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

Re: [Ifeffit] Using more than one E0
by Scott Calvin 07 Jun '04

07 Jun '04

Hi Wojciech, I have another suggestion. It is my secret, completely untested belief (which I am now revealing to everyone on this mailing list!), that some of the cases of "successful" fits using multiple E0's are masking problems caused by not considering a third cumulant. For those who may not know the role of this parameter, it in essence measures asymmetry in the distribution associated with a path. For example, if a pair of atoms are more likely to separated by a distance considerably larger than the mean separation than by a distance considerably smaller than the mean separation, then the third cumulant is positive. (The mathematical definition is that the third cumulant is the mean cube of the difference from the mean, in the same sense that sigma2 is the mean square of the difference from the mean.) In most cases, the third cumulant is small. Nevertheless, if it were 0 in all cases, then materials would not show any expansion with temperature! Through symmetry arguments, it is pretty clear that the third cumulant is most likely to be significantly nonzero for nearest-neighbor paths. What does this have to do with fitting different E0's? E0 and the third cumulant both affect the phase of the EXAFS signal, although they are weighted in different ways by k. Nevertheless, if a nonzero nearest-neighbor third cumulant is called for, allowing a different E0 for the nearest-neighbor instead would probably also improve the fit statistically. In this case, however, while the use of a third cumulant can be justified on physical grounds relatively easily, the use of a separate E0 is an arbitrary non-physical attempt to improve the statistics. So as far as I am concerned, I am more inclined, if my fit is not quite working out, to try allowing the third cumulant for paths in the first coordination shell to vary than I am to introduce multiple E0's. In fact, I usually do this at some point during the fitting process even if my fit is behaving fairly well to reassure myself that the third cumulant is 0 to within the uncertainty of the fit, and that constraining it to 0 is not distorting the values of the parameters I am interested it. Take all of this with a grain of salt; I wrote my dissertation on the third cumulant, and, to paraphrase Bruce, since I've spent a lot of time making a nice hammer, everything tends to look like a nail... --Scott Calvin Sarah Lawrence College > >I would like to address a couple of questions which are partially >related to my recent struggles in fitting some EXAFS data. I'm >trying to fit my data using several shells of different neighbors >including a few single scattering paths and also so multiple >scattering contributions (mainly collinear multiple scattering >paths) all calculated with the help of FEFF 8.20. Now, I found once >in the FEFFIT manual the following suggestion: one might consider >using several different E0's for different paths in order to improve >the fit. Ok, the explanation was based on some approximations coming >from FEFF code which include incomplete core-hole shielding, lack of >angular variations of the valence charge distribution and charge >transfer between atoms in polar materials. >My question is the following: does anyone of you have some >experience with such procedure? And if yes, shall than distinguish >between the first shell of nearest neighbors and the rest of the >atoms in terms of their E0 corrections (using 2 parameters)? Or >perhaps one can use separate E0's for each path?

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trouble with Atoms on Mac OSX
by Michel Jaouen 04 Jun '04

04 Jun '04

Hi folks, I'm using a PM (2X1.8 MHz processors) under OSX v 10.3.4 (Panther latest version). I have installed ifeffit-1.2.5a two weeks ago and used Atoms many times since. It works well till yesterday when I loose the ability to use the space group browser with an error reported on the herre attached file. It looks that I have a problem with Tk, but I don't understand why. I have tried to make a new install from scratch after putting in the trash the ifeffit and perl (the one I assume to be put by the iffit installer in the home/lib folder): it didn't fix the problem. I found rather puzzling to find several perl folders (one coming from ifeffit and one from Fink). Looking my environnement, I found the following: PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin. I therefore modify my profile making a setenv to force to use the perl from ifeffit without any change. So it seems some hidden file is responsible of this behavior. I must say that if I enter the space group by hand, Atoms runs (e.g. it creates the feff.inp file). If anybody has a solution, I will appreciate. Additional point: I have compliled feff7 using the GNU g77 from Fink, but it stops the run with a segmentation fault. Any hint? Best regards Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Debian packages
by Carlo U. Segre 04 Jun '04

04 Jun '04

Hello All: I have now packaged the latest horae (036) for Debian stable and unstable. There was a problem in previous versions for stable which I just now figured out how to fix and it involved making a back port of a newer perl module for the archiving/zipping of the project files. Sorry if this caused anyone problems. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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trouble with Tk on Mac OSX
by Michel Jaouen 03 Jun '04

03 Jun '04

Hi folks, I think somethings is broken with Tk. As reported in my previous e-mail I found a problem (I have not before 1st june!) with the space group browser of Atoms. In fact I have the same error with Artemis when pressing the fit button! The following message was trapped by Artemis: Artemiswarn/Users/mjaouen/.horae/stash/ARTEMIS.TRAPCODE(0x1e18a84) at /Applications/Ifeffit/bin/artemis line 1491 main::__ANON__('Tk::Error: unknown option "background" at /Library/Perl/ 5.8.1...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) l ine 488 Tk::Error('MainWindow=HASH(0x61e5d8)','unknown option "background" at /Library/Perl/5.8.1/darwin-thr...','Tk callback for .sgb.frame','Tk callback for . sgb.frame.ysbslice','Tk callback for .sgb.frame.ysbslice.corner','Tk callback for ..sgb','Tk callback for .sgb.button1','Tk callback for .frame.menubutton5.menu', 'Tk::__ANON__ at /Library/Perl/5.8.1/darwin-thread-multi-2leve...',...) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1627 What makes me crazy is that all was running smoothly before tuesday :-) Cheers Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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news
by Bruce Ravel 02 Jun '04

02 Jun '04

Hi everybody, Today I made another new release of the source code tarball and built a new Artemis executable for windows. Users of each of the three major platforms should read the notes below for information about this release. This will be the last release for a while. June and July will be very busy for me and I will have scant time to work on the codes until August at the earliest. I will be reading bug reports and suggestions and will address them when I get back to work on the codes -- so please continue to send them in. Hopefully whatever bugs are lurking in there will not prove too difficult to work around. This release attempts to fix a problem managing the project folder in Artemis, as reported by Stefano Ciurli. The new version works correctly for me, your milage may vary. If any of you will be at the ISSRNS conference in Zakopane Poland next week, please introduce yourself! I hope everyone has a great summer! (Or a great winter for those of you in the southern hemisphere!) B -------------------- O -------------------- Notes for each of the platforms follow: Linux (and other non-Mac OSX unixes): The source code tarball is on SourceForge and on my web site. If the horae_update script fails, try using the --mirror argument as described in the help text (horae_update -h). Mac OSX: There was no time to make a new installer package. For the time being, you can use the most recent installer package, then update to the latest source code tarball from the command line. This requires downloading the source tarball from SourceForge and unpacking it. Then, from the command line, type "perl Makefile.PL" then "make" then "sudo make install". The last step will prompt for the administrator password. If you run into trouble, ask on the mailing list and one of the Mac users should be able to help you. Windows: There was no time to prepare a new updater package for windows. Virtually all of the changes in my codes since the last updater package have been bug fixes to Artemis. So I have made a new Artemis executable and placed it here: http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/artemis_… If you are up to date with the most recent updater package, just download this executable and overwrite the "artemis.exe" file in the instalation directory: "C:\Program Files\Ifeffit" (or where ever you have ifeffit installed on your computer). -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b 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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trap file
by Stefano Ciurli 01 Jun '04

01 Jun '04

Hi Bruce, I installed the new horae (035) and played around with the ZnO tutorial using the new version of Artemis. I called the program in the directory where the ZnO dat file reside from the command line. The project apj1 (run with all the indications in the journal) worked smoothly. As soon as I try to read in the apj2, the following trap message pops up: # Artemis 0.7.005 # This file created at 00:19:09 on 31 May, 2004 # using darwin, perl 5.008001, Tk 804.027, and Ifeffit 1.2.5 # Workspace: /Users/stefano/.horae/stash/artemis.project.3/ The following message was trapped by Artemis on a SIGWARN: Artemis0.7.005warn/Users/stefano/.horae/stash/ARTEMIS.TRAPCODE(0x1e3dff8)/Users/stefano/.horae/stash/artemis.project.3/ at /Applications/Ifeffit/bin/artemis line 1562 main::__ANON__('Tk::Error: could not open /Users/stefano/.horae/stash/artemis...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 488 Tk::Error('MainWindow=HASH(0x8f44c)','could not open /Users/stefano/.horae/stash/artemis.project.3/...','main::nnnn_header at /Applications/Ifeffit/bin/artemis line 4386','main::read_path at /Applications/Ifeffit/bin/artemis line 10872','main::open_project at /Applications/Ifeffit/bin/artemis line ...','main::read_data at /Applications/Ifeffit/bin/artemis line 6901','main::dispatch_read_data at /Applications/Ifeffit/bin/artemis...','main::__ANON__ at /Applications/Ifeffit/bin/artemis line 586','Tk callback for ..frame.menubutton.menu.project_data',...) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1707 End of trap file. Exactly the SAME error message pops out when I try to save a fit as chi(k). Obviously I am stuck... Any help here? Again, there must be some problem with the perl libraries... HELP!!! Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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source tarball for horae-035
by Bruce Ravel 01 Jun '04

01 Jun '04

Hi folks, I just released the source code tarball for the latest version of my software. Those of you who use the source can run the horae_update script now. Or, you can grab the new version of the horae_update script from here and try it: http://leonardo.phys.washington.edu/~ravel/software/exafs/utilities/horae_u… The new version allows connection to a local proxy and grabs the tarball from SourceForge. Type "horae_update -h" for help on using the new features. This new version of horae_update is included in the tarball. This release is purely a bug fix release, mostly for Artemis. It addresses all the outstanding issues brought to my attention over the last week, including the problems related to the Mac OSX package. A windows executable will be made next week. Thanks to all the folks who provided bug reports for this release, including Shelly Kelly, Stefano Ciurli, Gleb Pokrovsky, and Peter Southon. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b 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 normalization and deglitching bugs
by Scott Calvin 01 Jun '04

01 Jun '04

Hi Bruce, I figured I'd post this to the Ifeffit list so that others could be alerted to similar problems, but I'll send you an Athena project file exhibiting this problem separately, so that everyone's in-boxes don't get cluttered with attachments. I'm using Athena 0.8.028 on Windows XP. First of all, on any file, including the copper data that comes with Athena, there is a bug. To see it, go to the deglitch screen, and change Emax by picking a point off the plot. Then replot. From now on, the green "tolerance" lines extend from Emax up to the end of the plot, rather than from Emin to Emax. This seems to affect only the screen display (i.e. it still deglitches the intended range), but it does make it harder to see what will get deglitched. The second behavior is best revealed with the project I am sending you separately. I am not positive it is a bug, but it doesn't match what I would expect. In the project I am giving you, the data is very glitchy (lots of Bragg peaks). Go down to the group labeled SBT/B Bi LIII Merge and plot in E-space with the post-edge line. Does it look right to you? It looks like the normalization line is considerably higher than it should be given the normalization range chosen, with only a few glitches above it. Is that something I don't understand about the way the post-edge line is chosen, or is it displaying the line wrong, or is it calculating it wrong? Thanks--the new features in Artemis are great, by the way. --Scott Calvin Sarah Lawrence College

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Updating problems.
by Dave Baker 28 May '04

28 May '04

Hello all. This message is directed mainly toward Bruce, but if anyone else has any suggestions, please feel free to contribute. For a while now, I have been using Athena and Artemis on my work computer with a broadband internet connection, and all the updates have auto-detected and installed without a hitch. The problem is that now, I want to use the programs on my home computer, for which I am simply too cheap to buy anything better than dialup service. The updater, unfortunately, has choked several times when trying to download and install the 9 updates it says I need. (In fact, one time the echo screen stated that all the updates were installed, but when I restarted and opened Athena and Artemis, I was confronted with the old versions of the programs.) I haven't seen any "new and fully updated windows installers" on either Matt's or Bruce's pages, and it isn't clear to me how to get at the update files without the assistance of the updater itself. (I seem to recall reading that one can simply unzip the ifup_00x.zip file in the Ifeffit directory, run make_bats.exe, and all will be well.) Is there a way I can use the broadband connection at school to grab the updates and install them myself on the home computer without the use of the updater? Or, is there a place that the updater stores the .zip files after it's done updating the program, so I can just grab them off the work computer? Thanks for your help! -Dave ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ --

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an update on the Mac OSX problem
by Bruce Ravel 28 May '04

28 May '04

Hi, I just wanted to let the mac users know that I have finally flushed out the problem that Stefano and Matt reported. There is most certainly a crippling problem with 0.7.004 on the Mac. In fact, the problm does not have to do with the Mac per se, but with the version of perl/Tk used to build the codes in the Mac installer. As some of you may be aware, the perl/Tk world is in the middle of a transition between two major versions of the toolkit. One of the challanges for me has been to write code that works seamlessly despite certain internal differences. It turns out that I finally traced the problem to a rather obscure difference between the older and new perl/Tk code bases. Fortunately there is an easy solution (although it will take me a while to find all the places where I need to apply it) and I think that I'll be able to post a new source code tar ball by the end of the day. Also fortunately, Windows users will not see this problem using the current builds of the windows executables. Note that the Mac installer currently has 0.7.003, so those who have installed the installer but not updated to 0.7.004 are unaffected. Finally, linux and other unix users who are using a perl/Tk 800 release will be unaffected. The bug is specific to perl/Tk 804. The amusing thing is that Stefano originally reported this as a problem loading an atoms.inp file. That turned out to be quite a red herring. The problem has nothing to do with the part of the code that handles atoms or feff files! Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b 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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