ifeffit and Feffit are different. Feffit's 'ikwindo = 2' caused some headaches (no one could remember them!) so 'kwindow=hanning' etc seemed better (if english-centric) for ifeffit. Other window functions are 'parzen' (linear sills), 'welch' (quadratic sills), and 'sine' (a sine wave over the whole range), and 'gaussian' (which is really weird: centered at dk2, with full width of 1/dk1, someone asked for it many years ago, it could probably be improved!). The next version of ifeffit will also have a window() command to make window functions without actually doing the FTs. --Matt

1 0

RE: [Ifeffit] Double dipping
by Kelly, Shelly D. 02 Dec '02

02 Dec '02

Hi Matt, I think that your reply sounds reasonable. Lets talk some more about this. > The other side of this is that I think it's more difficult than > generally acknowleged to over-interpret data. Most of the cases > I've seen are due to blatantly ignore the confidence limits or do > completely unfair things like fitting So2 to get 0.9+/-0.1, then > fix So2 to 0.90, fitting N, and claiming N to better than 10%. > Those are serious, but are the normal mistakes in analysis that > can happen with any data. If you fix s02 and then you fit N and get a error lets call it dn. Then the more generous estimation of the uncertainty for N is d(s02*n) = ds02*n + s02*dn. How would you estimate the error for N if you fix s02, R and sigma2? I will try to be more specific to my original problem. lets say that the original data set (s3) gives these results for the Ca shell. Ncas3=3.4+/-0.9 Rcas3=4.01+/-0.01 sigma2cas3=0.006+/-0.3 s02s3=1.05+/-0.10 Now I run another fit and I fix all the parameters except for Nca. This time I fit three data sets s3, s4 and s5 together and I get these results. Ncas3 = 3.2+/-0.1 Ncas4 = 2.5+/-0.4 Ncas5 = 2.0+/-0.4 What would you think would be an "appropriate" uncertainty? Surely 0.1 is too small for Ncas3 but 0.9 seems rather huge. So we have some limits but can I do any better than that? The difference is between these to extremes is quite profound. In one case we see a change in the value for Nca in the other we see nothing. Shelly > -----Original Message----- > From: Newville, Matthew G. > Sent: Friday, November 22, 2002 10:17 AM > To: 'ifeffit(a)millenia.cars.aps.anl.gov' > Subject: Re: [Ifeffit] Double dipping > > > Hi Shelly, > > > I would like to take a bunch of parameters (all of them that do > > not vary significantly from the known, as determined by > > individual fits to each data set) from this "known" data set > > and then fit the series including the "original" to see how a > > particluar parameter (the number of Ca atoms) changes as the > > ratio of U to Ca changes. I would like to hear a discussion on > > the fairness of this approach and how would you calculate the > > number of independent points? > > I think what you propose is fair, but you might need to be a > little more specific.... > > In general, I think it's fair to use parameters from one fit to > to another data set. Once one accepts the fact that there is > limited amount of information, getting hung up on trying to count > or enforce N_idp becomes pointless -- the data and estimated > uncertainties __WILL__ indicate how many parameters can be > determined with any confidence. > > N_idp is one statistic, it should not be construed as an exact > value nor a hard upper limit on how much data can be extracted > from data. Any attempt to use N_idp this way is abuse. > > The classic test is whether 100 very noisy scans (say, because > data was collected for 0.01s per point), has 100x more > 'independent points' as 1 scan that collected for 1.0s per point. > The 100 noisy scans __ARE__ independent, but when added together > with give exactly the same result as using the 1 clean scan. So > independent data does not mean you can determine you can > determine more parameters. > > The other side of this is that I think it's more difficult than > generally acknowleged to over-interpret data. Most of the cases > I've seen are due to blatantly ignore the confidence limits or do > completely unfair things like fitting So2 to get 0.9+/-0.1, then > fix So2 to 0.90, fitting N, and claiming N to better than 10%. > Those are serious, but are the normal mistakes in analysis that > can happen with any data. > > --Matt > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

2 1

notes for figures
by Bruce Ravel 22 Nov '02

22 Nov '02

Ning, I trust you will not mind if I respond to the ifeffit mailing list. You question is of general interest. > On Fri, 22 Nov 2002, "Ning Chen" <Ning.Chen(a)lightsource.ca> said: NC> Hi Bruce: I am wondering if it is possible to add note to the NC> figure inside the "Graphic window"? Hmmm.... no one has ever asked for that before. Good question! There is a way. It's not particularly convenient, but it's not particularly difficult either. Here is an example: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/tex… I made this first by clicking on the red "kq" button. Then, in the edit menu, I selected "Ifeffit buffer". At the bottom of the little window that popped up, there is a box with a label that says "Ifeffit>". That text box allows the user to interact directly with ifeffit by typing in explicit commands. Here is a picture: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ife… To get the text string in the plot, I typed: plot_text(x=7, y=-0.3, text="Hi Ning!") which tells Ifeffit to put the indicated text string at the indicated coordinates. The same thing could be done the same way in Artemis. Obviously, this could be made more user friendly by, for example, having Athena or Artemis prompt you to click on a spot in the plot window and then prompt you for a text string. I'll put that on the TODO list. Please note that using the plot_text command as I describe above will trigger the minor bug described by Matt earlier this week on this list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-November/000177.html 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/

2 2

Double dipping
by Kelly, Shelly D. 22 Nov '02

22 Nov '02

Hello All, I am new to this mailing list, so I hope my question is relevant. I have several EXAFS data sets that I want to simultaneously fit with one model. One of the data sets was modeled first and the results will be published separately from the rest. I would like to take a bunch of parameters (all of them that do not vary significantly from the known, as determined by individual fits to each data set) from this "known" data set and then fit the series including the "original" to see how a particluar parameter (the number of Ca atoms) changes as the ratio of U to Ca changes. I would like to hear a discussion on the fairness of this approach and how would you calculate the number of independent points? Shelly Kelly

2 1

Athena 0.8.007 and Artemis 0.5.003
by Bruce Ravel 22 Nov '02

22 Nov '02

Hi Folks, I just posted new versions of my two programs on my web site. The source tarball for Unix and OSX users as well as newly built windows executables are in their standard places. Most of the changes this time fix bugs that I discovered last week when I was visiting the wonderful folks at the Alberta Synchrotron Institute. The two most important changes fix the problems displaying the normalized background function and reading chi(k) data that is not on a uniform k-grid. Windows user who are new to Ifeffit: You just need to download the new executable files and drop them on top of the old ones in C:\Program Files\Ifeffit (or wherever you installed Ifeffit on your computer). The big installer file has *not* yet been updated to include these new versions. Unix, linux, or Mac OSX users: The source tarball now includes the ifeffit wrapper that comes with the main ifeffit distribution. Now, when you update ifeffit, it is no longer necessary to cd into the "wrappers/perl/" directory and build the perl wrapper. Instead the wrapper is built at the same time as Athena and Artemis. I am fairly confident that the wrapper gets compiled correctly. It works fine on my linux computer and on Mac OSX. Please let me know if you have any troubles with the compilation so I can fix the build scripts. As always, feel free to post questions, bug reports, or feature suggestions to this mailing list. Special thanks this time to Paul Fons and to all the folks at the ASI. 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/

1 0

Re: pgplot question
by Matt Newville 20 Nov '02

20 Nov '02

Hi Paul, On Thu, 21 Nov 2002, Paul Fons wrote: > I noticed (from early on) that although pgplot generated graphics show > all spectra labels on screen, when I save them to a file, that the > lowermost scan of a multiple scan plot always has the label missing. > Is this something that is Mac specific or is everyone suffering from > this problem? I want to try tracking it down a little (perhaps > including sending a note to the pgplot author if helpful). This is my fault -- a bug that's been on the to-do list forever, and never done. I believe this will also cause the same behavior: my.x = range(1,100,1)/10 my.y = sin(my.x) my.z = cos(my.x) newplot my.x, my.y, key='sin' plot my.x, my.z, key='cos' #everything is fine... plot xmax = 8 and the most recent 'key' gets lost. Making a hardcopy simply does a plot() with a different device, and so often tickles this error. Workarounds include adding the last trace twice, as in newplot my.x, my.y, key='sin' plot my.x, my.z, key='cos' #everything is fine... plot my.x, my.z, key='cos', color='red' which will then trick a second plot(). Anyway, it's all my fault, not PGPLOT's. Probably should fix it huh?? --Matt

1 0

Ifeffit 1.0075
by Matt Newville 13 Nov '02

13 Nov '02

Hi Everyone, Ifeffit 1.0075 is now available. There are some bug fixes related to erasing paths, which caused serious problems with artemis. There was also a change in the guts of how the Perl wrapper was built, as the older one failed to compile with gcc3.2 on RedHat 8.0. I have not tried this on Mac OS X, and don't foresee any problems, but if someone is brave enough to try it, please let me know if it fails. The most significant change in 1.0075 is the inclusion of Feff6 in the source tree and a Windows executable of Feff6 in the Windows installer. That right, there is now a free version of Feff6 included with Ifeffit!! The plan is to turn this version of Feff into a library that can be called directly from the perl and python scripts. That is, the 'run feff' button on TkAtoms might actually work someday!! If you're as thrilled about this as I am, don't hesitate to thank John Rehr repeatedly. There are new versions of sixpack, artemis, and athena in the Windows installer. The latest source code for these should be downloaded from Sam's and Bruce's web pages. Special Thanks to John, Sam, and of course Bruce, --Matt

4 6

ifeffit and feff
by Bruce Ravel 06 Nov '02

06 Nov '02

Ahmed, I trust you do not mind that I answer your question on the ifeffit mailing list. It seems of sufficiently broad interest that an answer in that forum is appropriate. You asked: AS> I received a note with the latest version of your software. In my AS> understanding that the latest version includes the Feff6L without AS> a license fee. Does this mean that by downloading the latest AS> version of ifeffit, so that I do not need to buy a license of AS> feff? Well, my answer is ether a qualified yes or a qualified no, depending on what your interests are ;-) *IF* you are interested only in the extended EXAFS features of Feff and *IF* you do not think that you need any of the more recent developments of Feff (most notably, self consistent potentials), then you probably do not need a license for Feff. Feff6L is free in both senses of the word -- it doesn't cost you any money and you may freely use, modify, and redistribute the code under the terms of its license. See this post from John Rehr to the mailing list about the Feff6L license: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-November/000169.html However, if you are interested in computing XANES, partial electronic densities of state, charge transfer or ab initio Fermi energies, you will need to license a copy of the latest version of Feff. If you are interested in the latest developments of such theoretical topics as self-consistent potentials, improved self-energies, S02 calculations, resonant scattering corrections, or a whole host of other features available in the latest Feff and not available in Feff6L, you will need to license a copy of the latest version of Feff. Feff6L is useful code for the extended exafs practitioner. If that were not true than Matt would not have been so effusive in his post yesterday announcing Ifeffit 1.0075. While Feff6L is useful and usable for exafs analysis, you must be aware that it is largely limitted to exafs analysis. If you need XANES calculations, you need a Feff8 license. All clear? 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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FEFF6L - Lite EXAFS only version of FEFF6 source code
by John J. Rehr 05 Nov '02

05 Nov '02

Dear Feff developers, In an effort to facilitate the development of EXAFS analysis software, the FEFF Project has made available the source code for a "lite" subset of the FEFF6 distribution sufficient for EXAFS analysis, named FEFF6L. Thus cross-sections and XANES capabilities of FEFF6 are disabled in FEFF6L. A copy of the FEFF6L distribution can be found (shortly) on the FEFF Developer download pages. The subroutines are distributed with a License that permits redistribution without a license fee; see the LICENSE in the distribution for details. c/////////////////////////////////////////////////////////////////////// c Distribution: FEFF6L c Copyright (c) [2002] University of Washington c c This software was prepared in part with US Government Funding under c DOE contract DE-FG03-97ER45623. c c Redistribution and use of this Distribution in source and binary c formats, with or without modification is permitted, provided the c following conditions are met: c c Redistributions must retain the above notices and the following list c of conditions and disclaimer; c c Modified versions carry the marking c "Based on or developed using Distribution: FEFF6L c Copyright (c) [2002] University of Washington" etc. The distribution FEFF6L should not be confused with the full distribution of FEFF6. Also the FEFF Project will continue to develop advanced versions of the FEFF codes which will be distributed with the UWOTT License and license fee. Comments on this EXAFS version are welcome. Sincerely, FEFF Project PIs J. J. Rehr A. L. Ankudinov

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Re: [Ifeffit] Debye factor and S02 correlation
by Bruce Ravel 05 Nov '02

05 Nov '02

jjr> I don't understand Bruce's remark. Incorporating prior knowledge jjr> into statistics is completely proper according to modern jjr> statistical theory. If two quantities are correlated and one jjr> knows one, then naturally the other is better determined. Well, leaving aside the question of whether one can call a Levenberg- Marquardt fit "modern", I agree that one can set a value and call it part of the model. One does that all the time in any fitting problem. But in that case you are asserting a value with no error bar. There is no situation where you can assert a value AND an error bar. My concern was your statement that you somehow knew the value of the error bar on S02. If it floats, you have to use the error bar the fitting algorithm reports. But the most important thing in my comment and the most important thing in the discussion on the topic of amplitude terms in exafs that we have seen in the last week on this list is that, in a difficult fitting problem (i.e. not copper), one rarely has reliable a priori knowledge of the *product* of S02, coordination, and the systematic uncertainties. Thus one rarely has a reliable prior in the Baysian sense. 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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rebinning data
by Carlo U. Segre 05 Nov '02

05 Nov '02

hello All: This is to bring back up a subject that was discussed a few months ago on the list. We have been diligently working on a python algorithm for rebinning XAFS data from high point density slew scans. I have been testing it and I hope that there will be a complete version available shortly. It is in the form of a unix filter which takes a few parameters (edge energy, energy above the edge where rebinning is to begin, step size in k for rebinning) and spits out a modified file for each input file. There are just a couple of small glitches in how it handles data points with the same energy (this causes athena to pop up an annoying dialog) but that should be solved this week. I am more than happy to send it to anyone who would like it. Matt, I remember that you had suggested that we send code. 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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Re: [Ifeffit] Debye factor and S02 correlation
by John J. Rehr 05 Nov '02

05 Nov '02

Matt's test of fitting the inelastic losses using So2 and an effective mean free path (via a constant imaginary shift Ei in the net lifetime width in FEFFIT) is quite interesting. In particular the results are consistent with our current understanding of the physics, namely that the inelastic losses are generally overestimated by the plasmon-pole self energy. Thus one expects Ei to be negative to compensate for errors in this self-energy model. Also it's particularly encouraging that one can fit *both Ei and So2*. I'm not too worried by the evident correlation between these parameters since they both smoothly affect the overall amplitude; what matters is the value of Ei when So2 is about 0.9. Matt wrote: >This seems like a fine approach to me, and it could be automated, >at least somewhat. Feffit/Ifeffit have Ei as a path parameter, >so setting So2 to 0.9 and floating Ei is possible right now. >Using Ei instead of So2 has a couple possible benefits: > 1. Not completed correlated with N (though see below!) > 2. Can accomodate measurement resolution issues. > 3. Might be a little easier conceptually on the new people. > >For one variation on the canonical 'Cu 10K first shell fit', >with sigma2 varying as well, I get these values: > So2 Ei chi_square r-factor > 0.93(0.03) 0.00(fix) 119. 0.0017 > 1.00(fix) 0.55(0.25) 128. 0.0018 > 0.95(fix) 0.14(0.24) 120. 0.0017 > 0.90(fix) -.29(0.23) 116. 0.0016 > 0.85(fix) -.75(0.23) 116. 0.0016 > > 0.87(0.14) -.58(1.27) 116. 0.0016 > >The last one had both So2 and ei (and sigma2!!) floating. The >correlation between them was 0.98, higher than that between So2 >and sigma2, which was a mere(!) 0.94. So it looks like, for this >data, So2 really does want to be ~0.90 +/ 0.05, and Ei wants to >be 0.00 +/- 0.25. As I read the numbers for the minimum chi_square, I would say that the results suggest Ei = -.52 +/- .3 I don't believe the error bar on So2 of +/- .14. Probably +/- .05 is more like it, so the error bar on Ei will be much smaller than 1.27. Also, I think if you look at plots of the fits, they look better with a slightly negative Ei. We would very much like to see more evidence for the inadequacy of the plasmon pole self energy. Thus I would encourage more fits to include E_i as a fitting parameter, with So2 kept under control (e.g. fixed or floating in a range 0.9 +/- .05, assuming edje jump is well defined). J. Rehr

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Re: [Ifeffit] Debye factor and S02 correlation
by John J. Rehr 04 Nov '02

04 Nov '02

Hi Everyone, I agree with Matt's assessment: > ... my view is that the >errors in the calculated mean-free path may have a much stronger >energy dependence than the errors in the calculated So2. From >the analysis point-of-view, I prefer to think of So2 as >k-independent, and put all k-dependent pieces go into lambda(k) >or F(k). Feff tries to include all loss terms as well as it can. There are two ingredients in the mean free path lambda(k) lambda_k approx k/[Im Sigma(E) + Gamma] 1) The core hole lifetime Gamma - FEFF estimates this by interpolating from tabulated values. This rough estimate should not lead to serious errors, in my view, since a 10% error in the lifetime translates to only few percent error at worst in the loss factor exp(-2 lambda R). 2) The self energy Sigma - FEFF uses an electron gas plasmon pole approximation. which can easily be off by 1-2 eV. This is the most serious error and leads to large energy dependent errors in lambda_k. >So2 _is_ calculated (if crudely in Feff6 and 7 -- I don't know if FEFF6-8 will make an atomic value of So2 if one sets S02 = 0 in the HOLE card. This approximation is unsatisfactory since it can't account well for the valence electron contributions or interference effects which dominate So2. I don't think it can be trusted - at least to better than 10%. >Luke Campbell's work on improved So2 is included in Feff8 yet). >So one might even expect that So2 should be 1, and even find it a Luke Campbell's routines are not in FEFF8 yet as they are not yet fully automated or ready to be integrated. This will us take some months. Moreover, Luke still uses a plasmon-pole self energy, which we want to improve. >little strange that it's usually around 0.9. Clearly, there are >loss terms that are not taken into account well enough in Feff. >My view is that it's not well known whether this is dominated by >an k-dependent term (ie, should be put into F or lambda) or a >k-independent term (So2). The remarkable bit of physics here is that interference terms between extrinsic and intrinsic losses and hence tend to suppress shake-up/shake-off effects. In any case, my suggestion in fits would be to treat the loss terms using a constant and an effective mean free path: a) set So2 = constant approx 0.9 b) fit the mean free path, e.g., by fitting the core-hole effective lifetime. I'd be interested in feedback on this suggestion. Can it be automated within FEFFIT? Cheers, John Rehr

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Debye factor and S02 correlation
by Dr. Paul Fons 04 Nov '02

04 Nov '02

I meant to send this off to the list (instead I sent it to Scott Calvin only). Ahh the wonders of email. I thought I would parrot back something I read in one of Bruce's tutorials (that seemed to work well for me), namely that the Debye factor, sigma has a k dependence while S02 does not. This means that if you can Fourier isolate the first shell (and you can assume a coordination number), you can determine a value for S02 by a fit using different k weights. You simply fit sigma for various fixed values of S02 (e.g. 0.6 - 1.0) and repeat the process for different k weights (e.g. k, k^2, k^3). The resulting plot of sigma vs. S02 will result in a straight line for a given k weighting. The three different k weights will intersect at a single point (or almost so) and the value of S02 at this point will be the value of S02 for the sample. While we are discussing S02, I thought I would ask a little more about it myself. 1. S02, the passive electron reduction factor is a term that encompasses many body effects, in particular the effect of the core hole. It is also as such said to have a "weak energy and path dependence" [J.J. Rehr and R.C. Albers in Reviews of Modern Physics, v. 72, no. 3 (2000)]. The question is how fair is it to assume that S02 is a constant independent of shell, or in other words should S02 be allowed to vary with shell (e.g. with significant multiple scattering contributions?) 2. I don't remember the paper offhand, but as I recall, in a paper by Bruce, the value of S02 was ascribed a value greater than unity. I didn't grok the explanation at the time, and was wondering if Bruce (or anyone else) in his ever-expanding knowledge of exafs has an explanation for when/if S02 can be greater than unity. Certainly if you consider Rehr's definition of the overlap integral of the N-1 electron wavefunction with and without a core hole, the value of S02 cannot be greater than unity[same reference, p. 636]. Any comments?

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Re: [Ifeffit] Re: Amplitude and the EXAFS equation
by John J. Rehr 30 Oct '02

30 Oct '02

Dear FEFF and IFEFFIT users, As Matt notes, >Feff tries to estimate many of the the physical processes >identified as So2. It also estimates lambda, but much more >crudely: it interpolates a fit to the *figures* from Rahkonen and >Krause (1974). Feff definitely does not include the energy >resolution of a Si(111) monochromator at 9keV. One of the biggest problems with the current FEFF calculation is that the mean free path lambda is calculated from the Hedin-Lundqvist electron gas self energy in the plasmon-pole approximation. This often overestimates the inelastic losses (too short mean free paths). The consequence of this is that the effective So2 must often be increased to compensate. For this reason, it is not unusual to see fits of So2 that that can exceed unity. Fortunately improvements are in sight. Luke Campbell's thesis focused in part on calculations of So2, and he was able to explain the So2 for Cu (about 0.9) to within a few percent. Also efforts are being made to improve the self energy. However, at present the theoretical So2 is typically 0.9 +/- 0.1. This of course, does not take into account possible errors in the value of the edge jump and corrections for experimental resolution which can affect fits to So2. John Rehr

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Re: Amplitude and the EXAFS equation
by Scott Calvin 30 Oct '02

30 Oct '02

Hi all, I thought I'd add my two cents: I agree with everything Bruce said (!), but I think it is worth emphasizing one aspect of this issue. Basically, unless I'm using a mutiple-element fit with some clever constraints (not yet available in Artemis, but soon, I gather), any determination of coordination number is likely to be pretty uncertain. Not only does N correlate completely with S02 for a single shell fit, it is also likely to correlate strongly with sigma2 (or the Debye or Einstein temperature or whatever I'm using as the free parameter). Multiple-shell fits help when I can use them, but if I don't know the coordination number for the first shell, how likely is it that I know the structure of the material well enough to fit outer shells? Although you may see coordination numbers determined by EXAFS with an "uncertainty" of 1 in publications, this is usually something like the uncertainty reported in IFEFFIT--it probabIy doesn't include systematic errors like the effect of assumptions concerning the Debye-Waller factor or S02. In most cases if I'm looking for a first shell coordination number via EXAFS I'm not counting on better than a factor of two accuracy. That may still be useful in some cases, but doesn't help distinguish between, say, tetrahedral and octahedral coordination. So, if I'm only looking for a factor of 2, and if I'm pretty sure my sample is homogenous and of a consistent and appropriate thickness, I'm happy to just constrain S02 to 0.90 or 0.85 or whatever, knowing that the arbitrary choice of S02 is probably introducing an uncertainty of less than 20% in the coordination number. Since this is still considerably less than I generally believe is introduced by other issues (such as the scheme used for the Debye-Waller factors), it's good enough for me. --Scott Calvin Naval Research Lab --

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Amplitude and the EXAFS equation
by Bruce Ravel 29 Oct '02

29 Oct '02

Hi folks, Today I received one of the top-ten most asked questions. I am going to take a stab at answering it here in an archived forum. I am sort of hoping to get a discussion going and get several people's viewpoints. An Artemis user observed in her email that, in the EXAFS literature, people often publish values for coordination number. She asked how one obtains that using Artemis/Ifeffit. If only there were an easy answer to this question! It turns out that, in the EXAFS equation, there are two terms that directly affect the amplitude. One is N, the coordination number (or one might say "the path degeneracy"), and the other is S02, the so-called passive electron reduction factor. S02 is, according to popular wisdom, chemically transferable. This means that if you somehow have determined S02 for a given central atom in one compound, you can use this value for some other compound. While this may be true, particularly if a standard and a sample are measured back-to-back under identical experimental conditions, it is not a safe course of action. The problem is that lots of empirical effects can also change the measured amplitude. These may include things like detector response, sample inhomogeneity, and those annoying gremlins that sneak into the hutch when you're not looking. Assuming, though,that you know S02 and you are confident that empirical problems are a small factor, then the "S02" path parameter can often be interpreted simply as the coordination. If, however, you are not confident of S02 or of the smallness of the empirical effects, the situation is somewhat more complicated. A common assumption is that you should be able to determine S02 *and* coordination simultaneously from data. This is, at best, extremely difficult to do with statistical significance and, at worst, flatly impossible. If you are fitting only one shell of data, then it is certainly impossible. Why do I say that? Well, consider how coordination (N) and S02 enter the EXAFS equation: N * S02 * F(k) chi(k) = ------------------ sin( 2kR + delta(k) ) exp(-2ksigma^2) 2kR This is the generic formula. In Feff, Ifeffit, and Artemis, this is the the expression for chi(k) for a particular path. The data chi(k) is fit by evaluating this equation for one or more paths then summing them up. In that equation, note that N and S02 are both multiplicative factors. If your fit considers only one path, then N and S02 have *exactly the same effect* on the equation. They cannot be measured independently. In the absence of knowledge about either N or S02, the only thing you can do is measure the product (N*S02). How does one then report on coordination in a journal article? You have to somehow interpret the product (N*S02) and determine how much of that is N and how much is S02. There is no generic answer to how that is done -- it depends on the details of the sample and the experiment. To return to last week's silly posts about training monkeys -- it is yet another reason why data analysis requires a thinking human being. If you are fitting many shells or many data sets (the latter is something that Artemis does not yet allow you to do -- it's coming soon!), then you may have enough information in your data to uncouple the correlation between N and S02 and somehow fit them independently. Again, there is no generic way of doing so -- each situation is different. It is common to do as I suggested above and determine S02 from a well known standard that was measured at the same time as your sample. If there are no significant empirical effects in the sample that do not exist in the standard, then the value of S02 is probably useful for your unknown sample. Armed with that, it is much easier to then determine coordination. The discussion up to now has been conceptual. How are the amplitude terms handled in Artemis. Well, start by taking a look at a screenshot of the path page from a recent version of Artemis: http://feff.phys.washington.edu/~ravel/software/exafs/images/artemis/artemi… Note that there is an entry box labeled "N" and another labeled "S02". The one labeled "N is filled with the path degeneracy when the feffNNNN.dat file is imported. The one labeled S02 is intended to be filled with a math expression used to describe all remaining terms that may effect the amplitude. In the example shown, I have left N equal to the value from the feffNNNN.dat file and set S02 to a very simple math expression. The variable "amp" is being floated in this fit to copper foil data and used to evaluate the S02 term in the EXAFS equation for each path. In this case I am using knowledge of the system to uncouple N and S02. This is a copper foil, thus I am confident that the coordination is as expected from crystallography. I am also confident that the empirical effects are negligible. Whatever value amp ends up being, I will interpret that as S02. Now suppose I want to measure a nano-particulate copper oxide. In such a system, I may expect coordination to be reduced relative to the bulk oxide. For that, I may do the following: 1. Run feff using the crystal structure of bulk copper oxide. This will give me a copper/oxygen path to use to fit the first shell of my nanoparticle. 2. Read that feff path into Artemis along with my data 3. Set amp to the value determine from the copper foil (this is done by selecting "set" rather than "guess" from the appropriate optionmenu on the "Guess, Def and Set" page in Artemis. 4. For the first shell path, set N to 1 (rather than what ever value it was in the feffNNNN.dat file) 5. Set S02 for the first path to this math expression: n_first * amp 6. On the "Guess, Def and Set" page, define n_first as a guess parameter and choose a sensible starting value. The N and S02 part of the screenshot above will then look something like this: ___ ___________________________________ N |_1_| * S02 |_ n_first * amp ___________________| Here I have fixed amp to represent the known value of S02, I have set the N term in the EXAFS equation to be 1, and I have made a math expression, "n_first * amp", that will be evaluated and used for the S02 term in the EXAFS equation. n_first will be adjusted in the course of the fit and can be directly interpreted as a coordination number. Is this the only way of dealing with coordination? Certainly not. Is this the "official" way of measuring coordination? No. There isn't one. Every situation is different. Should you apply this example to every one of your analysis problems? No way! Did this example help you understand how N and S02 are used in Artemis and Ifeffit? I hope so. May this example be applicable to some analysis problem you run into at some point in your career? Quite possibly. Do you need to think hard about every analysis problem and figure out the best way to deal with the problem of N and S02 being coupled parameters? Absolutely! Hope that helps, 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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detaching plot buttons in Athena on Windows
by Bruce Ravel 25 Oct '02

25 Oct '02

Hmmm.... the situation with the detaching plot buttons is actually worse than I thought when I wrote my last (and somewhat sarcastic) message. It turns out that the mechanism I used to handle the detaching and reattaching of the plot buttons will not work on Windows. It seems to be one of the very few things in perl/Tk that does not port from Unix to Windows. Unless I can find a better way, in the next release I will remove this option from the Plot menu on Windows. For now, just don't use it. Thanks for the report, Raul. It's appreciated, as always. 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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detaching plot buttons in Athena on Windows
by Bruce Ravel 25 Oct '02

25 Oct '02

Raul said: RB> I just downloaded your last exe files of Athena and Artemis. I RB> tried the detach plot buttons feature and I found that the Data RB> group card is gone. I've done this before and after loading some RB> data and it happened in both cases. Then I selected the replace RB> option and nothing happened except the message "this may take a RB> few seconds". So, there is no way to select any data after RB> select this option. Hmmm.... that's a problem.... I guess I forgot to test that little feature on Windows before releasing. Drat! Fortunately, the work-around is really obvious ;-) 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: Ifeffit digest, Vol 1 #70 - 1 msg
by Raul Barrea 25 Oct '02

25 Oct '02

Hi Bruce, I just downloaded your last exe files of Athena and Artemis. I tried the detach plot buttons feature and I found that the Data group card is gone. I've done this before and after loading some data and it happened in both cases. Then I selected the replace option and nothing happened except the message "this may take a few seconds". So, there is no way to select any data after select this option. Thanks Raul Barrea ----- Original Message ----- From: <ifeffit-request(a)millenia.cars.aps.anl.gov> To: <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Friday, October 25, 2002 12:00 PM Subject: Ifeffit digest, Vol 1 #70 - 1 msg > 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-admin(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. Athena 0.8.004 and Artemis 0.5.001 (Bruce Ravel) > > --__--__-- > > Message: 1 > Date: Thu, 24 Oct 2002 15:48:34 -0400 > To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> > Reply-To: ravel(a)phys.washington.edu > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: [Ifeffit] Athena 0.8.004 and Artemis 0.5.001 > > > Hi everyone, > > I posted a new source tarball (horae-005.tar.gz) and new windows > executables on my webpage today. Both Athena and Artemis have > significant new features and bug fixes. > > Athena: > The biggest new feature is the many new keyboard shortcuts. Here's > a summary: > Ctrl-t toggle marking of current group > Ctrl-p e plot current in energy > Ctrl-p k plot current in k-space > Ctrl-p r plot current in R-space > Ctrl-p q plot current in q-space > Meta-p e plot marked in energy > Meta-p k plot marked in k-space > Meta-p r plot marked in R-space > Meta-p q plot marked in q-space > Ctrl-k select group above > Ctrl-j select group below > It is now possible to do much more work with Athena without taking > your hands of the keyboard. > > You can now save derivative of mu(E) spectra to files. The > auto-alignment algorithm changed slightly. Let me know if it is > better or worse than before. You can detach the plot buttons from > the main window. That's rather wacky, but people may like it. See > the "Plot" menu. > > Artemis: > I fixed a half dozen really serious bugs that were discovered during > and after the recent analysis course at NSLS. I will certainly not > claim that artemis is bug-free -- you just have to go find new ways > to break it ;-) > > The most significant new feature is on the paths page. There is now > a little box for the degeneracy. It is filled automagically with > the degeneracy from the feffNNNN.dat file. It must be a number and > must not be a variable. I hope this will help clarify the inherent > confusion between N, S02, and other terms which affect the > amplitude. There are menu items for setting all degeneracies to 1 > or resetting them to their feffNNNN.dat values. > > Also I changed the background color of Artemis so that, if you have > both Athena and Artemis open at the same time, they are easier to > tell apart. > > The complete lists of changes and bug fixes are available on the web > site. > > Extra special thanks this time to Mark Jensen (YeS, i fiXeD YouR bUg), > Jia Liu (who was *very* patient in helping me track down some serious > Artemis bugs, thanks!), Shelly Kelly (whose mouse avoidance regimen is > proceeding nicely), and Scott Calvin (for color consultation). > > Have fun! > 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/ > > > --__--__-- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest

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Athena 0.8.004 and Artemis 0.5.001
by Bruce Ravel 24 Oct '02

24 Oct '02

Hi everyone, I posted a new source tarball (horae-005.tar.gz) and new windows executables on my webpage today. Both Athena and Artemis have significant new features and bug fixes. Athena: The biggest new feature is the many new keyboard shortcuts. Here's a summary: Ctrl-t toggle marking of current group Ctrl-p e plot current in energy Ctrl-p k plot current in k-space Ctrl-p r plot current in R-space Ctrl-p q plot current in q-space Meta-p e plot marked in energy Meta-p k plot marked in k-space Meta-p r plot marked in R-space Meta-p q plot marked in q-space Ctrl-k select group above Ctrl-j select group below It is now possible to do much more work with Athena without taking your hands of the keyboard. You can now save derivative of mu(E) spectra to files. The auto-alignment algorithm changed slightly. Let me know if it is better or worse than before. You can detach the plot buttons from the main window. That's rather wacky, but people may like it. See the "Plot" menu. Artemis: I fixed a half dozen really serious bugs that were discovered during and after the recent analysis course at NSLS. I will certainly not claim that artemis is bug-free -- you just have to go find new ways to break it ;-) The most significant new feature is on the paths page. There is now a little box for the degeneracy. It is filled automagically with the degeneracy from the feffNNNN.dat file. It must be a number and must not be a variable. I hope this will help clarify the inherent confusion between N, S02, and other terms which affect the amplitude. There are menu items for setting all degeneracies to 1 or resetting them to their feffNNNN.dat values. Also I changed the background color of Artemis so that, if you have both Athena and Artemis open at the same time, they are easier to tell apart. The complete lists of changes and bug fixes are available on the web site. Extra special thanks this time to Mark Jensen (YeS, i fiXeD YouR bUg), Jia Liu (who was *very* patient in helping me track down some serious Artemis bugs, thanks!), Shelly Kelly (whose mouse avoidance regimen is proceeding nicely), and Scott Calvin (for color consultation). Have fun! 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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Athena: problems at the Bi L3 edge
by Carlo U. Segre 23 Oct '02

23 Oct '02

Bruce: I have encountered some strange behavior at the Bi L3 edge. I have a file which runs out about 1200eV above the edge (13419eV). While Athena does find the high energy when setting the default normalization and spline ranges, it does not plot any of the data beyond 14220 (about 800eV above the edge). In fact, there seems to be a hard limit of about 800eV above the edge for all data and this translates into the k-space plot as well. I am now unsure of what effect this might have on the back transform if the defaults are not touched but certainly the graphical setting of limits for normalization, spline fit, fourier transform and back transform wil not work since the plot does not show the complete data range. Another problem I have found is that the Auto Align feature is somewhat unreliable and does not always yield a visually correct shift. I haven't characterized when exactly this happens but it has seemed to work once on a file and then not work later on the same two files. Cheers, 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 and templates
by Bruce Ravel 22 Oct '02

22 Oct '02

Hi folks, I received this question today: > The third question is about the fitting templates provided in your > software, such as firstshell, mixedshell, three shell, etc. How > can I predict which one is good for the fitting? What are the > differences among them? A bit of recent history. The templates are a feature of Artemis that I started working on just prior to last month's EXAFS course at NSLS. The concept seemed to be working pretty well for copper metal ($ironic_mode=1), so I decided to put the templates in the official release. The thing that the templates have been most useful for so far is to point out that Artemis remains almost completely undocumented. The templates are but one confusing part of the program. Once a user gets confused, there is no place (other than, of course, this mailing list) for the user to turn for information. Sigh. Let me start by explaining what the templates are not: They are not intended to be a complete description of any fit to any data set. That is, you cannot expect to choose an item from the Templates menu, click the big green fit button, and be ready to publish. The templates are intended to help you start a new fitting project by filling in many of the little entry boxes scattered throughout the program with reasonable first guesses for interesting parameters. Another way to say this is that the templates will hopefully help save you from having to do a certain amount of really tedious typing. As an example, the template called "firstshell" makes a non-stupid guess about what kinds of parameters you might want for a fit to the first shell of your data. You will almost certainly have to edit the guess/set/def parameters as well as the path parameters to get a fit to your data that is statistically valid and physically reasonable. Some of the templates ("threeshell" for example) do nothing at all at this time. So, to answer the questions directly: > How can I predict which one is good for the fitting? In a sense, none of them are. However, if you want to do a fit to the first shell, the "firstshell" template may be helpful. If you want to do a fit for which the correlated Debye model is valid, the "debye" template may be helpful. > What are the differences among them? Their names tend to explain the kind of situation in which they might be helpful. Let me end by saying my main point one more time in different language: Templates are the *starting points* for fits. Use them in that sense. They are NOT complete fitting models. Do not use them as such. Hope that helps, 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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SUIs
by Bruce Ravel 22 Oct '02

22 Oct '02

Matt said: MN> Bruce also points out (again, correctly) that we have very little MN> experience training monkeys. OK. You caught me in a little, white lie. Perhaps it is possible to train a monkey to do data analysis. In fact, all my experience is in writing GUIs for Ifeffit. I actually have no experience writing SUIs (simian user interfaces). Perhaps one of our eager users would be interested in doing the pioneering work in this field. ;-) 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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measurement uncertainty
by Bruce Ravel 22 Oct '02

22 Oct '02

Gustavo de Medeiros Azevedo said: GdMA> I''ve recently started using IFEFFIT, and I'm a bit confused on GdMA> the way it estimates the error bars. In the IFEFFIT Reference GdMA> guide, (page 38) you mention the variables epsilon_k and GdMA> epsilon_r, where the measurement uncertainty is stored. In GdMA> that same page, you remark that changing the values of GdMA> epsilon_k and epsilon_r will change chi_squared, Chi-reduced GdMA> but won't affect R_factor and the error bars. As far as I GdMA> understand, the error bars should given by the diagonal GdMA> elements of the co-variance matrix, multiplied by the square GdMA> root of Chi_reduced. In this way, I would expect that varying GdMA> epsilon_k or epsilon_r should affect the estimated GdMA> uncertainties. GdMA> Could you, please, clarify this point? Gustavo, Well, I live one time zone to the east of Matt, so I guess I'm seeing this before he does ;-) I'll take a stab at your question. epsilon_r is measured from the data by performing the Fourier transform of chi(k) and then computing the root mean square value of the magnitude of chi(R) between 15 and 25 Angstroms. The assumption is that, because of disorder and mean-free-path effects, any finite spectral content in that R range can only be due to white noise in the data. The relationship between epsilon_k and epsilon_r is established by the normalization of the Fourier transform. Because epsilon_R enters into the fitting metric, chi-square, when the fit is done in R-space (or epsilon_k for a fit in k space), you are correct that the value of chi-square and reduced chi-square are affected by the value of epsilon_r. The R_factor is just a percentage misfit and so is independent of epsilon. The error bars are independent of epsilon as reported by ifeffit, but the reason for this requires some explanation. The first question to ask at this point is whether it is valid to presume that the dominant error in the exafs measurement is the shot noise measured from the high-R portion of the Foruier spectrum. In most situations it is not -- that is, in most situations the shot noise is much smaller that detector non-linearity, sample inhomogeneity, errors in the theoretical fitting standards, errors in the empirical fitting standards, or a whole host of other problems you might have in a real experiment. Particularly at 3rd generation light sources, photon flux and the shot noise associated with it is the least of your problems. By a long stretch. Thus, the way ifeffit uses to estimate epsilon is manifestly wrong. It is way too small, thus chi-square is very large. Even for a fit that is clearly a good fit, such as the common example of a copper foil that comes with the Artemis, the reduced chi-sqare is much larger than 1. By the formalism of Gaussian statistics, we expect that a good fit has a reduced chi-square of about 1. So what's going on? Well, the problem is that ifeffit makes no attempt (since it operates within a Gaussian framework and not a Baysian framework) to estimate all the other sources of error besides shot noise. Thus it is almost always doomed to have reduced chi-square much larger than 1 (except in the odd case when the shot noise is quite large). So what about the error bars? The diagonal elements of the covarience matrix (i.e. the error bars) are much too small for the same reason that the reduce chi-square is too large, i.e. because epsilon has been vastly underestimated. Ifeffit then makes the assumption that the fit it just finished was, in fact, a good fit. It assumes that the reason that reduced chi-square is not near one is NOT because it is a bad fit, but rather because epsilon has been significantly underestimated. Multiplying the error bars by the square root of reduced chi-square is mathematically equivalent to re-evaluating the covarience matrix with epsilon set to the value it must be for reduced chi-square to equal 1. Thus, it is the mathematical equivalent of assuming that the fit is, in fact, a good fit. So finally, you asked how setting epsilon to some other value will effect the fit. The answer is "Not much." It will have some small effect in how the fit is evaluated numerically because chi-square may be of a different order of magnitude. However, because Ifeffit rescales the error bars under the assumption that the fit was good, manually changing epsilon will have little effect on the results. One more thing needs to be said. Because Ifeffit *always* assums that the fit is a good fit and reports statistics accordingly, it is the RESPONSIBILITY OF THE USER to actually evaluate the quality of the fit. Are the best fit values physically reasonable? Are the parameters highly correlated? Are the rescaled error bars of a reasonable size? Ifeffit cannot answer those questions. You must. And that, finally, is why a human needs to do data analysis. Sadly we cannot train a computer or a monkey to decide if the fit is, in fact, the one you want to publish. Hope that helps, 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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Re: Ifeffit digest, Vol 1 #67 - 1 msg
by Gustavo de Medeiros Azevedo 22 Oct '02

22 Oct '02

Dear Bruce and Matthew, I''ve recently started using IFEFFIT, and I'm a bit confused on the way it estimates the error bars. In the IFEFFIT Reference guide, (page 38) you mention the variables epsilon_k and epsilon_r, where the measurement uncertainty is stored. In that same page, you remark that changing the values of epsilon_k and epsilon_r will change chi_squared, Chi-reduced but won't affect R_factor and the error bars. As far as I understand, the error bars should given by the diagonal elements of the co-variance matrix, multiplied by the square root of Chi_reduced. In this way, I would expect that varying epsilon_k or epsilon_r should affect the estimated uncertainties. Could you, please, clarify this point? Best Regards, Gustavo Azevedo At 12:00 PM 17/10/2002 -0500, you 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-admin(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: using Artemis (Bruce Ravel) > >--__--__-- > >Message: 1 >Date: Thu, 17 Oct 2002 09:33:37 -0400 >To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] using Artemis >Reply-To: ravel(a)phys.washington.edu >From: Bruce Ravel <ravel(a)phys.washington.edu> > > >John, > >I think you replied to me rather than to the list, so I am answering >to list. > >You said: > > jjr> It's great to have the hints on artemis usage. My friendly > jjr> suggestion would be to complement this with sample input/output > jjr> so one can follow along a worked example. The "examples" in the > jjr> artemis source are somewhat useful in this respect, but hacking > jjr> one's way wasn't completely straightford for me. > >I have been thinking about how to provide useful, interactive examples >and documents for the programs. It's difficult. > >The example projects for Artemis are certainly incomplete works-in- >progress. > >There is a README file in the examples directory for Athena that is >helpful, but should, I guess, be an html file. The project files in >both programs' examples directories do have journal entries that help >explain what's going on and give suggestions for other things to do. > >The journals are accessible from the Edit menu in either program and >are a space for writing notes about the project. The journal is saved >in the project file along with all the data. The idea is that you have >a space to record note so that, in 6 months, you can recall why you >did all the wacky things in the project. Not using the journals? You >should be ;-) > > > >So, I agree that the examples are not all they could be. It is >actually hard for me to make good examples since I already know how >the programs work. Good examples are something the people on this >list could put together and contribute. That would be extremely >welcome and an excellent, non-programmer's way of giving something >back to Matt and I. > > > >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/ > > >--__--__-- > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest

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Re: [Ifeffit] using Artemis
by Bruce Ravel 17 Oct '02

17 Oct '02

John, I think you replied to me rather than to the list, so I am answering to list. You said: jjr> It's great to have the hints on artemis usage. My friendly jjr> suggestion would be to complement this with sample input/output jjr> so one can follow along a worked example. The "examples" in the jjr> artemis source are somewhat useful in this respect, but hacking jjr> one's way wasn't completely straightford for me. I have been thinking about how to provide useful, interactive examples and documents for the programs. It's difficult. The example projects for Artemis are certainly incomplete works-in- progress. There is a README file in the examples directory for Athena that is helpful, but should, I guess, be an html file. The project files in both programs' examples directories do have journal entries that help explain what's going on and give suggestions for other things to do. The journals are accessible from the Edit menu in either program and are a space for writing notes about the project. The journal is saved in the project file along with all the data. The idea is that you have a space to record note so that, in 6 months, you can recall why you did all the wacky things in the project. Not using the journals? You should be ;-) So, I agree that the examples are not all they could be. It is actually hard for me to make good examples since I already know how the programs work. Good examples are something the people on this list could put together and contribute. That would be extremely welcome and an excellent, non-programmer's way of giving something back to Matt and I. 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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Athena disappears instantly if a new graph is being presented.
by Bruce Ravel 15 Oct '02

15 Oct '02

Kotoro, This is a question of broad interest. I hope you don't mind that I forward it to the ifeffit mailing list. > On Tue, 15 Oct 2002, "Kotaro Sasaki" <ksasaki(a)bnl.gov> said: KS> Dear Bruce, I was an attender at EXAFS workshop at NSLS last KS> month; I have just updated the syetem of my computer from WINDOW KS> 98 to XP. Now ATHENA seems to run on this system. Yay! Sorry for the hassle. There are just too many operating systems and too few of us working on the software! The situation with 9x/ME is fragile. KS> However I encountered the following problem. When I try to replot KS> a new graph after closing a previous graph, the program is KS> suddenly shot down. This is a known problem with PGPLOT on windows. At this time neither Matt nor I know any better solution than "don't close the plot window." Just get in the habit of NEVER closing the plot window unless you are done with Athena (Same holds true for Artemis) and things should work OK. 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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using Artemis
by Bruce Ravel 14 Oct '02

14 Oct '02

Hi folks, Based on feedback from last months EXAFS course at NSLS and on some email I received last week, I decided there was a need to start working on a beginner's guide to using Artemis and Ifeffit for fitting data. Here is the URL for this new document: http://leonardo.phys.washington.edu/~ravel/software/exafs/startfitting.html Please feel free to send me comments. Feel free to edit it heavily or add material. I would like this to develop into a collaborative, community document. This is not meant to be a comprehensive guide to fitting. Nor is it intended to replace my book of analysis tricks at http://leonardo.phys.washington.edu/~ravel/course/notes/ It is intended to get people over the initial potential barrier of using Artemis and Ifeffit and start them down the road of using them cleverly and intelligently. 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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Athena 0.8.003 released
by Bruce Ravel 14 Oct '02

14 Oct '02

Hi! I just updated the source code tarball and the windows executable for Athena. I added several features last week while I was at the synchrotron and wanted to get them out there. New features include: 1. Energy calibration using the mouse. See the end of the Group menu. 2. Data smoothing. The Fourier filter smoothing is flaky and smoothing is a suspicious thing to do in any case. Take this feature with a grain of salt. 3. Save many marked groups as columns in a single data file. See the File menu. This is handy for exporting much data from Athena to a plotting program 4. Fixed a bug whereby the pre-edge line energy range was not being respected. 5. Athena will now tell you how many spline knots it intends to use. See the Data menu. Thanks to Shelly Kelly for the pre-edge bug and thanks to Dean Hesterberg, Suzanne whose-last-name-I-can't-remember, Kumi Pandya, and Mali Balasubramanian for several good suggestions. There are some new notes on the download page for Windows 9x/ME users and a new page about how to write a good bug report. Check 'em out! 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 ifeffit and Mac OS X
by Jeff Terry 11 Oct '02

11 Oct '02

Hi all, fink is not that hard to use. I believe that the firewall problem is due to the APS blocking the cvs port. I forget which one it is. Jeff

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new release of Athena
by Bruce Ravel 01 Oct '02

01 Oct '02

Hi folks, This morning I posted a new version of the source code package and a new windows executable for Athena on my web site. The changes in Athena include: 1. The ability to read a data file from a multi-element detector and have each channel be made into a separate group. This allows you to examine and discard individual channels before making a summation. 2. Added a simple log-ratio/phase-difference analysis. This can be accessed from the "Analysis" menu. It is currently undocumented, but if you already know how log-ratio works, it should be fairly clear what is going on. 3. Fixed (I think!) a bug in which reading in data and selecting the raw detector data type would crash the program on Windows. 4. Fixed a bug that made it impossible to save chi(q) data correctly. There are some outstanding problems with both the multi-element thing and the log-ratio thing. The most serious of these is one that effects a multi-element file with very many columns. It is quite possible for most of the columns not to be displayed in the column selection dialog. This will be fixed next time. I want to thank Dale Brewe and Oded Kleifeld for their useful bug reports. I also want to thank all of the participants and instructors of the recent EXAFS course at NSLS for putting Athena and Artemis through their paces. Several issues, mostly with Artemis, surfaced at the course and will get my serious attention this fall. *** For those of you receiving this who are not subscribed to the ifeffit mailing list, please consider subscribing. Go to http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/ and follow the instrctions. *** For those of you wanting to use the new Windows executable of Athena, grab it from the downloads page of my website (URL below in my .sig) and drop it on top of the old one in the C:\Program Files\Ifeffit folder. Please note that the installer has NOT been updated to include it. *** For those of you having strange problems on Windows 98, there are some links on my downloads page that may help you deal with certain inherent limitations of that charming operating system. 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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Re: Ifeffit digest, Vol 1 #60 - 1 msg
by Grant Bunker 30 Sep '02

30 Sep '02

Hi, Matt - you might also add that if the energy resolution is small enough (<3 eV say), differences in resolution don't affect the EXAFS, because the EXAFS oscillates much more slowly than the energy width, except perhaps right near the edge. Only in cases where the resolution (or core hole lifetime) is really large (>5 eV) will you see any noticeable effect, and the effect is smaller the farther above the edge that you go. The effect is always important for XANES though, and that can cause a slight change in the EXAFS analysis. If the resolution is large for one scan, and small for another, the detailed shape of the edge can be altered. If the edge position is judged by the first derivative maximum or some other metric of the edge shape, the nominal edge position could be shifted an eV or two. This isn't an issue as long as people don't overinterpret the edge positions, but it could confuse those who do. Similar things happen with thickness effects and particle size effects and self-absorption effects. It is of course straightforward to compensate for spectral the differences by convolution/deconvolution. thanks - grant On Mon, 30 Sep 2002 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-admin(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. experimental resolution (Matt Newville) > > --__--__-- > > Message: 1 > Date: Mon, 30 Sep 2002 10:09:06 -0500 (CDT) > From: Matt Newville <newville(a)cars.uchicago.edu> > To: Irina Pirog <pirog(a)ip.rsu.ru> > cc: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] experimental resolution > > Dear Irina, > > On Wed, 25 Sep 2002, Irina Pirog wrote: > > > > Dear Dr. M. Newville. I'm a researcher of X-Ray department at > > Physical Research institute of Rostov State university. In our > > laboratory we use UWXAFS code treating experimental data. I will be > > very gratitude to you, if you would answer me: how is experimental > > resolution is taken into account in UWXAFS. > > > > Sincerely yours > > > > Irina Pirog. > > This is an excellent question that I'm sure other people may have, so > I hope it's OK with you that I am responding to the Ifeffit mailing > list, which we've set up to share such questions about EXAFS and > Feff, Feffit, Ifeffit, etc. > > By itself, the UWXAFS programs (atoms, autobk, and feffit) don't know > what the experimental resolution is. In principle, the experimental > resolution is important only to the extent that it is different > between two measurements or between a measurement and a theoretical > calculation. For the UWXAFS programs, the only place this becomes > important is when comparing Feff calculations to data in feffit. > > Generally speaking, Feff includes terms that effect the resolution > and all other loss terms in the mean-free-path, lambda. Feff > includes contributions from the core-hole lifetime and some many-body > electron loss terms in lambda, but it does not explicitly put in an > experimental resolution. But Feff usually has a little too much loss > (ie, lambda is a little smaller than it should be), which turns out > to be fine for experiments , with a resolution of ~1eV or so. > > But sometimes you know what the experimental resolution is and > want to include it in the analysis. To account for that, > Feffit has an energy-broadening Path Parameter, ei, that gives > an additional broadening term in the EXAFS equation through > p^2 = (k_real + i/lambda)^2 + ei * 2m / hbar^2 > > where k_real and lambda are taken from the feff0001.dat file for > each path (though they are the same for any one Feff calculation), > and then, the k and lambda terms used in the EXAFS equation are: > k = Re[sqrt(p)] > lambda = 1/Im[sqrt(p)] > > To use this, you would have a feffit.inp with something like this: > > Path 1 feff0001.dat > id 1 path 1 > s02 1 amp_factor > ei 1 1.0 # add 1 eV broadening to Feff calc. > ... > > I mention the s02 parameter here because ei will be very highly > correlated with s02 (and sigma2). In fact, I'd guess that much of > the variation in the observed s02 parameter for different > measurements is actually due to differences in energy resolution. > > > Finally, you may be interested in using the greatly revised versions > of the UWXAFS programs, including graphical user interfaces for data > processing and fitting: > http://cars.uchicago.edu/ifeffit > > Ifeffit also uses a Path Parameter called ei with the same effect, > though the syntax would be slightly different: > > path(1, file=feff0001.dat, s02=amp_factor, ei= 1.) > > Anyway, I hope that answers the question, > > --Matt > > |= Matthew Newville mailto:newville@cars.uchicago.edu > |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 > |= Argonne Natl Lab fax: (630) 252-0436 > |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ > |= Argonne, IL 60439 USA > > > > > --__--__-- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest >

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experimental resolution
by Matt Newville 30 Sep '02

30 Sep '02

Dear Irina, On Wed, 25 Sep 2002, Irina Pirog wrote: > > Dear Dr. M. Newville. I'm a researcher of X-Ray department at > Physical Research institute of Rostov State university. In our > laboratory we use UWXAFS code treating experimental data. I will be > very gratitude to you, if you would answer me: how is experimental > resolution is taken into account in UWXAFS. > > Sincerely yours > > Irina Pirog. This is an excellent question that I'm sure other people may have, so I hope it's OK with you that I am responding to the Ifeffit mailing list, which we've set up to share such questions about EXAFS and Feff, Feffit, Ifeffit, etc. By itself, the UWXAFS programs (atoms, autobk, and feffit) don't know what the experimental resolution is. In principle, the experimental resolution is important only to the extent that it is different between two measurements or between a measurement and a theoretical calculation. For the UWXAFS programs, the only place this becomes important is when comparing Feff calculations to data in feffit. Generally speaking, Feff includes terms that effect the resolution and all other loss terms in the mean-free-path, lambda. Feff includes contributions from the core-hole lifetime and some many-body electron loss terms in lambda, but it does not explicitly put in an experimental resolution. But Feff usually has a little too much loss (ie, lambda is a little smaller than it should be), which turns out to be fine for experiments , with a resolution of ~1eV or so. But sometimes you know what the experimental resolution is and want to include it in the analysis. To account for that, Feffit has an energy-broadening Path Parameter, ei, that gives an additional broadening term in the EXAFS equation through p^2 = (k_real + i/lambda)^2 + ei * 2m / hbar^2 where k_real and lambda are taken from the feff0001.dat file for each path (though they are the same for any one Feff calculation), and then, the k and lambda terms used in the EXAFS equation are: k = Re[sqrt(p)] lambda = 1/Im[sqrt(p)] To use this, you would have a feffit.inp with something like this: Path 1 feff0001.dat id 1 path 1 s02 1 amp_factor ei 1 1.0 # add 1 eV broadening to Feff calc. ... I mention the s02 parameter here because ei will be very highly correlated with s02 (and sigma2). In fact, I'd guess that much of the variation in the observed s02 parameter for different measurements is actually due to differences in energy resolution. Finally, you may be interested in using the greatly revised versions of the UWXAFS programs, including graphical user interfaces for data processing and fitting: http://cars.uchicago.edu/ifeffit Ifeffit also uses a Path Parameter called ei with the same effect, though the syntax would be slightly different: path(1, file=feff0001.dat, s02=amp_factor, ei= 1.) Anyway, I hope that answers the question, --Matt |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0436 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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Fixed a major bug in Athena
by Bruce Ravel 20 Sep '02

20 Sep '02

Well, it took a mere two days for someone to find a serious bug in my "great" new release of Athena. Sigh.... ;-) In 0.8.000, there is a serious bug associated with deleting data groups ("Delete group" or "Delete marked groups" in the "Group" menu). The bug makes it impossible to select one or more of the remaining groups. The unselectable groups are below the group that was deleted, unless you have rearranged the list with Alt-u and Alt-d, in which case the unselectable groups will be hard to predict. I posted a source tarball (horae-002.tar.gz) and a new athena.exe for you Windows users. I strongly encourage upgrading if you installed the release from earlier this week. For those of you Windows users who are new to the ifeffit world, when I update my codes I usually post updated windows executables on my web site. Usually I do NOT rebuild the entire Windows installer. The way to use the updated executable is to download the .exe file from the Windows section of http://feff.phys.washington.edu/~ravel/software/exafs/download.html and replace the .exe file in C:\Program Files\Ifeffit (or where ever you actually installed Ifeffit on your computer) with the new one. Many thanks to Adam Webb for pointing out the problem and for *not* waiting until next week to tell me about it! 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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ifeffit 1.0074, new windows installer
by Matt Newville 18 Sep '02

18 Sep '02

Hi Everyone, As Bruce promised, there's a new windows installer for Ifeffit available that includes his latest versions of athena and artemis. There are also some fixes to ifeffit for phase-corrected FTs, and to both ifeffit and Feffit for semi-related bugs in which values from the debye() and eins() functions not always being updated, especially in 'no fit' mode. Ifeffit is now at version 1.0074. The standalone source code for the Feffit program has also been fixed, and is now at version 2.98. Hopefully, we'll get some Mac updates of these fairly soon. Let me know if there are any questions or problems, --Matt

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new releases of Athena and Artemis
by Bruce Ravel 18 Sep '02

18 Sep '02

Hi folks, Today I posted new source tarballs of Athena and Artemis on my web site. A new Windows installer will be available later today from Matt's web site. This time there are some big changes. 1. I am now distributing Athena and Artemis in a single source tarball called `horae-001.tar.gz'. http://homepage.mac.com/cparada/GML/HORAE.html 2. Windows users should download and install the new installer package because there are several new library and example files. I will continue the practice of posting replacement executables when I _next_ update Athena and Artemis. 3. I have started numbering Athena and Artemis differently. Both programs are getting within striking distance of becoming the magical 1.0. Because of that and other reasons, I want to start using actual version numbers rather than dates to identify the versions. Athena is starting at 0.8 and Artemis at 0.5. The version number on the source tarball will simply be an incremented counter unrelated to the version numbers of the programs. 4. I have made a very large number of changes to Artemis. I'll refer you to the change logs for all the details. In addition to many, many squished bugs, the most important change is that reading in feffNNNN.dat files now works in a much more sensible manner. You can read in individual feffNNNN.dat files or read in all at once by selecting the feff.inp file. In either case, the feffNNNN.dat files should be grouped in a sensible manner in the list in the skinny part of the window. 5. The other big new feature in Artemis is templates. This is a scheme I am working on to help automate the creation of fitting models. The idea is that after reading in data and a feff calculation, you can select, for example, "FirstShell" from the Templates menu. Artemis reads an external file which described a prototypical first shell fit and generates guess, set, and path parameters that hopefully are close to an appropriate fitting model. For copper data, you can hit the big green fit button right after reading in the template file and get a reasonable fit. Some tweaking is usually necessary, but the templates are a decent start. 6. The most interesting change to Athena is that you can now save your data as a "chi(k) record". This is a special file that has the same structure as a normal Athena project file, but which contains only a single entry. That entry is saved as chi(k) rather than as mu(E). The purpose of this kind of file is for reading into Artemis. The advantage of a chi(k) record over chi(k) column data is that the values for things like the Fourier transform parameters that you chose in Athena will be set in Artemis. As always, let me know about problems and feature requests, Enjoy, 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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athena and artemis on Mac OS X 10.2
by Dr. Paul Fons 06 Sep '02

06 Sep '02

I have successfully installed the latest tarballs for athena and artemis on Mac OS 10.2 (Jaguar) and thought I would share with the list the necessary steps to do the installation. 0. Install 10.2 and the latest development tools (included with 10.2) 1. install the latest patch for xterm from the sourceforge site: ceforge.net/projects/xonx/ and install Xfree86 4.2.0.1 2. rebuild the readline libraries within fink after updating from cvs (I use the fink unstable branch) 3. recompile Tk after making the following modification: in Tk/MMutil.pm replace the subroutine const_config with the following code: sub const_config { my $self = shift; my $name; foreach $name (grep /(%|\.(old|bak|q4|orig|rej))$/,keys %{$self->{PM}}) { delete $self->{PM}->{$name}; } my $flags = $self->{'CCCDLFLAGS'}; $flags =~ s/(-[fK]?\s*)pic\b/${1}PIC/; $self->{'CCCDLFLAGS'} = $flags; if ($^O eq 'MSWin32' && $Config{'ccflags'} =~ /-DPERL_OBJECT/) { $self->{'LDFLAGS'} =~ s/-(debug|pdb:\w+)\s+//g; $self->{'LDDLFLAGS'} =~ s/-(debug|pdb:\w+)\s+//g; } elsif ($^O eq 'darwin' ) { $self->{'LDDLFLAGS'} =~ s/-flat_namespace\s+//; $self->{'LDDLFLAGS'} =~ s/-undefined\s+suppress\s+//; if ( -e "$Config{'archlib'}/CORE/$Config{'libperl'}" ) { $self->{'LDDLFLAGS'} .= " -L\${PERL_ARCHLIB}/CORE -lperl "; } elsif ( -e "/System/Library/Perl/darwin/CORE/libperl.dylib" ) { $self->{'LDDLFLAGS'} .= " -L/System/Library/Perl/darwin/CORE -lperl "; } else { warn "Can't find libperl.dylib"; } $self->{'LDFLAGS'} =~ s/-flat_namespace\s+//; $self->{'LDFLAGS'} =~ s/-undefined\s+suppress\s+//; } elsif ($^O =~ /(openbsd)/i) { # -Bforcearchive is bad news for Tk - we don't want all of libpTk.a in all .s o-s. $self->{'LDDLFLAGS'} =~ s/-Bforcearchive\s*//g; } return $self->MM::const_config; } The only thing that is different is a new conditional block in a if block, but I thought it would be easier just to copy and paste. This hack was taken from Bug's Macintosh Page at http://www.lehigh.edu/~sol0/Macintosh/X/ptk/. It turns out it is no longer necessary to hack the dynamic library loader dylib. After changing the subroutine const_config in MMutil.pm, mumble the usual incantations: perl Makefile.PL make make test sudo make install 4. rebuild the ifeffit source cd ifeffit/src/macosx make clean make sudo make install cd ../../wrappers/perl perl Makefiile.PL make sudo make install cd ../python sudo python setup.py install 5. Rebuild athena and artemis cd athena perl Makefile.PL make sudo make install cd artemis perl Makefile.PL make sudo make install You are done! Caveats: I (being perverse) have not done the installation exactly this way. I have compiled xfree86 4.2.99.1 from the online cvs sources and have in addition installed perl 5.8.0. This is a little more complicated (but not much). I also found that ifeffit was looking for a library libg2c.a and made a symbolic link from /usr/lib/gcc/darwin/2.95.2/libg2c.a to /usr/local/lib so that the ifeffit compilation could proceed normally. I am not sure if this step is necessary for all. I don't think perl 5.8.0 and the newest build of Xfree86 are necessary (but on the other hand that is all I have and can't check the alternatives). The version of perl installed by 10.2 is still 5.6. Any questions? Send me email if you have problems and I will help if I can. Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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athena and artemis updates
by Bruce Ravel 26 Aug '02

26 Aug '02

Hi Folks, I have just posted new source tarballs and windows executables for both athena and artemis. Both packages have significant new features and bug fixes. Please read the two special notes at the end of this announcement regarding a couple of bugs that I know about. I will be on vacation the rest of this week -- so I don't want anyone finding new bugs until next week! Athena: 1. fixed a problem that prevented one from plotting a chi(k) record (such as from feff's chi.dat file) 2. fixed a problem in which unmatched parentheses in the header of a data file would seemingly cause Athena to hang. Please note, that this was fixed by having Athena append the necessary close parens to title lines with unmatched open parens (i.e. by having Athena alter some title lines!) 3. Several usability improvements, including ability to specify a data or project file from the command line, remembering preprocessing parameters between files, and remembering the name of an input project file and using it as the default for saving a project file. 4. When records are saved as mu(E) or norm(E) column data, the e0 shift is applied before saving 5. project files now identify the operating system, perl version, and ifeffit version used to create the file. This makes project files more useful to me when submitting them with bug reports. (This was done without affecting compatibility in either direction.) (This is also a new feature in Artemis.) 6. several minor bug fixes Artemis: 1. The big box on the feff page is now filled with a schematic interpretation of the feff calculation. SS and colinear MS paths are highlighted and right-mouse clicking over a path description pops up a useful menu http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… 2. Began work on a templating system. This means that you can read in some data and a feff calculation, then select, say, the "FirstShell" template and Artemis will fill in guess, set, and path parameters with a model that should run to completion and may even be a decent stab at the fit you want to do. Note that the "Templates" menu does nothing on Windows at this time. Although this is undocumented, you can poke at it to see how it works. 3. Changed the color of the "fit" and "ff2chi" buttons. (See the screenshot mentioned above) 4. Several bug fixes and minor usability improvements. For complete details see the change logs in the tarballs or at http://leonardo.phys.washington.edu/~ravel/software/exafs/notes/ OSX users: It is the intended behavior of Athena and Artemis to remember the path whenever you use a file dialog and to use that path as the default the next time you use a file dialog. I am told that Athena does not behave this way on OSX. I am aware of the problem, but have not yet worked to fix it. All users: On your computer, there are probably a few seconds between the outline of Athena or Artemis window appearing on your screen and having all the features of the window be completely rendered. In that time, it is tempting to "jump the gun" and hit control-f so that the file dialog will appear just as soon as perl/Tk finishes rendering all the widgets. Doing this cause a minor race condition that will impede Athena's ability to monitor how much memory you are using and cause many scary-looking messages to be written to standard output. I haven't figured out how to prevent one from doing this, so my advice for the moment is to be patient and let the program finish rendering before using keyboard shortcuts. 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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athena and artemis under Mac OS X 10.2
by Dr. Paul Fons 26 Aug '02

26 Aug '02

I have successfully installed 10.2 on my Mac and found that, after a recompile readline is just fine. The only problem I am having is with Tk which is broken due to trouble with the new dynamic linker library. The author of the last hacked dyld loader Stephen.O.Lidie(a)lehigh.edu is working on a new version of dyld as we speak (write). It should be done tomorrow (hopefully) he says. What I wanted to add here is to warn people *not* to use to old hacked version of dyld on the new 10.2 as it will almost certainly break the system (e.g. every command as well as the OS uses the dynamic library loader). I will let the list know when things are working. For the moment I have my pismo laptop running 10.1.5 until I get this sorted out on my dual 500 MHz G4 desktop. Mac OS X 10.2 does seem nice and fast! Paul

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Warning: ifeffit users on Mac OS X
by Jeff Terry 24 Aug '02

24 Aug '02

Hello, If you are dependent upon ifeffit under OS X, DO NOT install the 10.2 upgrade. This upgrade breaks the readline library which is needed by ifeffit. A quick web search showed this to be a known problem with no current solution. Readline does not currently compile under 10.2. I tried a cursory effort compilation which resulted in many missing symbols. Jeff

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Warning:ifeffit on OS X
by jterry94＠mac.com 24 Aug '02

24 Aug '02

Do not install OS X 10.2 if you rely on ifeffit under OS X. The readline libraries break and ifeffit cannot be used. A quick web search revealed that others have seen the problem and a quick attempt to recompile readline by myself has failed: missing symbols. Jeff

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ifeffit 1.0073 released
by Matt Newville 19 Aug '02

19 Aug '02

Hi Everyone, I've posted Ifeffit 1.0073, both source code and Windows installer, on the ifeffit download page. Following the earlier discussion of interpolation schemes for continuous scan data, this source code has added 'interp=' options ('interp=line', 'interp=quad', 'interp=cubic') to the spline() and bkg_cl() commands. There are no other major changes to the base library, but a few minor improvements and bug fixes in the source. The Windows installer includes the latest (I believe!!) of athena, artemis, sixpack, and even gifeffit. Also, on Windows, the GrWin plot window now raises to the top at every plot(), cursor(), and zoom() command. Enjoy, --Matt

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symmetry in Atoms
by Bruce Ravel 19 Aug '02

19 Aug '02

Here is an interesting question that was waiting in my mailbox this morning. I thought folks on the ifeffit list might also find it interesting and, in any case, it seems useful to have the question and the answer in the ifeffit list's archive. B The attached EXCEL file is the structure data for Fe17Y2 referred from Pearson's Handbook. Actually I get FEFF.inp file by Atoms using the input data as attached list. I wondered, howevere, how Atoms recognize site symmetry thorough the Atoms.inp data. My question is that the input data for each symmetric site should fulfill the site symmetry like as following list. In case of Fe17Y2 (No. 194), when I input (0 0 1/4) then Atoms will automatically recognizes this is 2b site. But when I input the number (0.1672 0.3344 0.9874) for 12k-site, how Atoms recognizes this is 12k site. Or if input numerical numbers do not fulfill the symmetry condition, then how Atoms deal with it. Thank you for your attention. space group number : 194 setting : 1 Hermann-Mauguin : P 6_3/m 2/m 2/c Laue group : 6/mmm point group : 6/m mm positions 24 l x,y,z -y,x-y,z -x+y,-x,z -x,-y,z+1/2 y,-x+y,z+1/2 x-y,x,z+1/2 y,x,-z x-y,-y,-z -x,-x+y,-z -y,-x,-z+1/2 -x+y,y,-z+1/2 x,x-y,-z+1/2 -x,-y,-z y,-x+y,-z x-y,x,-z x,y,-z+1/2 -y,x-y,-z+1/2 -x+y,-x,-z+1/2 -y,-x,z -x+y,y,z x,x-y,z y,x,z+1/2 x-y,-y,z+1/2 -x,-x+y,z+1/2 12 k x,2x,z -2x,-x,z x,-x,z -x,-2x,z+1/2 2x,x,z+1/2 -x,x,z+1/2 2x,x,-z -x,-2x,-z -x,x,-z -2x,-x,-z+1/2 x,2x,-z+1/2 x,-x,-z+1/2 12 j x,y,1/4 -y,x-y,1/4 -x+y,-x,1/4 -x,-y,3/4 y,-x+y,3/4 x-y,x,3/4 y,x,3/4 x-y,-y,3/4 -x,-x+y,3/4 -y,-x,1/4 -x+y,y,1/4 x,x-y,1/4 12 i x,0,0 0,x,0 -x,-x,0 -x,0,1/2 0,-x,1/2 x,x,1/2 -x,0,0 0,-x,0 x,x,0 x,0,1/2 0,x,1/2 -x,-x,1/2 6 h x,2x,1/4 -2x,-x,1/4 x,-x,1/4 -x,-2x,3/4 2x,x,3/4 -x,x,3/4 6 g 1/2,0,0 0,1/2,0 1/2,1/2,0 1/2,0,1/2 0,1/2,1/2 1/2,1/2,1/2 4 f 1/3,2/3,z 2/3,1/3,z+1/2 2/3,1/3,-z 1/3,2/3,-z+1/2 4 e 0,0,z 0,0,z+1/2 0,0,-z 0,0,-z+1/2 2 d 1/3,2/3,3/4 2/3,1/3,1/4 2 c 1/3,2/3,1/4 2/3,1/3,3/4 2 b 0,0,1/4 0,0,3/4 2 a 0,0,0 0,0,1/2 The attachment contained this: Fe17Y2 "structure type" "Pearson Smmbol" "space group" No Fe17Ho2 hP44 P6_3/mmc 194 Wyckoff x y z occupncy Y1 2b 0 0 0.25 0.41 Y2 2c 0.3333 0.6666 0.25 0.35 Y3 2d 0.3333 0.6666 0.75 1 Fe1 4e 0 0 0.1103 0.28 Fe2 4f 0.3333 0.6666 0.1049 0.71 Fe3 6g 0.5 0 0 1 Fe4 12j 0.3341 0.964 0.25 1 Fe5 12k 0.1672 0.3344 0.9871 1 And my response: Well, you made it very easy for me to answer your question by including the symmetry table for your space group in your email. The answer is that Atoms reads a data base of the space group symmetries. For your example, #194, the data base entry contains this information: x,y,z -y,x-y,z -x+y,-x,z -x,-y,z+1/2 y,-x+y,z+1/2 x-y,x,z+1/2 y,x,-z x-y,-y,-z -x,-x+y,-z -y,-x,-z+1/2 -x+y,y,-z+1/2 x,x-y,-z+1/2 -x,-y,-z y,-x+y,-z x-y,x,-z x,y,-z+1/2 -y,x-y,-z+1/2 -x+y,-x,-z+1/2 -y,-x,z -x+y,y,z x,x-y,z y,x,z+1/2 x-y,-y,z+1/2 -x,-x+y,z+1/2 which you will recognize as Wyckoff's position "l". Atoms doesn't exactly distinguish between Wyckoff's position l and position b. Instead it assumes that everything is position l and discards repeated positions. To understand this, apply the symmetry operations in the list above to the position (0,0,1/4). You will notice that 12 of them generate the position (0,0,1/4) and 12 of them generate (0,0,3/4). Atoms notices that and discards 11 of each. So, you see, position b is not actually different from position l, it's just degenerate due to symmetry. Atoms will notice these degeneracies a posteriori and does not need to know about the a priori. So, where did Wyckoff get his notation scheme from? Well, the Wyckoff positions are simply ordered in terms of decreasing degeneracy. Position a is the most degenerate and the highest lettered position is the non-degenerate one. This is not actually a useful notation scheme because there is no consistency between space groups. That is, position "c", for example, in group 194 has no relationship to position "c" in any other space group. The last thing worth mentioning is that Atoms works with 5 significant digits. If you use, as you suggest, (0.1672 0.3344 0.9874) then Atoms will find the correct amount of degeneracy. However, how you write (1/3, 2/3, z) is very important. Atoms 3.0 is able to read the string "1/3" as a coordinate. However if you choose to write coordinates in decimal notation, you must be careful. (0.33333, 0.66667, z) is fine and will generate 4 positions. (0.33, 0.67, z) will have problems related to numerical precision. Hope that's clear, 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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Atoms 3.0beta7
by Bruce Ravel 15 Aug '02

15 Aug '02

Hi folks, I released a new version of Atoms today which includes one small (but possibly important) change from the previous version. I learned that the database entry for a specific space group (I -4 3 d, #220) was in error. I fixed this and made a new release. There is a new tarball and Windows executable on my web site. If you are a windows user, you will also need to install the new version of the space_group.db file, as per the instructions on the downloads page. I also updated WebAtoms on Matt's server. This error has ABSOLUTELY NO IMPACT on any other space group. Indeed, without an atoms input file using the affected space group, you would never notice the problem. This underscores an interesting aspect of crystallography. While group theory tells us that there are 230 possible space group, nature seems to prefer using only a small subset of them. Indeed, in all the years since I started working on Atoms, I have not seen an example of a crystal in this space group until this week. The collection of input files that I distribute with Atoms for the purpose of testing the code includes examples of less than 80 space groups. Anyway, here is the input file that lead me to the error in Atoms' space group data base: title = Cu3As Domeykite title = Iglesias, J. E., and Nowacki, W., title = Zeitschrift fur kristallographie, kristallgeometrie, title = kristallphysik, kristallchemie, v. 145, pp. 334-345 (1977). space = I -4 3 d a = 9.6190 core = Cu rmax = 8.0 atoms ! elem x y z Cu -0.02930 0.12020 0.18760 As -0.02980 -0.02980 -0.02980 One might notice that the old Fortran version of Atoms handles this input file correctly. The irony of that is not lost on me, particularly in light of my frequent and loud trumpeting of the advantages of the new version over the old version. Thanks to Elspeth Barnes for bringing this problem to my attention. 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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athena 2002.08.14
by Bruce Ravel 14 Aug '02

14 Aug '02

Hi, I put a new tarball and Windows build for Athena on my website this afternoon. There are only a few changes since last week, but they are interesting enough to merit a new release. 1. I fixed a problem in the display of the group list. When deleting groups, slightly more vertical space was removed than had been allocated when the group was listed. This lead to a misalignment that was particularly apparent when deleting many groups. 2. I now do the thing where the cursor changes to a stop watch (an hourglass on Windows) whenever Athena is doing anything time consuming. That keeps you from clicking buttons as a bad time and also gives you a visual cue when lengthy procedures finish. 3. I put in more careful checks of memory usage. I had a bug report that was traced back to a large quantity of data overflowing Ifeffit's static memory space. I now check memory usage more frequently and issue a warning message when the amount of memory is running short. The scheme is not foolproof. It is still possible to overflow the memory before triggering a warning, but Athena should catch many situations in which this might happen. 4. It is now possible to create a "background group". That is a data group which is listed in the groups list and which contains as its data the background function computed from another data group. This is useful for at least three things, including directly comparing different background functions, comparing a background function to a background computed by FEFF and read from the 5th column of xmu.dat, and investigating low-R phenomena such as multi-electron effects or the so-called atomic xafs. 5. Project files now identify the version of perl, the version of ifeffit, and the operating system of the computer along with the version of Athena used to create the file. This is information I need when I am sent a project file as part of a bug report. There is no problem with backwards compatibility -- project files without this information will be read without problem. And project files continue to be transferable between platforms. The tarball and the Windows exe are in the standard places. Special thanks to Raul Barrea for a very useful bug report which lead to most of this week's new features. 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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athena 2002.08.08 and artemis 2002.08.08 released
by Bruce Ravel 09 Aug '02

09 Aug '02

Howdy folks, This afternoon I put new source tarballs of Athena and Artemis on my website. I also build Windows executables of both programs for dropping on top of a current ifeffit installation (with the Splashscreen commented out!). These can be found in the standard places. These are mostly bug fix releases, although each program got one major new feature. For Athena the highlights are: 1. the column selection dialog now makes a stab at figuring out if you have transmission or fluorescence data. How it does this is configurable (so that it'll work well on your data files) but currently undocumented. Ask on this list if you want to know. 2. fixed a bug in the auto-align feature wherein the e0 shift of the alignment standard was ignored 3. fixed a horrid bug in the merge code where I added the e0 shift to the k-array when merging in k. (yikes!) 4. write a message to the Echo area if the plot multiplier is set to 0, which is usually not a good choice 5. added some complicated logic to avoid plotting groups if any relevant range is backwards. For example, if fft_kmin is greater than fft_kmax for a group, that group will not be plotted in R or q space and a (hopefully) helpful message will be printed to the echo area. 6. a few other minor problems were fixed and some usability issues on Windows were addressed (mostly having to do with raising small windows to the top of the screen) For Artemis the highlights are: 1. If you right-click on a word in one of the entry boxes for path parameter math expressions on a Path page, a menu will pop up which allows you to easily set that word as a parameter. It's very useful, but a little hard to explain. Here are some screen shots that might help: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/be… http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/af… In the first picture, I right-clicked on the word "amp". After selecting the "guess" option from the menu, the view is switched to the GDS page and focus is given to highlighted box so you can start typing. This feature works sensibly for parameters which already exist and for those that have not yet been defined. 2. fixed a problem which prevented saving path data in any space 3. fixed a problem reading a project file with multiple feff calculations 4. a few other fixes to functionality and usability Extra special thanks to Mark Jensen, Paul Fons, and Kumi Pandya for useful bug reports and to Shelly Kelly for suggesting the right-click thing in Artemis. Enjoy and, as always, let me know what needs fixin' 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: ifeffit and perl 5.8.0
by Carlo U. Segre 01 Aug '02

01 Aug '02

I am still using Atoms beta5 myself because I have not been successful in getting beta6 to compile. I just hadn't gotten around to figuring out if it was me or a real problem. Carlo On Thu, 1 Aug 2002, Dr. Paul Fons wrote: > > > I have now gotten perl 5.8.0 to work with both athena and artemis. As > Carlo said in an earlier message, the binaries of 5.6 and 5.8 are not > compatible and it necessitates rebuilding compiled packages. There is > an OS X problem as well in that the make install command for perl 5.8 > doesn't seem to overwrite all of the files so I manually deleted the old > installation and did a make install in the perl 5.8 directory. The > weird thing is that only tkatoms (B6) doesn't recompile. I can't even > do a perl Makefile.PL without getting an error. Any ideas? > > > Here is a clip: > > perl -v > This is perl, v5.8.0 built for darwin > ... > > > [etld1220:~/Ports/Atoms-3.0beta6] paulfons% perl Makefile.PL > dyld: perl Undefined symbols: > _Perl_safefree > _Perl_safemalloc > _Perl_saferealloc > _Perl_sv_2pv > _perl_call_sv > _perl_eval_sv > _perl_get_sv > > -- Carlo U. Segre -- Professor of Physics 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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Re: Ifeffit digest, Vol 1 #42 - 1 msg
by Raul Barrea 01 Aug '02

01 Aug '02

Hi Bruce, I've downloaded the exec file you've posted in your web site. Atoms and the periodic table work fine but Athena and Artemis don't work. Maybe there is something missing. Are the dll's the same for the old and new versions of the exec files? Thanks Raul Barrea BioCAT/APS ----- Original Message ----- From: <ifeffit-request(a)millenia.cars.aps.anl.gov> To: <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tuesday, July 23, 2002 12:01 PM Subject: Ifeffit digest, Vol 1 #42 - 1 msg > 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-admin(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. serious athena bug fix (Bruce Ravel) > > --__--__-- > > Message: 1 > Date: Mon, 22 Jul 2002 18:15:24 -0400 > To: ifeffit mailing list <ifeffit(a)millenia.cars.aps.anl.gov> > Reply-To: ravel(a)phys.washington.edu > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: [Ifeffit] serious athena bug fix > > > Hi folks, > > Today Shelly Kelly pointed out a serious bug in the code that merges > spectra. Spectra merged as mu(E) or norm(E) have not ever been > calculated correctly. There were several problems -- the worst was > that the e0 shifts for all groups involved in the merge were ignored. > This resulted in numerous problems with the merged spectra. > > I think I have fixed the problem -- at least the sample data that > Shelly gave me now gets merged correctly. There is a new source > tarball on my web site. > > I also added a couple of trivial features to both athena and artemis. > The first is a splash-screen, i.e. something to look at in those > endless seconds between double clicking on the icon and having the > program spring to life on the screen. I also added several keyboard > shortcuts for common tasks in both programs. You can see what these > are by examining the menus in the menubar. > > > I also added something new to my web site. Athena and Artemis change > much faster than Ifeffit these days. The bad part of this is that > Windows users don't get to take advantage of my updates as often as > unix and OSX users. So today I added a section to the downloads page > with links to the executables of my four programs. I doubt I will > update the executables as often as I update the source tarballs. But > when I do, I'll post the executables on the downloads page. > > The idea of these individual executables is that you replace the > executable in the C:\Program Files\Ifeffit\ folder with the new one. > These executables now found on my downloads WILL NOT RUN CORRECTLY > outside the context of a properly installed ifeffit package. But if > you have installed Ifeffit using the installer from Matt's web page, > you will be able to drop my new executables in place. > > 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/ > > > --__--__-- > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest

3 2

Perl 5.8 and ifeffit
by Dr. Paul Fons 31 Jul '02

31 Jul '02

I have now gotten perl 5.8.0 to work with both athena and artemis. As Carlo said in an earlier message, the binaries of 5.6 and 5.8 are not compatible and it necessitates rebuilding compiled packages. There is an OS X problem as well in that the make install command for perl 5.8 doesn't seem to overwrite all of the files so I manually deleted the old installation and did a make install in the perl 5.8 directory. The weird thing is that only tkatoms (B6) doesn't recompile. I can't even do a perl Makefile.PL without getting an error. Any ideas? Here is a clip: perl -v This is perl, v5.8.0 built for darwin .... [etld1220:~/Ports/Atoms-3.0beta6] paulfons% perl Makefile.PL dyld: perl Undefined symbols: _Perl_safefree _Perl_safemalloc _Perl_saferealloc _Perl_sv_2pv _perl_call_sv _perl_eval_sv _perl_get_sv Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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Carlo's message and perl 5.8.0
by Bruce Ravel 31 Jul '02

31 Jul '02

Hey, I just thought I would drop a short note to the list explaining in fewer words what Carlo said. The bottom line is that 5.8 and 5.6 are not binary compatible. This is an annoyance that affects many things, including the ifeffit interface. The solution is to go to the place where you unpacked ifeffit and cd to the wrappers/perl/ directory. Rebuild the ifeffit interface by doing make clean perl Makefile.PL make make install I don't think you'll actually need to reinstall athena, but it couldn't hurt. This is not a OSX-only, or debian-only problem. We will all have this annoyance when we get around to updating to perl 5.8 That doesn't make me happy, but I'll deal. Starting to distribute a big tarball with the ifeffit interface bundled with all my codes will actually go along way towards solving that problem. And, if you are not updating to perl 5.8 (or don't even grok what this discussion is about), then you will probably not be affected by this issue. Thanks Carlo! B Bruce Ravel e-mail: ravel(a)phys.washington.edu URL: http://feff.phys.washington.edu/~ravel/

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Perl 5.8.0 packages (fwd)
by Carlo U. Segre 31 Jul '02

31 Jul '02

In reference to the recent mail about Perl 5.8.0. This is specific to the Linux Distribution (Debian) that I use but it explains why version 5.8.0 is not drop in compatible with athena and artemis. Carlo -- Carlo U. Segre -- Professor of Physics Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre ---------- Forwarded message ---------- Date: Wed, 31 Jul 2002 23:18:29 +1000 From: Brendan O'Dea <bod(a)debian.org> To: "debian-devel-announce(a)lists.debian.org" <debian-devel-announce(a)lists.debian.org> Cc: Debian Perl List <debian-perl(a)lists.debian.org> Subject: Perl 5.8.0 packages Resent-Date: Wed, 31 Jul 2002 08:20:14 -0500 Resent-From: debian-devel-announce(a)lists.debian.org Perl 5.8.0 packages are currently being tested in a staging area: deb http://auric.debian.org/~bod perl/$(ARCH)/ deb-src http://auric.debian.org/~bod perl/ the principal reason for a staging area is that these packages are not binary compatible with the previous perl packages, which means that all binary (XS) modules and programs embedding a perl interpreter will need to be rebuilt. The complete list of packages which will require a rebuild may be obtained by running: apt-cache showpkg perlapi-5.6.0 perlapi-5.6.1 libperl5.6 In addition, since the perl 5.8.0 packages break binary compatibility I've chosen to enable ithreads which may affect some of the packages listed above--notably if packages embedding an interpreter declare their own xs_init subroutine rather than generating one with ExtUtils::Embed::xsinit may need to add a pTHR argument to that function.

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(no subject)
by Bruce Ravel 29 Jul '02

29 Jul '02

Paul said: PF> Just for fun, I tried installing the new perl 5.8.0 release on PF> Mac OS 10.1.5. The perl installation went fine (all the tests PF> passed that should), however, when I tried to reinstall ifeffit, PF> problems ensued. The installation attempt (the very tip) is PF> pasted below. Is this a sign of problems to come? I don't know PF> perl well enough to know where these modules came from. For the PF> moment my resolution is to install perl 5.6.1 (a slight upgrade PF> from the default 5.6.0 included with the OS) I haven't tried perl 5.8.0 myself yet. I presume that there will not be any issue with my code, but obviously I haven't tested it. My best suggestion is to install the ifeffit wrapper by itself without athena. (If you are using an older ifeffit distribution which has an athena subdirectory under wrapper/perl/, delete the athena subdirectory before building the wrapper.). Then install athena afterwards. My next, and more annoying, suggestion, is to clean up any traces of ifeffit's perl inteface (i.e. any instances of the files Ifeffit.pm, Ifeffit.bs, and Ifeffit.so) then try again. All of this points to something that I brought up on the list a while ago and which Matt has been advocating for. It would probably be best to make on big package with the the Ifeffit/perl inteface and my programs all bundled together and distributed separately from Ifeffit. I'll look into that next month. 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 and Athena
by Bruce Ravel 28 Jul '02

28 Jul '02

Hi Folks, I belive that I have solved the problems that I discussed earlier today for athena and artemis on both windows and unix. I have uploaded new tarballs and windows executables to the "downloads" page. Mark Jensen and Raul Barrea have confirmed that the windows executables posted today work as expected when you drop them into an existing Ifeffit distribution. Thanks guys! Sher Alam informed me of the problem with the missing module in the tarballs. I believe that I have solved that problem, but I would be grateful if you would let me know how it works for you, Sher. I also fixed yet another problem with merging in energy space which was discovered by Shelly Kelly. I believe that I have it working correctly now, but I am sure someone will let me know if that's not the case! This bug is fixed in today's tarballs AND Windows executables. Thanks to Mark, Raul, Sher, and Shelly. I am, as always, quite grateful. 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/

2 1

continuous scan data
by Matt Newville 28 Jul '02

28 Jul '02

Hi Everyone, I made some small, probably incomplete, progress on dealing with the problem of continuous scan (or QEXAFS) XAFS data for which the XAFS data is sampled on a fine energy grid -- 1eV was used for the data Raul posted. As mentioned earlier, Ifeffit currently uses a fixed k-grid of 0.05Ang^-1 for chi(k). At k = 10Ang^-1, this corresponds to energy steps of nearly 4eV. Any scheme to use "all the data" to map to chi(k=10) may be tricky. The basic approaches are 1) better interpolation algorithm. 2) change the k-space grid size. 3) doing some sort of averaging of the data around a particular k value. At this point I've tried the first 2 of these. More details are posted at http://cars9.uchicago.edu/ifeffit/qexafs/ including data files and some plots figures. This is all with 'experimental' versions of ifeffit. First, I made the interpolation scheme used for the translation of chi(E) to chi(k) in the spline command have a few options: 'linear' using two surroundings data points 'quadratic' or parabolic using three data points 'cubic spline' put a cubic spline through all the data points Linear interpolation is not very satisfying. The results from 'quadratic' and 'cubic spline' are very similar. The next thing I did was to change the k-grid spacing from 0.050 to 0.025 and to 0.010 Ang^-1, and repeated the use all 3 interpolation schemes. Using 0.050 is noticeably different from 0.025, while 0.025 and 0.010 seem pretty similar to me. This was all done by changing the kgrid at compile time, which will be possible in 1.0073. I also played around with trying to make the kgrid and size of the FFT array variables that can be set at run-time. This seems highly desirable for cases like this. Surprisingly to me, it also seems possible. I have a *highly* experimental version that allow kgrid to be set at run time. In favorable conditions, it even works correctly. There are still some severe bugs with this version that I do not fully understand, and I doubt I'll have much time to work on it soon. But if anyone is very eager to try it, I'd be willing to send it. I have not yet tried implementing any 'averaging of adjacent points' such based on a rolling boxcar or a convolution with a Lorenztian. I could be persuaded to try such things, but at this point I'm not sure what the right thing is. Finally, coming back to the interpolation of the continuous scan data, the data Raul sent has some systematic effects going on that might complicate these comparisons. The effects can be seen from the un-interpolated chi(k) data: http://cars9.uchicago.edu/ifeffit/qexafs/orig_data_zoom.png and the attempts to interpolate this data: http://cars9.uchicago.edu/ifeffit/qexafs/kgrid_zoom.png It looks like there are systematic trends due to insufficient precision (only 4 digits in the mu(E) data). I don't know enough about the electronics used to know if this is intrinsic to the measurements or not. Also, does anyone know how accurate the energies are with this kind of data? Thanks, --Matt

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Re: GIFeffit bugs
by Matt Newville 28 Jul '02

28 Jul '02

Hi Raul, On Fri, 26 Jul 2002, Raul Barrea wrote: > I was working with Gifeffit for windows and I save a session > file as ifeffit.sav but I couldn't open it again. Could you > please check it to see what can be wrong? Yes, GIFEFFIT is not handling the opening of files in directories with spaces in their name. It appears that save files are written correctly and can be read from a directory without a space in the name, but not if there is a space in the name. Should be easy to fix. > I found that log(my_logfile.log) is not working properly in > the windows version of GIfeffit. The program literally > crashes. A visual fortran run time error window appears. This > is not a serious bug but I think you must know it. I think this is related to all the other problems that result in a Visual Fortran Error of the form: forttl: severe (38): error during write, unit -1, file CONOUT$ .... which are come from GUIs that have no DOS console associated with them for simple print statements to be sent. These messages should not be necessary, but making sure that they never happen is harder. A solution should be fairly easy. I hope to post a version with fixes for both of these problems later today or tomorrow. > By the way, have you had any time to find a solution to the > interpolation routine to include all the statistics available > in the experimental data? I've made some progress, but not a complete solution. I'll send a separate post on this later today. --Matt

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Re: [Ifeffit] athena / artemis
by Bruce Ravel 25 Jul '02

25 Jul '02

Hi folks, On Monday I was rushing to get updated versions of Athena and Artemis finished so I could go on a two day trip to NSLS on Tuesday and Wednesday. In my rush, I posted broken versions of Athena and Artemis on my web site. Upon my return, I found my mailbox overflowing with reports of problems. For the Windows users: I belive that Matt correctly identified the problem. I, of course, installed the logos for the splashscreens on *my* computer, but forgot that no one else would have them installed on theirs. That's none too bright! Matt sent me personal email while I was gone stating that he is almost ready to release 1.0073. So here is what I propose. I'll build new executables that do not use the splashscreens and wait for 1.0073 to release that feature. In the future, I'll try very hard to remember to post any new files that need to go into the distribution. Thanks to Mark Jensen, Raul Barrea, and Matt for downloading the executables and reporting back with their problems. For the Unix users: The splashscreens appear to be a problem for unix types as well. The code which handles the splashscreen makes use of a perl module that I had thought was part of the standard distribution but which, in fact, is not. The solution is simple. I'll include the missing module in the source tarballs for athena and artemis and post the new tarballs later today. Thanks to Sher Alam for pointing out this problem. I'll send mail out to the list later today when the new executables and tarballs are in place. Once again, thanks to all of you for taking the time to provide feedback. Your help is very much appreciated. 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: FT padding
by Matt Newville 23 Jul '02

23 Jul '02

Dear Marcus, Recently, Marcus Karolewski wrote: > Dear Matt, > > I have been looking thro' your (highly informative) PhD thesis today in the > hope of finding some discussion about the zero padding used in FT > operations on XAFS data, but there doesn't seem to be any direct reference > to the reasoning behind it, although I gather you padded your data up to 25 > A-1. > > I realise that FT padding makes the data look nice in R-space, but I'd like > to ask whether you know of any other benefit to be gained from it. To my > way of thinking, there seems to be a definite drawback to padding insofar > as one ends up with data that consist mostly of interpolated points in R > space. This would seem to make a mockery of the fitting criteria which > strictly should be based on the actual number of points justified by the > range of the expl data. I would be very interested to hear your comments if > you can find the time. Excellent question! I hope it's OK if I CC this to the ifeffit mailing list, as it's relevant to a current discussion there on interpolating QEXAFS data, and because others might be interested or have opinions on this as well. Short answer: Yes, zero-padding is mostly to make the data look nice in R-space. A mockery of the fitting criteria?? I wouldn't go that far! Just for reference, the important values for the FTs are: kgrid: the k-grid spacing needs to get 'all the features'. N_fft: the FFT should use a number of points = a power of 2, even if zero-padding is used. rmax: the largest frequency that can be seen. rgrid: the resulting grid spacing in R should be small enough to avoid missing real features in R-space. Ifeffit uses kgrid=0.05Ang^-1 and zero-pads chi(k) to have N_fft=2048. The outputs from feffit also use these values. rmax and kgrid are simply related: rmax = pi /(2* kgrid) ~= 31.4 Ang for kgrid=0.05 The spectra above Rmax are a mirror image of the lower-R portion of the spectra: chi(R) = chi(2*Rmax-R) for R > Rmax 31.4Ang is much further than the XAFS really extends, but we can use the high portion to estimate the noise in the signal (feffit does this). So, we probably wouldn't want to go to kgrid=0.10 & rmax=16Ang. In fact, we might be tempted to use a smaller kgrid. The spacing of the R-space data, rgrid, is given as rgrid = pi / (kgrid * N_fft) For N_fft=2048 and kgrid=0.05Ang^-1, rgrid~=0.03Ang. If we had N_fft = 512, we'd have kmax = 0.05 * 512 = 25.6Ang-1 which is probably reasonable -- I've seen a few data sets past 25Ang^-1, but these are rare. We'd also have rgrid = pi / (0.05 * 512 ) = 0.122 Ang This has the advantages of giving data points in R that is closer to the 'real spacing' of "pairs of independent data points" in R-space: Delta R ~= pi / (K-range). The emphasis here should be on the 'approximate' sign. It is tempting to interpret this formula as "my independent data points are exactly 0.XXX Ang apart", but this is a serious overstatement. A better interpretation is that distances separated by less than (2pi/K-range) will be very difficult to distinguish. Using a coarser R spacing does make the fits faster. In fact, feffit (the program) does NOT use N_fft = 2048 when doing the fits -- it uses either 256, 512, 1024, or 2048 depending on the data k-range. This does indeed speed up the fits (for all output arrays, N_fft=2048 is used to make the plots prettier). Long ago (when computers ran on diesel), N_fft=128 was also allowed, but this was not reliable because there was a good chance of getting stuck in a 'false minima' with data that sparsely spaced in R. I've seen such false minima happen a few times, and took out the option of using N_fft = 128. Because it's painful to constantly switch N_fft, ifeffit currently uses kgrid=0.05 and N_fft = 2048 throughout. I have started working toward having these be changeable at will inside the program, but this still causes a few problems at the moment. Anyway, I wouldn't say that using zero padding and a large N_fft is really cheating much. It's really just oversampling the data. An FT is linear, so zero-padding does not change your data (much), but just convolves the 'independent data points' with Gaussian functions. Finally, zero-padding does change your data some because it means that you are asserting that chi(k)=0 for k>kmax. A better approach would be to pad with random noise at a level consistent with your data. This could be done, I suppose, but has not been done yet. Hope that helps, --Matt

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serious athena bug fix
by Bruce Ravel 22 Jul '02

22 Jul '02

Hi folks, Today Shelly Kelly pointed out a serious bug in the code that merges spectra. Spectra merged as mu(E) or norm(E) have not ever been calculated correctly. There were several problems -- the worst was that the e0 shifts for all groups involved in the merge were ignored. This resulted in numerous problems with the merged spectra. I think I have fixed the problem -- at least the sample data that Shelly gave me now gets merged correctly. There is a new source tarball on my web site. I also added a couple of trivial features to both athena and artemis. The first is a splash-screen, i.e. something to look at in those endless seconds between double clicking on the icon and having the program spring to life on the screen. I also added several keyboard shortcuts for common tasks in both programs. You can see what these are by examining the menus in the menubar. I also added something new to my web site. Athena and Artemis change much faster than Ifeffit these days. The bad part of this is that Windows users don't get to take advantage of my updates as often as unix and OSX users. So today I added a section to the downloads page with links to the executables of my four programs. I doubt I will update the executables as often as I update the source tarballs. But when I do, I'll post the executables on the downloads page. The idea of these individual executables is that you replace the executable in the C:\Program Files\Ifeffit\ folder with the new one. These executables now found on my downloads WILL NOT RUN CORRECTLY outside the context of a properly installed ifeffit package. But if you have installed Ifeffit using the installer from Matt's web page, you will be able to drop my new executables in place. 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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Re: continuous scan data
by Webb, Samuel M. 19 Jul '02

19 Jul '02

Matt -- What we've used at DND-CAT is a box-car type averaging to grid the data. Basically, impose a 0.05 A-1 grid and bin all points that lie between a starting and ending point of each point on the grid. Of course, at DND we have data that has been collected at 12.5 kHz, so there are plenty of points to average and get statistical information with... Sam

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Re: Ifeffit digest, Vol 1 #38 - 6 msgs
by Raul Barrea 18 Jul '02

18 Jul '02

Hi Matt, first of all I'd like to say that I have been using Iffefit and Athena for a while and I found both packages very easy to learn and use. I've been following the discussion about how Ifeffit and also athena manage continuous scans and finer grid in energy space. We work in continuous scan mode at BioCAT, so our energy grid cannot be change during the scan as step scans usually do and our energy grid is aprox 1 eV per point, so when we transform this grid to k space we get a not even grid and for most of our point the grid is really smaller than 0.05 A-1. I was very curious about the statistics and how ifeffit and Athena calculate the interpolation. I took one of our scans taken at the Cu K Edge and I remove every other point from it. In order to preserve the grid in the very first region of K I just substitued the high K region from 6 to 13 A-1 with this "new" grid. I found that the results of the original data and the modified data are exactly the same, so the interpolation is not considering the missing points. I've also removed a group of three consecutive points of a goupr of five from the grid (in the same k region) and I found the same results. It will be very usefull if you could include into your package other method that consider every measured point. As you said in your last mail working with finer grid could be a non trivial change but if you could include a better interpolation method will be great. Attached you will fine the three files with the original data and the modified ones (senc-full.xmu; senc-1.xmu and senc-3.xmu). Thanks Raul Raul A. Barrea, PhD Senior Research Associate Illinois Institute of Technology 7900 S Cass Av. BioCAT/APS, Bldg 435B Argonne, IL 60439

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Re: continuous scan data
by Webb, Samuel M. 18 Jul '02

18 Jul '02

Hi all... I've been reading the list about the continuous scan data lately and it looks as if the main issue getting a oversampled grid onto the "standard EXAFS" grid. We've collected a lot of continous scan data DND-CAT at the APS and basically have a routine to bin the data so it resembles a normal step scan (this way you don't loose the statistics and use every point) and then feed it into IFEFFIT. I'm not sure how similar the MR-CAT setup is to the DND collection, but it may be that the conversion process is very similar. To that effect, I have integrated those scipts into an averaging program (now called Sixpack) and analysis suite that uses IFEFFIT. One future development that I hope to add to the program is to be able to read a variety of formats, and allow user definable formats. Until that is complete, it would be simple for me to expand the functionality of what's there to include the MR-CAT continuous scan format... This solution might be able to circumvent the current problems of the splining you have. *********************************************** Street address for courier deliveries: Sam Webb SSRL/SLAC Bldg. 137, MS 69 2575 Sand Hill Rd. Menlo Park, CA 94025 Letters and other mail: Stanford Synchrotron Radiation Laboratory P.O. Box 20450, MS69 Stanford, CA 94309-0210 Phone: (650)-926-3734 FAX: (650)-926-4100 E-mail: samwebb(a)slac.stanford.edu ***********************************************

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Ifeffit 1.0072 released
by Matt Newville 18 Jul '02

18 Jul '02

Hi Everyone, I figured that it had been long enough for version 1.0071, so posted version 1.0072 today. This version has several small feature improvements and bug fixes. There is also a fairly substantial changes to the 'configure ; make ' on Unix, so that the perl and python extensions are no longer built during this process, but have to be built after installation of the library, with the 'normal method' for these languages: cd wrappers/python python setup.py install cd wrappers/perl perl Makefile.PL ; make install This change greatly simplifies the work of the configuration script and is much more reliable. The other major change is that the internals of macro handling were largely rewritten so that nested macros work correctly in all cases (including on windows). Related to that, macros that are run by feffit() and minimize() at each iteration of the fitting loop now run correctly as well. I have a Windows dll ready, but am having difficulty making standalone executables from the ravelware perl scripts. Hopefully that will get worked out soon so that a new Windows installer with the latest athena, artemis, and tkatoms, as well as gifeffit and samxas will be possible. I've also started (but haven't gotten very far on) an annoted collection of ifeffit scripts, intended to be something of a 'how-to' or 'cookbook' for ifeffit commands that will complement the documents and FAQ. Any suggestions or comments on this would be very welcome. Finally, I am really expecting that 1.0072 represents a nearly complete version of Ifeffit 1.0. I believe the XAFS analysis functionality is more-or-less complete at this point. I'm willing to fix bugs, and add small features, but would like to try to leave this version stable and to start working (even if slowly!) on much more significant changes that would eventually become Ifeffit 2. Thanks, --Matt

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Dopants in ATOMS
by Bruce Ravel 18 Jul '02

18 Jul '02

Hi, One of the most common inquiries that finds its way into my mailbox is why the dopants capability in Atoms does not do what the user expects. Typically, the user expects Atoms to write a magical feff.inp file that correctly accounts for the dopants in the material such that FEFF can be run using this magic input file to generate fitting standards or a XANES calculations for the doped material. I get this question so often, that I want to post a response to both the feff and ifeffit mailing lists with an obvious subject line. Then, in the future, I (or even you!) can just point the curious to this posting. ----------- O ----------- First off, this topic is covered in the Atoms document http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Atoms/Atoms/A… See section 3.4, Dopants. I also discuss this issue in Chapter 10 of the lecture notes for my course on EXAFS Analysis Using FEFF and FEFFIT. http://leonardo.phys.washington.edu/~ravel/course/notes.pdf The discussion in this posting applies to the old versions (2.50 and earlier) of Atoms as well as to the current version. ----------- O ----------- Atoms is, except in extremely contrived situations, not capable of writing a proper feff.inp file for a doped material. This is not a programming shortcoming of Atoms, but a number theoretic limitation imposed by the physical model used by FEFF. In the feff.inp file, there is a big list of atomic coordinates. The reason that people like using Atoms is because, without Atoms, it is a pain in the ass to generate that list. The virtue of Atoms is that it automates that annoying task for a certain class of matter, i.e. crystals. FEFF expects a point in space to be either unoccupied or occupied by a specific atom. A given point may be occupied neither by a fraction of an atoms nor by two different kinds of atoms. Let's use a very simple example -- gold doped into fcc copper. In fcc copper, there are 12 atoms in the first shell. If the level of doping was, say, 25%, then Atoms could reasonably use a random number generator to choose three of the 12 first neighbor sites and replace them with gold atoms. However, what should Atoms do with the second shell, which contains 6 atoms? 25% of 6 is 1.5. Feff does not allow a site to be half occupied by an atomic species, thus Atoms would have to decide either to over-dope or under-dope the second shell. This problem only gets worse if the doping fraction is not a rational (in the number theory sense) fraction, if the material is non-isotropic, or if the materials has multiple sites that the dopant might want to go to. Because Atoms cannot solve this problem correctly except in the most contrived of situations, I decided that Atoms would not attempt to solve it in any situation. If you specify dopants in Atoms' input data, the list in the feff.inp file will be be made as if there are no dopants. This leads to two big questions: 1. Why are dopants allowed in Atoms? 2. How do one deal with a doped sample? The first question is the easy one. Atoms does many things other besides feff.inp generation. Calculations involving tables of absorption coefficients and simulations of powder diffraction and DAFS spectra can use dopant information quite well. The second question is the tricky one and the answer is somewhat different for EXAFS as for XANES. The chapter in the PDF file mentioned at the beginning of this posting discusses one approach to analyzing EXAFS of doped materials. In this posting http://cars9.uchicago.edu/feff/feffusers/msg00022.html Scott Calvin adds his two cents worth. The bottom line for EXAFS analysis is that most dopant problems require running FEFF many times to deal with the wide variety of local environments one finds in a doping problem. One of my papers, A Combined EXAFS and First Principles Theory Study of Pb(1-x)Ge(x)Te, B. Ravel, E. Cockayne, M. Newville, and K.M. Rabe, Phys. Rev. B 60, #21, pp. 14632-14642 (1999). discusses a very thorough approach to one particular case of a doped material. The best approach to simulating a XANES spectrum on a doped material that I am aware of also involves running FEFF many times. One problem a colleague of mine asked me about some time ago was the situation of oxygen vacancies in Au2O3. After some discussion, the solution we came up with was to use Atoms to generate the feff.inp for the pure material. My friend then wrote a little computer program that would read in the feff.inp file, randomly remove oxygen atoms from the list, write the feff.inp file back out with the missing oxygens, and run FEFF. He would do this repeatedly, each time replacing a different set of randomly selected atoms and each time saving the result. This set of computed spectra was then averaged. New calculations were made and added to the running average until the result stopped changing. If I remember, it took about 10 calculations to converge. This random substitution approach would work just as well for dopants as for vacancies. I hope that is helpful. 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 and athena updates
by Bruce Ravel 17 Jul '02

17 Jul '02

Hi folks, So, today I tried to actually analyze some data that is long overdue for some attention. I didn't get much analysis done, but I did find and fix lots of bugs in Artemis and Athena. Artemis: ** fixed a bug which precluded using third or fourth cumulants in fits (that was rather serious!) ** clicking buttons in the plot options section does redisplay ** data gets plotted in R when reading data files, project files, or feffit.inp files ** fixed a bug which made every item in the "select paths for fitting" menu fail ** title lines now get correctly restored from project files ** a few internal changes that affect how fits get run and results get displayed Athena: ** now using the sort argument to read_data, as was discussed in some mail earlier today ** disable "save as" menu items for spaces that do not make sense for the current record ** fixed a bug in how markers get displayed in energy plots ** fixed a few other minor bugs, see CHANGES file for details New source tarballs are now on my website. Regards, B P.S. I have been working pretty hard lately on the codes and making lots of releases. Indeed, this is my fourth tarball announcement during July! That's the open-source philosophy -- "release early and often". I don't really expect everyone to update their system everytime I announce a new tarball. Therefore, I am trying to make it clear what the major changes are so you can decide if you need to upgrade. Athena and Atoms are pretty stable these days -- you probably only need to upgrade if a change addresses a bug that you have noticed yourself. Artemis, on the other hand, is changing pretty dramatically. Each release lately has addressed some serious usability issues. It may even be useful soon ;-) -- 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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new source tarball for Artemis
by Bruce Ravel 16 Jul '02

16 Jul '02

Hi folks, I posted a new source tarball for Artemis on my website. Lots of improvements this time, including: ** a check to see that all guess parameters are used and that all math expressions use parameters that have been defined ** rearrangement and improvement (I hope!) of the page for defining guess, def, and set parameters ** fixed more problems that cropped up after deleting individual feff paths or entire feff calculations. I know I said I had fixed this in the last release, but this time I think I mean it!! ** many more features of Artemis can operate on the group of selected paths, including deletion of paths, exporting path parameter values, and editing path parameter values ** fixed a problem where, in certain situations, the array containing the background function refined during a fit was overwritten by another array. This resulted in messed up plots after doing fits with background refinements. ** and a bunch of minor things -- see the CHANGES file for details A windows update will follow soon. 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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new releases of Atoms, Athena, and Artemis
by Bruce Ravel 11 Jul '02

11 Jul '02

Hi all, I just wanted to follow up Matt's announcement of the Windows preview release yesterday. It includes versions of my programs that have been updated in the last two weeks. For those of you who are linux, unix, or OSX users, source code tarballs of the latest versions can be found on my web site. For Atoms the big changes are mostly in the parts of the code that compute absorption cross sections from the McMaster, Elam, or other tables. Several bugs were fixed, including some severe problems in the McMaster tables and a bug which resulted in negative (i.e. unphysical) normalization corrections in some situations. For Athena the changes are fairly numerous and include bug fixes, changes to the column selection dialog, changes to the behavior of the groups list, and a few other things. For Artemis, I have squashed a lot of bugs which lead to strange behavior or crashes. Many of the problems had to do with deletion of feff paths. That is now fixed and should work as expected. As always, poke at them and let me know what needs fixing. Special thanks this time to Simon Bare and Paul Fons for very helpful bug reports. 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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Test Windows Installer for Ifeffit++
by Matt Newville 09 Jul '02

09 Jul '02

Hi Everyone, There's a new version of the ifeffit windows installer available at http://cars.uchicago.edu/ifeffit/src/iffsetup_jul09.exe This installer uses ifeffit 1.0072 and includes the latest versions of atoms, athena, and gifeffit, and now includes artemis, sixpack, and a few other applications. The main point of this release is to check the installation process and the running of all the newly available programs. I'm expecting that we'll need to make some minor changes to some of the applications, but I'd like to get a release that can be stable for several months, so would greatly appreciate as much testing of these versions as possible. So, all you Windows users out there, here's your chance to help out! Please try this installer out, and trying running all the programs. If any of them don't run or crash immediately, please let us know. The installer is now 20Mb, and expands to a directory that uses about 50Mb. If this is a problem, please let us know: we could probably split the distribution into separate installers for different programs. Thanks, --Matt

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The so-called ravelware packages
by Bruce Ravel 05 Jul '02

05 Jul '02

Hey, Today Matt asked me why I don't make one big tarball with Atoms, Athen, and Artemis all in it. Apparently a few people have complained to him about problems upgrading them one at a time. I think that having one big tarball is a great idea and, in fact, I have been looking forward to the day when all three would be basically stable and ready for real work. Atoms and Athena are there. Artemis should be soon. I'll probably keep with the separate tarballs thing for my own convenience for a short while longer, but I suspect that in the next couple of months I'll start doing one huge tarball. If anyone has a compelling reason for me *not* to do so, speak up! 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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New source code releases for Atoms and Athena
by Bruce Ravel 05 Jul '02

05 Jul '02

Hi Folks, I just uploaded new source tarballs for Atoms and Athena to my web pages. For Athena, I corrected two small and somewhat obscure bugs that I found last week. One had to do with the behaviour of the "fix step" button and the other with how Cromer-Liberman normalizion parameters were handled internally. For Atoms, most of the reason for the new release was to correct mistakes in the absorption library. 1. The McMaster tables now have a correct entry for the element Re 2. The McMaster tables now corectly handle energy ranges between the L2 and L3 edges 3. The function that computes the normalization correction has much more error checking and has a few little bugs corrected. It should never return a negative normalization correction any more 4. A few small changes to WebAtoms, which also benefits by the items above. 5. A new item in the TkAtoms File menu -- a submenu labeled "Recent files". The idea here is that you can easily return to an atoms.inp file you had been looking at earlier in your TkAtoms session. As currently implemented it is functional, but behaves a little oddly. The order of the entries is backwards of what you may expect (i.e. most recent file is last in the list) and the list never gets truncated. I got tired of fiddling with it, so I declared it "functional enough";-) Check out http://feff.phys.washington.edu/~ravel/software/exafs/ for the latest. Next week I hope to build new Windows binaries of all three of my programs based on Matt's most recent release of Ifeffit, so keep you eyes on this mailing list for that announcement. As always, comments, suggestions, feature requests, and bug reports are very welcome. 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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my programs on OSX
by Bruce Ravel 24 Jun '02

24 Jun '02

Hi folks, I received an email from a new user last week praising Francois on his helpful pages (http://www.univ-mlv.fr/~farges/atomsX/) explaining how to get Atoms up and running on OSX. Now I have a question for you OSX gurus on this list. Can someone write up a web page to supplement this explaining how to get Ifeffit (and, by extension, Athena and Artemis) up and running on OSX? Or perhaps this exists, in which case I need the URL so I can make a link on my web pages. Eventually, I would like there to be some kind of (Fink-based, I suppose) installer package for OSX, but for the moment it would be nice to at least give some guidance to the inspired and dedicated OSX users. 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/

2 1

(no subject)
by Bruce Ravel 24 Jun '02

24 Jun '02

Hi, I fixed several bugs in Artemis last week and today I posted a new source code tarball. The changes include: 1. fixed several bugs in displaying and using different FT window choices 2. fixed some bugs affecting deletion and rereading of feff calculation. 3. added the ability to turn on and off the "include this path in fit" button for the set of selected paths (i.e. all the paths highlighted in orange in the list on the right). I also reorganized the pull-down menus for including/excluding paths from the fit. 4. paths included in the fit are listed in black text, paths excluded from the fit are listed in a different color. also things not intended for plotting (such as the GSD listing) are printed in italics. this all gives some visual cues to help use the contents of the list effectively. 5. fixed (I hope!) a serious problem which manifested itself by having the data appear as a bizarre starburst-like plot in k-space. Several people had noticed this already. These are all pretty significant usability improvements. Special thanks this week go to Paul Fons for helping me track down several of these problems. As always, grab the latest from http://feff.phys.washington.edu/~ravel/software/exafs/ 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 source code update
by Bruce Ravel 18 Jun '02

18 Jun '02

Hi, I fixed the following four problems with artemis reported to me last week: 1. a really bad bug triggered by using capital letters in parameter names 2. a strange end-of-line problem when artemis was run on unix using feffNNNN.dat files made on windows 3. the "View paths.dat" button will look for "paths.dat" or "path00.dat", i.e. it will find the paths file from feff6 or feff8 4. several related bugs in how the functional form of the FT windows were chosen and displayed on the screen I updated the source tarball and posted it on my web site. http://feff.phys.washington.edu/~ravel/software/exafs/ Artemis currently has the unfortunate, complimetary problems of lacking documentation while being a complex and unintuitive program. The best suggestion I can make for now for learning to use it is to check out the two project files in the examples/Cu/ directory. They are the ones with the .apj extensions. If you are a feffit user, you can import your `feffit.inp' files. If you have never used feffit before, I would recommend reading Chapters 2 and 4 of the `notes.pdf' file found on the web page for my "EXAFS Analysis Using FEFF and FEFFIT" course: http://leonardo.phys.washington.edu/~ravel/course/ Between that and examining the project files, hopefully Artemis will make some kind of sense. Thanks especially to Mark Jensen and Michael DeLeon for their email in the last few days. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Naval Research Laboratory, Code 6134 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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Mark Jensen's artemis bug report
by Bruce Ravel 14 Jun '02

14 Jun '02

Hi, Yesterday, Mark Jensen alerted me to two problems in the current version of artemis. The first is a situation wherein artemis ignores certain guess parameters. The second is a situation in which artemis fails to display the header information from the feffNNNN.dat file as in this screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/artemis/ar… The first problem is due to the fact that artemis gets confused by capital letters in parameter names. That is, "deltar" is ok, but "deltaR" is not. This will be fixed in the next release. The work-around for this problem is to avoid capital letters in parameter names. The second problem was for the somewhat strange situation of running artemis on a unix machine and having made the feffNNNN.dat files on a windows machine. Because of a mistake that I made in the code that fills in the text box in the picture above, artemis got confused by the different end-of-line conventions on windows and unix. How embarassing! This will also be fixed soon. The work-around is to run feff and artemis on the same kind of computer. I want to thank Mark for the excellent bug report and for his help in troubleshooting. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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XAS GUIs
by Webb, Samuel M. 14 Jun '02

14 Jun '02

Hi All... Just wanted to post this to the audience here. I've been working on a set of GUIs for XAS preprocessing and fitting and I think they are just about ready for testing by a broader audience. The first program is SamView and performs basic averaging of scans, energy calibration, deadtime correction and viewing of raw data. At this point, it is specialized to read only certain file formats, but the capability will be expanded in the future. Since my focus has been at SSRL recently, it will read binary and ASCII formats from SSRL, as well as from DND-CAT at the APS. In summary, it is essentially a graphical version of MAVE, MCALIB, and MDEAD for those who have used EXAFSPAK at SSRL. The second program (SamXAS) is a XAS fitting routine. It has a GUI interface to IFEFFIT for FEFF fitting of XAS, a linear combination fitting routine for XAS and XANES, and an interface for creating FEFF single scattering paths (if Feff8 is installed on your system). It also has a fitting routine to account for fluoresence self absorption with out prior knowledge of the sample composition. These are all in their infancy, but I'm looking for feedback on how to improve them, with out replicating the magnificnet work of other contributors. The documentation for both is essentially non-existent, but there are a few sample workspaces and data files included to get you started. Familiarity with IFEFFIT is definitely a plus. The programs can be downloaded from www.stanford.edu/~swebb. Thanks! Sam Webb SSRL samwebb(a)slac.stanford.edu

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First attempts to use Artemis
by Mark Jensen 13 Jun '02

13 Jun '02

Dear Everyone: I'm not sure if this is a bug report or a dopey user report for Artemis, but I am having a problem with Artemis on two Red Hat 7.3 systems with Feff8. The data files load and are displayed in the PGPlot window. I can load and display FEFF paths in the windows too. (Nice touch Bruce. Ravel-ware is great!). However, :( , the path information is not displayed in the path text box like the last picture in Bruce's poster shows. That's not a killer problem in my mind. The real problem is that I can only fit 0 or 1 variable, no matter how many I set as guessed. It appears that Artemis/ifeffit is only varying the guessed variable associated with the first path variable on whichever tab (Basic parameters or Other parameters) is visible (i.e. S02, OR the third cummulant). It won't vary both S02 and the 3rd cummulant and it won't vary any guessed variables that appear in the other path parameters. It doesn;t appear to matter how many different paths I include. If there isn't a guessed variable in either the S02 or third cummulant path, none of the guessed variables is varied. The values of all guessed variables that are not varied always return from ifeffit as 0.0. Any thoughts Mark Jensen ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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rendering problem with Athena
by Carlo U. Segre 08 Jun '02

08 Jun '02

hello Bruce: I have noticed a rendering problem with Athena in Linux. I am attaching a PNG screenshot of the offending screen. As you can see, the lowest part of the "Background Removal" subwindow is showing only the top and it is impossible to read it. Since the window will not resize, it is not just a question of enlarging it. I use a Debian testing system and I would be happy to tell you what libraries are installed if you let me know which ones are relevant. Carlo -- Carlo U. Segre -- Professor of Physics 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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Ifeffit: spline with a standard
by Bruce Ravel 23 May '02

23 May '02

Hi, Earlier today Michael Green asked Matt a question of the variety "How do you do ______?" Athena (and artemis) may provide some help with regards to questions like that. If you look in the Edit menu, you will see a item that says "Display Ifeffit buffer". This shows a text box which displays all text strings that have been sent by athena to ifeffit. This is useful to folks who want to learn ifeffit's syntax. To use the example that was just posted to the mailing list, one could read some data and a feff chi.dat file. Then plot the data in mu(E) and the background without a standard. Then tell athena to use the chi.dat file as a standard and replot in energy. Because the standard was changed, the spline will be redone using the newly chosen standard. All of the ifeffit commands to do this will be written to the ifeffit buffer for your examination. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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: spline with a standard
by Matt Newville 23 May '02

23 May '02

Hi Michael, This seems like a question that others might have, so I hope it's OK that I'm sending this reply to the ifeffit mailing list too. On Thu, 23 May 2002, Michael Green wrote: > I can't figure out how to use a standard for background > removal in G.I.FEFFIT or IFEFFIT. Is there a way to do > this? Table 4 of the Refman lists a chi_std data type, but > I didn't find any mention of it anywhere else. Yes. In ifeffit, it would go like this: #### # background-removal using known chi(k) data read_data(file= data.xmu, label= 'energy xmu', group= dat) read_data(file= standard.chi, label= 'k chi ', group= std) # without standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1) # with standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1, k_std=std.k, chi_std = std.chi) #### That is, you read in the spectra for the standard, and use it's "k" and "chi" arrays for "k_std" and "chi_std". Hope that helps, --Matt

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divorce and OSX
by Bruce Ravel 23 May '02

23 May '02

Hi, There are two more issues that I wanted to comment on, but my last message was really long, so I am writing a new one. 1. Matt suggested an amicable divorce as a way of trying to avoid many of the installation problems that we have been having recently. I would suggest a separation rather than a divorce. Ifeffit and the apps might resolve their marital issues in the future and choose to get back together. But for now, for the sake of the kids, I think a separation is a good idea. I freely confess that many of the installation problems are either due to programming mistakes I have made or due to inherent problems in how perl modules get built. It seems imprudent that Matt and Ifeffit should suffer for those reasons. And, as Matt pointed out, my codes are evolving and releasing faster than Ifeffit itself. While it is certainly less convenient for the end user to have to install several packages than a single one, it is even less convenient if the whole kit 'n' kaboodle fails because of an error in a single app. A separation is thus a very good idea. The separation works well for unix users, where it is a simple matter to grab, say, the athena source tarball and install it on top of a functional ifeffit. It is a little less convenient for the windows users. I suppose a solution is that *I* build a new windows installer package based off of Matt most recent ifeffit release when I release new source code tarball. That's not a complete solution because Sam will certainly have a different release schedule than I will. I vote that Matt, Sam, and I put off dealing with that until dealing is unavoidable. 2. Could Paul, Francois, or Chuck summarize for us the status of ifeffit + X + perl + tk + my codes on OSX? (Although I chuckled when I read it, I cannot bring myself to actually use the word Ravelware ;-) Specifically I am interested in a clear statement of how difficult it is to get my codes up an running on a virgin system and how much time it takes. I am also interested in the prospects for providing a click-n-install package for OSX users. I just gave a poster at the NSLS users meeting on my software and showed one of Francois's pictures of Atoms running on OSX. I presume that it will spark some interest. Also, NRL's beamlines at NSLS are Mac shops (thanks to Johnny Kirkland, deacon of the church of the mac) and I'll want to be running the codes there. Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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installation issues
by Bruce Ravel 23 May '02

23 May '02

Wow! I was gone for three days and a whole flurry of interesting issues came up. ;-) First off, I must thank Mark Jensen for these kind words: MJ> Ever since the Windows version of Athena was released, I've been MJ> hooked. I'm blushin'. Then Mark said: MJ> After an apparently successful installation, neither Athena nor MJ> Artemis ran, saying that they couldn't locate FileDialog.pm, MJ> widgets.pm, or Chemistry/Elements.pm (depending on the MJ> program). I was unsure where to get these files, or why they MJ> weren't where they were supposed to be, but the MJ> Chemistry/Elements.pm file made me wonder if that wasn't part of MJ> Atoms3.0. Indeed it is. After installing Atoms, Athena and MJ> Artemis both appear to be working correctly. So, Bruce might want MJ> to make a change in the intall.unix file to say that Athena (or MJ> Artemis) requires PGPlot, IFeffit, and Atoms. and Paul followed up with PF> Although I had "cleaned" and reinstalled several times athena and PF> Tk, I hadn't given a second thought to tkatoms -- it had no PF> relation to athena, right? wrong! Upon reintalling tkatoms, PF> athena worked. For starters, I am pleased that you both were able to solve your immediate problems. I am lucky to have such smart users. This exchange, though, underscores a serious problem. Eventually I intend to tie atoms, athena, and artemis (and a feff gui, should I or someone else ever get around to writing it) into a more cogent package. At the current stage both of the software development and of my understanding of the needs and challanges of GUI EXAFS software, it is a great convenience for them to be distinct programs. Still, as Paul pointed out, there are some ties between the codes. I use some object inheritance in athena and artemis, so they do share some code already. And one small feature of athena is only enabled if one of modules from Atoms is installed. So I have put myself in an awkward state of having neither a unified suite of programs nor three disjoint programs. Clearly what I need to do is to make a "clean room" for myself. That is, I need a place where I do not have any of my own software installed. Then I can install the tarballs individually or in any combination. If I do this, I should be able to avoid the problems that Paul and Mark reproted to this list. Thanks you both for the excellent feedback. I have said it before and I'll say it many times in the future -- this stuff is much better thanks to you guys providing feedback. Why having an out-of-date atoms resulted in the error that Paul described is a bizarre mystery to me. And why lacking atoms gave Mark an error about widget.pm is equally strange. I'll look into all of it and certainly will work on the installation scripts. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Athena Run Time Error Solved!
by Dr. Paul Fons 22 May '02

22 May '02

I wrote earlier that upon trying to install athena on a colleagues powerbook, I ran into problems with an undefined value in a call to the perl standard routine configure. e.g. Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. It turns out that the problem was related to an earlier windows-related post (aka the Ravel-ware post). Although I had "cleaned" and reinstalled several times athena and Tk, I hadn't given a second thought to tkatoms -- it had no relation to athena, right? wrong! Upon reintalling tkatoms, athena worked. There must be a perl module that is installed only with tkatoms that is required by athena. Consistent with this is the observation that artemis worked out-of-the-box (e.g. a simple make) without problem. In any case all is solved. It might be a good idea however to investigate this issue further as I am fairly sure that this problem will come up again (not with me though!). In my case (on my own machines), I installed all three programs (tkatoms, athena, and artemis) and never ran into the problem. Paul

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Run time error with athena
by Dr. Paul Fons 21 May '02

21 May '02

I have been using athena and just installed the latest version (5.16) on a colleagues G4 powerbook running Mac OSX (10.1.4). This machine is ostensibly running the same set of basic software, namely same version of perl, Tk, python, and pgplot, but he gets a runtime error when he attempts to read in some data while I don't. It would help if there were some suggestions as to how to narrow down the problem. Upon opening a prj file (the example file, ga.prj in the examples folder), the following gibberish appears: Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. main::set_properties at /sw/bin/athena line 1775 main::fill_skinny at /sw/bin/athena line 923 main::read_record at /sw/bin/athena line 4306 main::read_file at /sw/bin/athena line 1973 [\&main::read_file,0] Tk callback for .frame.menubutton2.menu Tk::__ANON__ at /Library/Perl/darwin/Tk.pm line 228 Tk::Menu::Invoke at /Library/Perl/darwin/Tk/Menu.pm line 530 (command bound to event) It seems to be referring to a perl module called configure. Any ideas? Thanks. Dr. Paul Fons Senior Research Scientist National Institute for Advanced Industrial Science and Technology Optoelectronics Institute Energy Electronics Institute Umezono 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 paul-fons(a)aist.go.jp lines below are in Japanese: 〒305-8568茨城県つくば市梅園1-1-1 主任研究官ポール・フォンス

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GIFeffit, Athena and Artemis Installation
by Mark Jensen 21 May '02

21 May '02

Bruce, Matt, and everyone: Ever since the Windows version of Athena was released, I've been hooked. I couldn't wait for a Windows version of Artemis, so after a week of pondering the best way to re-introduce Linux to my PC, I have installed Linux, PGPlot, Ifeffit, Athena and Artemis this morning. I had a problem that others doing a "Ravel-ware" installation for the first time might run across. After an apparently successful installation, neither Athena nor Artemis ran, saying that they couldn't locate FileDialog.pm, widgets.pm, or Chemistry/Elements.pm (depending on the program). I was unsure where to get these files, or why they weren't where they were supposed to be, but the Chemistry/Elements.pm file made me wonder if that wasn't part of Atoms3.0. Indeed it is. After installing Atoms, Athena and Artemis both appear to be working correctly. So, Bruce might want to make a change in the intall.unix file to say that Athena (or Artemis) requires PGPlot, IFeffit, and Atoms. There is one other problem that I have not solved. Ifeffit runs fine, but when I try to run GIFeffit, the "splash window" pops up for a split second and then I get 2 error messages before the program shuts down. The errors are File "/usr/local/gin/gifeffit", line 3, in GIFeffit.GIFeffit (sys.argv[1]) File "/usr/lib/python1.5/site-package/Ifeffit/GIFeffit.py" line 285, in __init__ self.iff_dir = os.getenv('IFEFFIT_DIR) Attribute Error: getenv Does anyone have any thought? Have I missed something obvious in the installation? Mark Jensen ---------------------------------------- Mark Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 (630) 252-3670 (630) 252-7501 FAX mjensen(a)anl.gov

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New pgplot in fink unstable branch
by Dr. Paul Fons 17 May '02

17 May '02

There is a new version of pgplot in the unstable branch of fink which breaks the ifeffit install process. The only thing that needs to be changed is to include the two "library" like arguments: -framework Foundation -framework AppKit to the linking arguments (or compile arguments). The location of the pgplot library has also been changed to (the now standard location) /sw/lib/pgplot. I can see how to make the changed to the Makefile in src/macosx without trouble, but I am thrown a little by the python setup (it seems somewhat convoluted). What changes need to be made there to reflect the new link arguments and the new location of the pgplot library? Thanks.

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athena update
by Bruce Ravel 16 May '02

16 May '02

Hi folks, I guess I have been a busy boy this week. There's another release of athena on my web site. New stuff includes: 1. A couple bug fixes and several changes to the layout of the main window. 2. An automated alignment algorithm which works by varying an e0 shift to minimize the difference spectra of the derivative of two mu(E) spectra. I would not place great trust in this algorithm, but it think it will often provide a good first guess for the e0 shift. It works well for the EuTiO3 data that is included in the examples. You can use this algorithm from the alignment dialog or from the data preprocessing options in the file selection dialog. 3. Athena now checks to see if input data is monotonically increasing in energy (or wavenumber for chi(k) data). If it is not, Athena spits up an error message and refuses to read the data. This choice seems safe, but I am open to suggestions for other ways to treat the non-monotonic data. 4. A y-axis offset plotting parameter. This is most useful for stacked plots like in this screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ath… This was done by setting the y-axis offset for the first data group to 0.5 and to -0.5 for the third data group. Enjoy, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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uh oh!
by Bruce Ravel 15 May '02

15 May '02

So, has anyone downloaded the athena tarball I released yesterday and noticed that you cannot plot chi(k) with any k-weighting other than 1? Yikes! How embarassing! That bug will certainly be fixed in the next release. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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non-monotonic data
by Bruce Ravel 14 May '02

14 May '02

Matt, Can you explain what ifeffit does when it reads a mu(E) data file which has non-monotonically increasing energy values. Specifically what happens to data like this: # energy xmu # ---------------- 1 0.1 2 0.15 2 0.15 3 0.18 4 0.2 end so on. Ifeffit throws up one of these two sets of error messages: spline: energy data appears out of order pre_edge: energy data appears out of order or spline: energy and xmu are different length? I understand that non-monotonic data will give problems in the intepolations and elsewhere, but what does ifeffit actually do in this case? FWIW, I plan to have athena check data as it is read in to verify that the energy array is monotonic up (or down, in which case the data will be reversed) before trying to do anything with it. But I remain curious about what ifeffit chooses to do. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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new Athena, first release of Artemis
by Bruce Ravel 13 May '02

13 May '02

Howdy folks, Today I am pleased to announce a new release of Athena and the first release of Artemis. These are source code only releases -- I have not yet built Windows binaries. But those of you on unix machines can grab the latest and try them out. Get the latest from the normal spot: http://feff.phys.washington.edu/~ravel/software/exafs/ See some Artemis screenshots at the bottom of http://feff.phys.washington.edu/~ravel/software/exafs/screenshots.html Athena: The new features are: 1. An on-line document in the Help menu 2. Plotting difference spectra and making data groups containing difference spectra 3. Plot chi(E) (by which I mean k-weighted chi(k) but with the x-axis converted to energy) 4. Several minor improvements to the on-screen display and to the example files Artemis: Be kind. This is an initial release. ;-) Many features are missing. Many features that are present may not work quite right. But it does fit and plot. That's a big step! It cannot currently do multiple data sets, but it can handle feffNNNN.dat files from multiple feff calculations. Probably the best way to start using Artemis is to open the example project file for FCC copper (examples/Cu/cu.apj). Artemis can currently plot things in k, R, or q. It can do fits or simply evaluate the path parameters and do a sum of paths like ff2chi. To start a project of your own, do the following: 1. Read in a chi(k) data file by selecting "Open data" from the File menu. 2. Read in a feff calculation by selecting "Open FEFF calculation" form the File menu and selecting the feff.inp file from the relevant feff calculation. (You need to have already run feff, Artemis is expecting to find the feffNNNN.dat files.) 3. Click on "Guess, Set, Def" in the column on the right and define some fitting parameters. 4. Click on "Data' in the right column and set the fitting and FT parameters. 5. Click on all the paths that you want to include in the fits and define the path parameters. Like in FEFFIT, this is the time consuming part of the process. I am open to suggestions for helpful functionality in that part of the code. 6. Once that is all done, click on the Fit button. 7. Make plots by selecting things to plot from the right column and clicking on the appropriate plot button. The list uses extended selection, thus you can click and drag to select multiple items. You can also control-click to select multiple, disjoint items for plotting. Play around, let me know what breaks and what needs to be added. Remember that Athena changed A LOT in the first few months as Shelly and Matt and others gave me feedback. It took a while, but she went from a shaky, buggy beginning to being a useful, solid utility. Artemis will get there, too, but I need your help to get through the initial growing pains. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Problems running athena/tkatoms
by Norbert Weiher 12 Apr '02

12 Apr '02

Dear friends, seems to be that I'm another guy having problems in setting up athena/tkatoms ;) I browsed the archives but found nothing that helped me to get them running. Here is the story: tkatoms worked well - then I installed the newest version and get: weiher> tkatoms.pl ...(lots of messages like the following)... Bareword found where operator expected at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, near "12 normal" (Missing operator before normal?) Unquoted string "normal" may clash with future reserved word at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, <RC> line 186. couldn't read bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm": Datei oder Verzeichnis nicht gefundenerror reading bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm" at /usr/lib/perl5/site_perl/5.6.0/i586-linux/Tk/Submethods.pm line 37, <RC> line 186. for athena it seems that it can't find the ifeffit.so libs - although they are installed (as well as the perl wrappers) and pass all test runs. I get: weiher> athena Can't load '/usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so: undefined symbol: G77_getenv_0 at /usr/lib/perl5/5.6.0/i586-linux/DynaLoader.pm line 200. at /usr/local/bin/athena line 50 Compilation failed in require at /usr/local/bin/athena line 50. BEGIN failed--compilation aborted at /usr/local/bin/athena line 57. I'd really love to get the packages on their way which has never been a real problem. I don't know why the new versions don't compile on my system. The requirements are all fulfilled (perl > 5.0, new Tk version...). Can anyone help me with my problems? The system is a SuSE linux box (V7.2) with kernel 2.4.4 compiled. Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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Reverse Monte Carlo
by Dr. Paul Fons 10 Apr '02

10 Apr '02

Athena and ifeffit are all running fine (now I am just waiting for artemis) so I thought I would ask a silly question about reverse monte carlo. I have taken multiple edge data on a (nearly amorphous) buffer layer comprised of S, O, and Zn. I was wondering about applying reverse monte carlo to look at some prototypical structures. Has anyone ever used Rmca (http://www.studsvik.uu.se/Software/rmc/rmc.htm) I found this using SINCRIS at the IUCr which stated that there were unix and vms versions of the software. On the ftp server I only found a os independent fortran program (which relies apparently on os dependent subroutines for which only vms and windows NT are available on the site). Is there a real unix version out there? Any opinions on the value of rmc for getting an idea of what is going on structure wise? Dr. Paul Fons Photonics Research Institute National Institute for Advanced Industrial Science and Technology Ministry of Economics and Trade Umezono 1-1-1 Tsukuba, Japan 305-8568 tel. 81-298-61-5636 fax. 81-298-61-5615 paul-fons(a)aist.go.jp Lines below are in Japanese 独立行政法人産業技術総合研究所光技術部門〒305-8568 茨城県つくば市梅園1-1-1 産総研つくば中央第2 E-mail: paul-fons(a)aist.go.jp, Tel. 0298-61-5636, Fax. 0298-61-5615

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online help bug in tkatoms
by Bruce Ravel 28 Mar '02

28 Mar '02

Howdy folks, Today I received a bug report regarding the on-line help feature in tkatoms. I belve that this problem only affects unix systems. The problem is that, when selecting "Help with Atoms" from the help menu, you may get an error dialog telling you, among other things "Error: Can't set -file to `tkatoms.pod' for Tk::Pod=HASH(0x8f06fe0)" The cause seems to be an error in one of my installation scripts and it should be fixed in the next release (sometime in the indeterminate future -- I am mostly working on artemis right now). If you don't feel you can live without the online help, I think you can make the problem go away by copying by hand the file `tkatoms.pod' from /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/ (or whatever similar directory it ended up in on your system) to /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/lib/ which is where it should have gone in the first place, except for the bug in my installation script wherein I left out the "lib/" part. Regards B Carlo, if you haven't already, you may be interested in subscribing to our mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Update athena problems
by Norbert Weiher 28 Mar '02

28 Mar '02

Dear friends, I tracked down the athena installation problems to the point that it's definitively a bug in the perl wrapper for ifeffit. Even re-compiling my gcc suite didn't solve this problem. All suggestions given by Matt and Bruce have not been successful so far. Maybe someone here got athena running on a linux box (I have SuSE 7.2) and experienced the same? Could it be the gcc version I use (2.95.3)? Include paths, etc seem to be okay. The build of the wrapper works, but the make test still aborts with the message I posted... gifeffit & ifeffit work fine. Any new suggestions on this issue? Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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volunteerism....
by Bruce Ravel 27 Mar '02

27 Mar '02

Hi Folks, Matt said: > From a political viewpoint, I think we'd need a volunteer to keep > the scripts in working order for Win95/98/ME. Unless that happens, > I don't consider "upgrade to 2000" to be an unreasonable response. I want to second this request. It's really hard for Matt and I to stay on top of all these different platforms. The 9x/ME series of OS's is sufficiently different from 2000/NT/XP (I run 2000 under VMWare on my linux box) that it is hard for us to keep up. I would be happy to help a volunteer 9x/ME tester/debugger get up and running. The biggest chore is learning how to use the program that Matt and I chose for building the Windows installation package. That's not hard -- I had it mostly figured out in a day. Then Matt said: > Also from a political viewpoint, could we encourage 'A fellow' > to post such problems here? I get lots of email from people about Atoms and, of late, about Athena. I have taken to pointing out the web entry point to our mailing list whenever I answer a question from someone who may not be a subscriber. I encourage all of you to encourage anyone around you who may be interested in our software to subscribe. As ifeffit and friends have been finding a wider audience, more problems have been cropping up. This is a natural part of growth and is very healthy. With the help of all of you on this list, Matt and I will be able to make a much better package. Finally, some suggested reading from freshmeat, the software repository: The Importance of Non-Developer Supporters in Free Software http://freshmeat.net/articles/view/156/ How to Report Bugs Effectively http://freshmeat.net/articles/view/149/ B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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 digest, Vol 1 #10 - 1 msg
by Guilhem DEZANNEAU 27 Mar '02

27 Mar '02

Hi, i actually work with Windows 95 (version 97) OS and encountered similar messages : - too many parameters - environment out of memory for all programs of the ifeffit package Nevertheless, even if these messages appear, the programs TkAtoms, Gifeffit run without problems... It is not the case for APT that stays without running... Guilhem DEZANNEAU ___________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français ! Yahoo! Mail : http://fr.mail.yahoo.com

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ifeffit on Windows ME
by Bruce Ravel 26 Mar '02

26 Mar '02

Howdy folks, I got an interesting bug report a few days ago which I could only partly address. A fellow asked me: > I have installed the IFEFFIT package in my computer (WIN ME). The > installation software seems to work ok. However, when I try to run > the *.bat files, I have the following message, repeated twice: "out > of environment space". Despite these messages athena, gifeffit and > ifeffit are runnig ok. However, tkatoms.bat and apt.bat don't run > at all. I understand that the "out of environment space" problem results from the rather awkward way the old Windows operating systems handled "conventional" memory and the amount of memory dedicated to holding the values of environment variables. It seems reasonable that this message turns up when our .bat files are run since they add to the environment. I suppose that an environment that is already nearly full could be tipped by our .bat files. See, for example, http://www.pcguide.com/ts/x/sys/operrEnvironmentSpace-c.html The second part of the question stumps me. Why do three of the codes work, but tkatoms and the periodic table not run? The tkatoms executable is, in fact, larger than athena, but the periodic table is smaller. And the periodic table does not use Ifeffit, which should make its memory demands even smaller. So does anyone have any wisdom for Windows ME? ("Upgrade" and other snippy comments are not helpful! ;-) Has anyone been able to use these codes on 98 or ME? B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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] iFEFFit and Tcl
by Bruce Ravel 11 Mar '02

11 Mar '02

John said: jjr> Maybe, I misunderstand, but presently we do have Python-2.0.1 jjr> installed. Does anyone know what version of Python is needed to jjr> have Tkinter? A quick search on google turned this up: http://www.python.org/topics/tkinter/

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Re: [Ifeffit] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Matt, Thanks for the comments: > For G.I.Feffit, I think it's just a matter of getting a version > of python with Tkinter built-in. If perl/Tk were installed, > I'd guess that athena and tkatoms would run fine too. These > are both (python/Tkinter and perl with Tk) a small amount of Maybe, I misunderstand, but presently we do have Python-2.0.1 installed. Does anyone know what version of Python is needed to have Tkinter? Also, both tkatoms and athena appear to run fine on our SGI (at least for the jobs I've run). Only gifeffit seems to be problematic. John

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new Athena release, version 2002.03.08
by Bruce Ravel 11 Mar '02

11 Mar '02

Hi, I just posted a new release of the athena source code. I have not yet made a new windows binary. This version is 2002.03.08. New in this release: ** Phase corrected Fourier transforms (requires ifeffit 1.0069 or later) which make use of tables of central atoms phase shifts as I discussed on the feffdevel list http://cars9.uchicago.edu/feff/feffdevel/msg00082.html ** Spline clamps, both high and low, but with discrete, menu-chosen scaling factors. This is not yet documented, but the basic idea is that you can put restraints at the high and low end of the spline range in the autobk algorithm to coerce the spline to go through the data at those points. Try autobk with the high clamp set to Strong -- very cool! ** a few bug fixes -- as always ;-) Kind of a small list, but PCFTs and spline clamps are both fairly major bits of user functionality, so it seemed worth making a new release. As always, point your browser at http://feff.phys.washington.edu/~ravel/software/exafs/ for the latest. B P.S. Those of you to whom I sent this message by blind carbon copy should go to http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit and subscribe to Matt's great, new ifeffit mailing list. In the future all announcements will be made there. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Everyone, I'm simply delighted to see all the effort/success in getting gifeffit/ifeffit/ etc. going on OSX. However, I'm curious about the status on SGIs. Although I've gotten ifeffit to build and install using SGI's cc compiler (setenv CC cc), it appears that gifeffit does not work yet even with the latest release of ifeffit. Some symptoms, which may or may not be relevant: 1) from the ifeffit make install: Making install in wrappers Installing python extension Distutils works Testing for Tkinter and Pmw ===== WARNING WARNING WARNING ===== Tkinter is NOT installed, or was not found G.I.FEFFIT will not work. Pmw 0.8.5 is already installed. Great! 2) from wrappers/tcl cd /usr/local/src/ifeffit_1.0b/wrappers/tcl 44# sh Build cc -fpic -g -c -I../../src/lib ifeffit_wrap.c -o ifeffit_wrap.o cc ERROR parsing -fpic: unknown flag *** Error code 2 (bu21) This is not an urgent matter; ifeffit/gifeffit/athena/tkatoms, etc all appears to work fine on my laptop and desktop running various RH LINUX OS. But we still love our SGIs. Cheers, J. Rehr

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Re: [Ifeffit] Some thoughts on gifeffit
by Bruce Ravel 11 Mar '02

11 Mar '02

Paul said: > Also one of the things I used to do with the unix environment was to > set up a series of different autobak files with different rback > settings so I could see the effect of moving the fit window. It was > nice to be able to compare all of these in the same graphic window For what it's worth --- this can be done in Athena fairly easily. 1. Read in your mu(E) data. 2. Using the Group menu, make several copies of that data group. 3. Set Rbkg as desired in each copy. 4. Mark all the copies. 5. Click the purple k or R buttons. It would be nice to have a way of probing individual parameters for single groups without explicitly making copies. If anyone pipes up in support of that idea, I'll throw it on the todo list. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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 and Tcl
by Matt Newville 11 Mar '02

11 Mar '02

Hi Tsu-Chien, > >> Has anyone tried to use Tcl/tk 8.4a4 with G.I.FEFFit? > > > > Yes. G.I.FEFFIT works on MacOS X. Installing the python > > package from Fink and then building and installing the > > Ifeffit-python wrapper will install G.I.FEFFIT. > > > What I mean is Tcl/Tk for MacOS X. Just found this interesting page: > <http://www.oreillynet.com/pub/a/mac/2001/10/26/tcl_osx.html?page=4> Ah, sorry I misunderstood. I have not tried to build the Tcl/Tk wrapper on MacOS X, but I'm pretty sure it would be possible and fairly easy. In fact, Tcl/Tk is available from Fink, and installing the python module must also install this, since python/Tkinter uses Tcl/Tk. Right now, the Ifeffit build on MacOS X does not try to build the Tcl extension, but it would be easy to add this. I believe it could be as easy as this: create TclSetup.in in ../wrappers/tcl: #---- LIB_PLT = -L/sw -lpgplot -L/usr/lib -lX11 -lpng LIB_F77 = -lg2c -lm LIB_IFF = -L../../src/macosx -lifeffit INC_IFF = -I../../src/lib CC = gcc CFLAGS = -g -O2 LDFLAGS = #----- and type 'sh Build'. I believe that 'tclsh test.tcl' will then work, running a simple test that doesn't do much besides prove that ifeffit runs from Tcl. I do not know much about how 'packages' are properly installed with Tcl/Tk, and haven't been very good about keeping the Tcl extension up-to-date. That's mostly because I don't actually use tcl myself. If someone else wanted to use tcl and ifeffit together, and/or take over this module, that would be great! --Matt

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An Athena mini-tutorial
by Bruce Ravel 11 Mar '02

11 Mar '02

Hi folks, In the absence of a real document, I want to write something down to help people get started with Athena. Here goes.... First, Athena, like gifeffit, is an attempt to automate the creation of ifeffit commands. The beauty of ifeffit's command interface is that it is very flexible, both in terms of functional flexibility and in terms of writing wrappers. The annoying part of ifeffit's command interface is that you have to remember a lot of syntax and do a lot of typing. Essentially, Athena does a lot of typing for you. Second, Athena has two features that may not be obvious to folks who have used Mac-xafs or win-xafs or some other extant package. (1) There are no buttons that say "Remove background" or "Fourier transform". There are only buttons that say "Plot in energy" or "plot in R". Athena is clever about keeping track of what needs to be done and doing all necessary analysis steps in the background before plotting. So, if you change the k-weight for the Fourier transform, Athena knows to redo the forward and backward transforms as needed but not to redo the background removal. If you change Rbkg and plot in energy only, the background removal will be done. And so on. (2) You can "mark" groups and perform various actions on single groups or on ensembles of marked groups. So it is easy to plot single groups or ensembles of groups with a few mouse clicks. What's more the analysis steps are taken care of automagically for single groups or for ensembles of groups. Now I am going to describe specific features of Athena: ***** Reading in data Athena reads ASCII data using ifeffit, so all the rules that apply to ifeffit also apply to Athena. Basically, Athena expects that data will be in the form of column data, possibly with headers. Athena can directly read mu(E) or chi(k) data. It can also read raw data straight from the beamline. See http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/col… You can then construct mu(E) data by selecting columns for the numerator and denominator. In the screen-shot, I show selecting It and I0 columns as the numerator and denominator for transmission data. There is a natural log button which should be clicked for transmission data. You can also handle multi-element detector data in a very rudimentary way by selecting multiple numerator columns for fluorescence data. You will notice that there are options in the File menu for reading single or multiple files. This is annoying but necessary. The standard file dialog does not do extended selection, the motif-like file dialog does extended selection but is unfamiliar to most people. Extended selection is very useful -- if you extendedly select a group of identically formatted files, Athena will only give the column selection dialog for the first one. The button labeled "Set preprocessing parameters" is beyond the scope of this post, but may become clear to you once you grok all the features of Athena. ***** Selecting and marking groups Once you have read in some data, you will probably want to plot it. You select a group by clicking on its name in the skinny frame on the right. When you select a group, its name will be highlighted in orange and its parameter values will displayed in the form on the left. When you click on a *red* plotting button, the selected group will be plotted. To the left of the group's name is a little check button. You mark a group by clicking the checkbutton on. When you click a *purple* plot button, all marked groups will be over-plotted. ***** Setting parameter values You can only directly edit the parameters for the selected group because only the selected group has its parameters displayed. There are ways of setting the parameters of other groups to the values of the selected group. In the Group menu is and option for setting the values of all parameters of all other groups to the values of the currently selected group. There is another option for setting all parameters of all marked groups to the values of the currently selected group. There is also fine grained control over setting parameters which is described in the next section. ***** Mouse clicks on labels When you pass the mouse over a label in the frame displaying all the parameter values, you will notice that the text and background change color. This is a visual cue that the text is sensitive to mouse clicks. Clicking the left mouse button on a word that has changed color will display a little bit of text in the echo area at the bottom of the window which explains in a few words the purpose of that parameter. Clicking the right mouse button will pop up a menu which allows you to set that parameter for other groups to the value of the currently selected group. The functions in the Group menu explained above work on all parameters, this right-click function works only on that specific parameter. ***** Plotting options You can independently control how single and marked group plots are made by choosing different options in the Plotting Options section at the lower right hand corner of the window. There is one notecard for each plotting space. Red buttons are for single group plots and purple buttons are for marked group plots. I suggest poking at these buttons to see what kinds of plots you can make. The plot ranges for the x-axis are set in this space as well. You may need to think about these values. For example, the data alignment function (described below) uses the values of Emin and Emax. Typically, you would want to restrict the plot to a few tens of volts above and below the edge so you can see the details of the edge for alignment. ***** Palettes The options in the Edit menu all pop up a new window with notecards which display all sorts of textual information. Perhaps the most useful is the ifeffit buffer which allows you to monitor the communication between Athena and ifeffit. ***** Project files You have the options of saving data in a variety of column formats, including mu(E), norm(E), chi(k), chi(R), and chi(q). You can also save a "project file". Which is an Athena specific which records the state of your Athena session. It will record data and parameters in a big ASCII file that is hard for a human but easy for Athena to read. Athena's project files are different from ifeffit's PAD files. They exploit the object oriented nature of its internal data structures to save the state of an ensemble of groups, even if the data in that ensemble is unrelated one to the other. ***** Deglitching The deglitch menu has two options in it, deglitching and truncating. Deglitching is for removing spurious points throughout the data set, truncating is for removing all data points after a specified point. Deglitching can be done point-by-point or algorithmically. The point-by-point is done by clicking the "Select a point" button, then clicking on the plot. The "remove point" button will then become active. Clicking it will remove the point from the group. The algorithm is a bit more complicated. There are three parameters which set margins above and below the data in a range either in the pre-edge or the post-edge. Any data points which extend outside these margins will be removed. To understand this better, try reading the data file uhup.003 and plying around with the algorithmic deglitching parameters. Eventually you will make it look like this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/deg… Clicking the "Remove glitches" button will remove the four points outside the margins. ***** Aligning Alignment can be done using raw mu(E), normalized mu(E), or the derivative of mu(E). I think this one is pretty easy to understand. The "Standard" is the fixed reference. The "Other" is the group to be energy shifted. When you click the + or - buttons, the other group's e0 shift is incremented and the two data sets are replotted. See this: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ali… ***** Merging Merging works on all marked groups. You can merge in any of the plotting spaces. The average and standard deviation of marked groups are calculated. The average, the average + the std. dev., and the average - the std. dev. will be plotted. The standard deviation will be written to output column data and to project files. There is more stuff to explain. I have not discussed macros, plot multipliers, clamps, phase corrections, Cromer-Liberman normalization, hints, the Plot and Mark menus, data preprocessing, detector data, pluck buttons, autobk standards, feff data, and a few other things. But hopefully this is enough to get people started until I write a proper document/tutorial. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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Some thoughts on gifeffit
by Dr. Paul Fons 11 Mar '02

11 Mar '02

I just brought up gifeffit this morning -- and I can already say I like it. I was wondering about some simple changes (perhaps I can do some of these myself once I get a little more sophisticated) 1. It would be nice to have legends on the pgplot window -- colors are nice but if one is comparing different data sets, it is really hard to tell them apart (especially if the page is printed). Also one of the things I used to do with the unix environment was to set up a series of different autobak files with different rback settings so I could see the effect of moving the fit window. It was nice to be able to compare all of these in the same graphic window -- it doesn't seem like this can be done anymore (am I right about this?) 2. In terms of documentation, a nice intro would be to highlight the differences between gifeffit and the more traditional unix command line version to help new users get up to speed -- again I am willing to write some of this (if help is needed), but I still need to get up to speed myself! 3. I am not 100% sure of this, but it seemed that when, for example, I had the plotter open and subsequently read in a new data set in another window or defined a new array, the pop-up menus in the plotter window weren't aware of the new data set (at least not immediately). One last thing, on the ifeffit homepage, it is stated that feffit is included in the distribution, but is not stable -- what is unstable and what are the limitations of the feffit module within gifeffit currently, e.g. is it something I can use to fit data? Last thing -- but really should have been first. Thank you for putting all of this effort into ifeffit and then sharing it with the rest of the community. Many people are benefiting from your efforts. Bruce's course (which is still a developing entity I believe) is also of great help in learning more about the different approaches to data analysis. It is my impression that while there is a fairly good collection of knowledge regarding exafs (and less so for xanes), this information is scattered in many different locations (and some of it is very dated). Having a reference in a easy-to-find place is a real benefit to the community at large. It also would have the advantage of being dynamic in that it doesn't have the birth (and death) cycles of commercially published material. I guess all of this is obvious, but I just wanted to say thanks (again). Paul

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Athena runs
by Bruce Ravel 11 Mar '02

11 Mar '02

Chuck asked: CB> BTW, does Artemis have any requirements, other than its own perl CB> files, that are beyond ifeffit/atoms/athena? Nope. It works just like athena. There are a lot of widgets that are used to generate ifeffit text which gets piped to the ifeffit library. Then stuff gets plotted by pgplot. So if athena works, artemis will work. CB> Now to actually learn a bit about how to -use- ifeffit, tkatoms, CB> and athena! Matt's ifeffit tutorial (see the documents page on the ifeffit site) is quite nice and will give you an overview of all the main functions. The reference is also good -- I consult it all the time as I write my codes. It is, however, a bit behind the current version. Still, it's very useful. If you have ever used atoms, tkatoms will be quite straightforward. Athena is lacking documentation. I am going to post something this morning under a different subject line which will, I hope, get you started. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/PGPlot/AquaTerm
by Tsu-Chien Weng 10 Mar '02

10 Mar '02

> 3. Has anyone run ifeffit using aquaterm? > Yes, I just tried newplot() with PGPlot/AQT, not in rootless XFree86. Since I'm a new user, I've not tried many functions in iFEFFit. Has anyone tried to use Tcl/tk 8.4a4 with G.I.FEFFit? Tsu-Chien <Chien>001000</Chien> === PGPlot/AquaTerm === 1. cvs AquaTerm 0.3 from aquaterm.sourceforge.net. 2. cp AQTProtocol.h, aqdriv.m to /usr/local/src/pgplot/drivers 3. mkdir sys_macosx, then cp g77_cc_AQT.conf and iand.c to it. 4. mkdir /usr/local/pgplot and copy over drivers.list. Add a line: AQDRIV 0 /AQT 5. /usr/local/src/pgplot/makemake /usr/local/pgplot 6. Modify makefile: DRIVERS=nudriv.o aqdriv.o aqdriv.o: $(DRVDIR)/aqdriv.m $(MCOMPL) -c $(MFLAGC) $(XINCL) $(DRVDIR)/aqdriv.m 7. make === iFEFFit === 1. download readline-4.2a from GNU and install libreadline.a to /usr/local/lib. 2. modify ifeffit_1.0b/src/macosx/Makefile a. #X_LIBS b. READLINE_LIBS = -L/usr/local/lib -lreadline c. NSLIBS = -framework Foundation -framework AppKit d. PGPLOT_LIB = -L$(BASEDIR)/pgplot -lpgplot -L/usr/lib $(NSLIBS) Note: I downloaded gcc3.1/g77 from <http://floyd.liunet.edu/~gkhanna/g77.dmg.gz>. The version of /usr/bin/cc is 2.95.2 and it has problem like /usr/bin/ld: /usr/lib/crt1.o relocation overflow for relocation entry 33 in section (__TEXT,__text) (displacement too large)

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Mac OS X: athena, tkatoms, gifeffit all working!
by Matt Newville 09 Mar '02

09 Mar '02

OK, After installing perl/Tk, tkatoms (3.0beta5) installed without problems. Since I had already installed the ifeffit perl extension, and perl -e 'use Ifeffit;' was already working without complaint, the tkatoms interface to ifeffit ran fine. I also verified that a 'Powder' calculation ran and plotted to its canvas, and that the Chantler, Elam, and CL resources worked for absorption calcs. I couldn't get a plot in the DAFS window, but that could be operator error. After this, I reinstalled the ifeffit perl extension (though it may not have been necessary), and ... athena runs. It seemed to run perfectly, though I didn't try everything. There is a problem with athena saving hardcopies, but I think that will be easy to fix. In short, I believe everything is working on MacOS X. The necessary ingredients seem to be: From http://fink.sourceforge.net/ fink components: rootless X-windows, an X window manager (eg, orobus, sawfish, windowmaker), g77, python, and PGPLOT. From http://www.Lehigh.EDU/~sol0/Macintosh/X/ptk/ the perl/Tk fix for dyld follow instructions carefully!!! From http://cpan.perl.com/ perl's Tk800 build from source: > Perl Makefile.PL ; sudo make install From http://feff.phys.washington.edu/~ravel/software/exafs/ tkatoms build from source: > Perl Makefile.PL ; sudo make install From http://cars.uchicago.edu/ifeffit ifeffit.tar.gz, unpack and install: base lib: > tar xvzf ifeffit.tar.gz > cd ifeffit_1.0b/src/macosx > make > sudo make install perl extension + athena: > cd ../../wrappers/perl > perl Makefile.PL > sudo make install python extension + gifeffit: > cd ../../wrappers/python > sudo python setup.py install Edit .cshrc, adding if (! $?DISPLAY) setenv DISPLAY 0.0 setenv PGPLOT_DEV /xwindow # PGPLOT window dies with ifeffit setenv PGPLOT_DEV /xserve # PGPLOT window stays up. Then, with X-Darwin running, tkatoms, ifeffit, gifeffit, and athena should all run from a normal Terminal.app. I haven't tried these steps on a fresh MacOS X box, so there may be a missing step or two. Thanks Chuck, Francois, Paul, and Bruce for all the help. Now, can anyone else get all this to work? --Matt

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Athena runs
by Charles Bouldin 08 Mar '02

08 Mar '02

>From: Bruce Ravel <ravel(a)phys.washington.edu> > > >Well, it is certainly a step in the right direction to actually >install the perl interface to Ifeffit before attempting to use Athena ;-) Well, okay(!) :), I never said I knew what I'm doing here, although I certainly know a lot more than 2 weeks ago. I did what Matt said, and also cleaned up what may have been a small version difference in the ifeffit distribution, and then, as Matt suggested: > cd ..... src/macosx; make clean ; sudo make install > cd ../../wrappers/perl ; perl Makefile.PL ; sudo make install and it all works! At least I get the tk panel for Athena...I don't know how to drive it yet. So, I agree with Matt...ifeffit, atoms and tk interfaces seem to be working. We should now put our heads together and try to refine the directions for all this....I'm pretty sure I could repeat it all from scratch, but it would take a while. Now to actually learn a bit about how to -use- ifeffit, tkatoms, and athena! BTW, does Artemis have any requirements, other than its own perl files, that are beyond ifeffit/atoms/athena? Chuck

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Re: [Ifeffit] The road to Athena... (and Artemis too!)
by Bruce Ravel 07 Mar '02

07 Mar '02

The fact that the wrapper for python worked as it was occurred to me after I hit the send button. How does the loader work on BSD? Does it expect libraries to be in certain standard places? Perhaps Chuck ended up with the ifeffit library in some non-standard place and so needs to fix that, set an environment variable (like on SGI), or fix the loader configuration (like on linux). Anyway, I am glad to hear that such good progress is being made. I wish I could contribute more to the immediate problem. Do post the screen messages from the build, as Matt suggested. I mostly grok perl's strange and numerous messages (which must say something bad about me .... ;-) I wanted to mention that this week I made some good progress on Artemis (I had all of Monday at home watching a contractor poke holes in my walls!) There are still alot of clunky interface problems, but Artemis will run to completion a fit with one data set using any number of feff calculations and it will plot the results in a manner that rsembles Athena. That is, you can select the data, the fit, and/or any number of paths from the list in the skinny panel on the right and click a button for plotting in k, R, or q. Model building needs a lot of work, but its usable. I would love if the Mac effort could succeed soon -- that would somewhat increase the number of alpha testers ;-) B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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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The road to Athena...
by Charles Bouldin 07 Mar '02

07 Mar '02

Bruce sez to try this to test if things are in place for Athena: >#!/usr/bin/perl -w >use Tk; >use Ifeffit qw(get_scalar); >use Tk::Dialog; >my $x = get_scalar('etok'); >my $top=MainWindow->new(); >$top->Label(-text=>"Ifeffit sez etok=$x") ->pack(); >$top->Button(-text=>'Done', -command=>sub{exit})->pack(); >MainLoop; I tried it and got: >[h196132:~/Desktop] charlesb% perl test_ifeffit.pl >Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5/darwin >/sw/lib/perl5 /System/Library/Pe >rl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl >/Library/Perl /Network/Library/Perl >/darwin /Network/Library/Perl /Network/Library/Perl .) at >test_ifeffit.pl line 3. >BEGIN failed--compilation aborted at test_ifeffit.pl line 3. But then I realized I needed to At 12:01 PM -0600 3/7/02, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > cd ../../wrappers/perl > perl Makefile.PL > sudo make install So, I did that, but now I get >[h196132:~/Desktop] charlesb% perl test_ifeffit.pl >dyld: perl Undefined symbols: >_ifeffit_ >_iff_exec >_iff_get_array >_iff_get_echo >_iff_get_scalar >_iff_get_string >_iff_put_array >_iff_put_scalar >_iff_put_string >_iffgetarr_ >_iffgetecho_ >_iffgetsca_ >_iffgetstr_ >_iffputarr_ and I'm not sure why this is happening. However, this feels close to working. More suggestions?

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How to run ifeffit from terminal.app
by Charles Bouldin 07 Mar '02

07 Mar '02

Thanks to helpful folks on usenet, who seem amused that Maccies are starting to ask such basic questions, here is how to run ifeffit from terminal.app: >: Wow, this sounds close to a solution to something I've been puzzling >: over. I have Xwindows installed and I can use pgplot from an xterm >: running under XDarwin, but I can NOT run pgplot from Terminal.app. If I >: try I get a message: >: PGPLOT /xw: cannot connect to X server >: I tried putting the DISPLAY=:0.0 export DISPLAY into .xinitrc and >: .cshrc, to no avail. Basically, I don't know what I'm doing here :) and >: I am just blundering about. > >That command is for sh/bash, not tcsh. For tcsh, you want > setenv DISPLAY :0.0 > >If you're going to put it in your .cshrc file, then use > if( ! $?DISPLAY ) setenv DISPLAY :0.0 >so it won't override DISPLAY if it's already set, such as by >a forwarded X11 connection. There were several interesting replies, one of which was basically, "I know how to fix it, but I refuse to use c shells". What's -that- about?

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Status of ifeffit, atoms, athena, etc on MacOS X
by Charles Bouldin 06 Mar '02

06 Mar '02

This may be the first message on the mailing list? It is a message mostly composed of questions: I have ifeffit and atoms running just fine on MacOS X, thanks to Francois' hard work figuring some things out and Matt's quick port of ifeffit. 1. Does anyone have Athena running? 2. Is anyone able to run ifeffit from Terminal.app, as opposed to running it from an xterm? When I try this, I get an error message, "PGPLOT /xw: cannot connect to X server". When I do ps -aux | grep pgp I see a process charlesb 3239 0.0 0.1 67316 672 std- S 0:00.04 /sw/pgplot/pgxwin_server -display :0.0 so clearly I need to something to tell terminal.app about the pgplot server? Anyone have advice on this? I just don't know where to look beyond this point. Why do I care about this distinction? (1) Terminal.app supports cut/copy/paste, (2) terminal.app is scriptable, which means that you can define define macros, or use script menu to put in common command blocks. In principle, this means that you could use Applescript studio to control ifeffit from a mac-native gui. 3. Has anyone run ifeffit using aquaterm? I'm very heartened by the recent rapid progress and hope that it can continue.

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Ifeffit Mailing List
by Matt Newville 05 Mar '02

05 Mar '02

OK, after two short weeks waiting for the APS firewall to allow the mail server to work, it appears that the Ifeffit mailing list is now really open for business! You can join this list or read the archives from http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/ Thanks, --Matt |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0443 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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Ifeffit Mailing List
by Matt Newville 21 Feb '02

21 Feb '02

Dear Friends of Ifeffit, Over the past few weeks there has been quite a bit of email flying back and forth about Ifeffit and a variety of related subjects: building on MacOS X, installations scripts for Win32, phase-corrected FTs, Tables for Feff calculations, and a bug report or two. It's been quite a challenge for me to keep up with it all! At Bruce's suggestion, and in an effort to cut down on the amount of repeated and partial information, I set up a mailing list for Ifeffit. You can join this list or simply read the archives. You do not have to join the list to post a message. To join the list or browse the (currently very short!) archive, go to http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ Of course, you can still send me mail about Ifeffit, but please consider using this list for Ifeffit-related mail. Since these messages will be put in a public archive, anyone with similar questions, or answers, will be able to see the messages. Thanks, --Matt |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0443 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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Welcome!
by Matt Newville 20 Feb '02

20 Feb '02

Dear Friends, Welcome to the Ifeffit Mailing list. This list is intened for announcements, questions, and discussion of Ifeffit and related programs (including, but not limited to Feffit, Autobk, Atoms, G.I.Feffit, Athena, and Diffkk). It is also intended for discussion of the Analysis of XAFS and related spectroscopies. Although there is a separate mailing list for Feff Users and Development (see http://leonardo.phys.washington.edu/feff) questions and discussion of how Feff relates to XAFS Analysis, and the use of Feff calculations in XAFS Analysis are welcome here too. Thanks, --Matt Newville |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0443 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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