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

RE: [Ifeffit] Some questions about ATOMS and FEFF
by Barton, David (DG) 16 Jan '05

16 Jan '05

Patrick, Welcome to the mailing list! This list is an excellent forum for newcomers and veterans alike. > 2) Running the FEFF6 software directly or through the Artemis > bundle, I never get any "chi.dat" output file as a weighted sum of the > individual This feature is built into Artemis. After you run the FEFF calculation with Artemis and choose which paths to import, just highlight the paths in the DATA & PATHS window that you would like to sum and then choose DATA-->SUM OF PATHS-->SELECTED DATA PATHS from the menu. This will produce the chi(k) sum which can be plotted along with your data set. A shortcut to this menu item can also be found by right-clicking on the selected paths and choosing DATA-->SUM OF PATHS-->SELECTED DATA PATHS. I often use this feature to get a rough feeling for the relative contributions of each path in the calculation by plotting the SUM along with all of the individual paths. Have Fun, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA Ph: (989) 636-4753 Fax: (989) 638-6225 Email: dgbarton_remove_me(a)dow.com > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Patoo > Sent: Sunday, January 16, 2005 9:07 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Some questions about ATOMS and FEFF > > > Hi, > > I am just starting to work with the ARTEMIS/ATHENA software suite for > EXAFS data processing and analysis and a newcomer in this > mailing list. This project is really very nice and useful for > the EXAFS community and > I really enjoy to learn how to use it. > I read most of the documents which are available on the website and > around, but I have already two questions : > 1) in the "feff.inp" command file, what are the options of the cards > CONTROL and PRINTS > 2) Running the FEFF6 software directly or through the Artemis > bundle, I > never get any "chi.dat" output file as a weighted sum of the > individual > "feffNNNN.dat" individual path contribution. Is there any forgotten > option to get it ? > > Thanks in advance for your help > > Patrick > > -- > *********************************************************** > Dr. Patrick Judeinstein > R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 > I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) > Université Paris-Sud, 91405 Orsay Cedex - France > Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + > 33 (0)1 69 15 81 05 > > e-mail : pjudeins(a)icmo.u-psud.fr > web site : http://patoo.hope.free.fr > > *********************************************************** > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Some questions about ATOMS and FEFF
by Patoo 16 Jan '05

16 Jan '05

Hi, I am just starting to work with the ARTEMIS/ATHENA software suite for EXAFS data processing and analysis and a newcomer in this mailing list. This project is really very nice and useful for the EXAFS community and I really enjoy to learn how to use it. I read most of the documents which are available on the website and around, but I have already two questions : 1) in the "feff.inp" command file, what are the options of the cards CONTROL and PRINTS 2) Running the FEFF6 software directly or through the Artemis bundle, I never get any "chi.dat" output file as a weighted sum of the individual "feffNNNN.dat" individual path contribution. Is there any forgotten option to get it ? Thanks in advance for your help Patrick -- *********************************************************** Dr. Patrick Judeinstein R.M.N. en Milieu Orienté, (UMR 8074), Bâtiment 410 I C M M O (Institut de Chimie Moléculaire et des Matériaux d'Orsay) Université Paris-Sud, 91405 Orsay Cedex - France Tel : +33 (0)1 69 15 70 17 ou ++ 33 (0)1 69 15 47 68 ; Fax + 33 (0)1 69 15 81 05 e-mail : pjudeins(a)icmo.u-psud.fr web site : http://patoo.hope.free.fr ***********************************************************

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re:fits
by k-kupiecki＠northwestern.edu 15 Jan '05

15 Jan '05

Thank you Bruce and Shelley! I just wanted to thank Matt, Bruce and everyone involved with IFEFFIT/Artemis/Athena... it has been a Godsend.... I couldn't have stumbled on it at a better time (I'm frantically trying to analyze about 4 beamtimes worth of SEXAFS data for papers and my thesis and WINXAS wasn't really working out for me)!!!!! Does anyone have any suggestions for additional literature in regards to better understanding the quality of fits and the parameters involved?.... or perhaps know when we might be able to expect a updated version of the Artemis literature? (What is currently there has helped me sooo much that I've been checking for an update every couple of weeks hoping to get see sections 2.2-3.2..... ) Also.... I guess I've realized that only knowing IFEFFIT with Artemis I kinda take things for granted (like I didn't know that IFEFFIT was having problems, in certain cases since I had only been checking the "Results" and the error messages on the bottom of the window....) which meant I missed errors like this in the IFEFFIT (since I didn't notice anything unusual in the "Results"): ............ # Do the fit! ## fitting difference of Cov_0_06ML_bl1435_111703.chi and one or more paths ... ## === data set #1 of 1 feffit(1-8, group=data0_fit, chi=data0.chi, k=data0.k, kweight=2.00, rmin=1, rmax=4, kmin=2.5, kmax=15, dk=2, kwindow=kaiser-bessel, fit_space=R, do_bkg=no, data_set=1, data_total=1) feffit fitting 1 data sets fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... fitting ... no uncertainties estimated! fit gave a warning message: too many fit iterations. try again with better guesses or a simpler problem. ............................................... I guess my question is.... is there anything else I should be looking for in the IFEFFIT printout that I might not otherwise notice by just using Artemis and looking at the error messages and "Results"? Thanks for the input! Sincerely, Kristine Witkowski Northwestern University

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another bug
by Norbert Weiher 13 Jan '05

13 Jan '05

Hi Bruce, sorry to bother again - here's the issue: I fit a given spectrum say in kw=2, choose as plotting option "kw". If I plot the fit and the data, only the data gets the correct kw, the fit is displayed with kw=1. If I select kw=1,2 or 3, everything is fine. The problem exists also when exporting the fits to a file... I noticed this in diana and artemis... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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horae-048 with Athena 0.8.037 and Artemis 0.7.014/DR008
by Bruce Ravel 13 Jan '05

13 Jan '05

Hi folks, I just released the latest source tarball for linux, unix, and Mac OSX. Copies can be found on SourceForge and on my web site. A windows updater and Carlo's debian packages should follow soon. A new windows executable of the development version of Artemis can be found along with some notes on its use at http://leonardo.phys.washington.edu/~ravel/software/exafs/diana/ This is mostly a bug fix release. I have addressed almost all of the problems reported in the last 10 days on the mailing list. (I think the lone exception is the control-click problem Paul reported yesterday.) Additionally, I have added a new feature to the development version of Artemis. In the Theory menu, you can now find an entry that reads "Quick first shell theory". This is in response to the thread started by Carlo the other day. This prompts you for a concise description of a single shell scattering problem -- absorber and scatterer species, distance, coordination geometry, edge -- and produces a quick-n-dirty feff calculation suitable for a quick-n-dirty first shell fit. I wrote a document page -- just click on the document button at the bottom of the quick first shell theory dialog. Try it out -- it should make sense once you poke at it a bit. As I said yesterday, this release is probably the last one for at least a couple of months. There is some chance that I might update the source code tarball in that time, but I lose my ability to make windows executables tomorrow. I am keeping my fingers crossed that the windows executables that I just built and that will be in the next updater will prove to be solid. 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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personal news
by Bruce Ravel 12 Jan '05

12 Jan '05

Hi! I wanted to let all the good folks on the mailing list know about an imminent change in my life. This coming Friday will be my last day with my current employer, the Naval Research Lab. I will be taking a 7-week vacation, then starting a new position at Argonne working in the Environmental Research Division. My responsibilities there will include helping to build an XAS station on the Sector 10 bending magnet. My new boss knows all about the software and has encouraged me to continue working on it. Yay! For the coming 7 weeks, I'll only be posting to the mailing list sporadically. For two of those weeks, I will be traveling for fun outside of North America and I have no intention of looking at a computer during that time! Before the end of the week I intend to have a new source code tarball and new Windows executables of Athena and both versions of Artemis. Until I am settled in at the new job, it is unlikely I will update the codes, even in the event of a serious problem. Once I get to Argonne in early March, I look forward to meeting all of you whom I do not know and who pass through the APS. A period of transition is an excellent opportunity to look back upon and evaluate recent times. The last three years in which I have been working on the programs have been some of the most rewarding of my career. It has been enormously gratifying to see so many people get involved in my efforts at the level of sending me bug reports and feature suggestions and working with me to improve the quality of the codes. And it has been enormously fun to see this mailing list grow into a real community populated by some of the friendliest, smartest, and most helpful people that I know. Many of you have made a real impact on the product of my three years of labor. I am thankful for that and I hope that you see a bit of yourselves every time you fire up the codes. 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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look what happens when you go away for a day!
by Bruce Ravel 12 Jan '05

12 Jan '05

Hi! Yesterday I spent the day away from the office. This morning I saw an impressive number of bugs and other issues reported in the short span that I wasn't paying attention. ;-) ** Mauro mentioned a problem changing between the raw and column views of a log file. I cannot reproduce this behavior. Mauro, can you send me a project file that demonstrates this? ** Paul mentioned a number of problems regarding data import. At least one of them seems to be the same problem Michel Jaouen mentioned in private email the day before. Matt, in his response, explained the problem exactly. Silly bug by me. ** Chachi mentioned a confusing error message from Feff. Matt explained the situation. The next versions of both the stable and development branch of Artemis will issue a much clearer error message in the situation Chachi reported. I will make a new release of the source code tarball this week. A windows updater package will follow shortly. 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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Bug in Artemis Rename horae-047
by Paul Fons 12 Jan '05

12 Jan '05

Thanks for the new version Bruce -- here is a quick bug report: I was bitten by a rename bug in diana (not carefully documented yet) so I tried artemis thinking things would be smoother. Upon renaming a feff calculation in artemis (horae-047), the rename window opens (I used the control key to make the pop up menu appear and chose the rename this feff calculation from there), and I enter the new name. Good. Wait, the rename window opens again (with the default name FEFFx -- where x is the original name of the calculation). I get an error when I try entering the name again (noted below). The changed name is already reflected in the list on the right after the first renaming. Something similar happened in diana as well. This should be easy to reproduce, let me know if you need more details. Paul <Key-Return> (command bound to event) at /Applications/Ifeffit/bin/artemis line 1586 main::__ANON__('Tk::Error: Can\'t call method "focus" on an undefined value a...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 488 Tk::Error('MainWindow=HASH(0x1e04a58)', 'Can\'t call method "focus" on an undefined value at /Applicat...', '<Key-Return>', '(command bound to event)') called at /Applications/Ifeffit/bin/artemis line 13619 eval {...} called at /Applications/Ifeffit/bin/artemis line 13619 main::Echo('There is already a Feff calculation named "Sbcore"!') called at /Applications/Ifeffit/bin/artemis line 13631 main::Error('There is already a Feff calculation named "Sbcore"!') called at /Applications/Ifeffit/bin/artemis line 4673 main::rename_feff() called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 247 eval {...} called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 247 Tk::__ANON__('Tk::Menu=HASH(0x1ea6660)', 'active') called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x1ea6660)', 1) called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 406 eval {...} called at /usr/local/lib/perl5/site_perl/5.8.6/darwin-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1796 Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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ARTEMIS export error
by Norbert Weiher 12 Jan '05

12 Jan '05

Dear Bruce, just tried to export some data to a file using the "save selected groups as" command. He gives me the message "You cannot save more than -2 groups to a single file". That's a step back compared to the limit of 15 I we had before :) Went quickly through some of my fits - but it is the same everywhere. I attached an example file. Hope it helps... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher(a)manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468

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RE: Ifeffit Digest, Vol 21, Issue 17
by crojasa＠unmsm.edu.pe 11 Jan '05

11 Jan '05

Hello. When i run feff on artemis, for a FeCo system , It appears a error message: Feff 6L.02 Fatal error : To many atoms in ATOMS list . Maximum is 5000 Which is the problem, Feff6 not support above 500 atoms?? wait your replys Chachi

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