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

RE: [Ifeffit] Two edge problem (in the same scan)
by Kelly, Shelly D. 26 Jan '05

26 Jan '05

> -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel > Sent: Wednesday, January 26, 2005 1:30 PM > To: asg2(a)lehigh.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Two edge problem (in the same scan) > > > Hello everybody, > > I have a question/problem. Last year during the EXAFS course at NSLS, I > > had requested Bruce if it is possible to analyze the data with two > > edges. For example, I have the data for As and Se K-edges, which I > > collect in the same scan. In WinXAS program, I can section the edges and > > analyze them separately. At that time, the program was not able to > > perform these edges or the sectioning. Have we reached this possibility. > > I tried again using the latest updated Athena, but it seems not to be > > working. Can you please tell me whether the sectioning or dealing with > > two edges in the same spectra can be done > > I don't unfderstand why "sectioning" is necessary. What precludes you > from reading the data set a second time and setting e0 to be appropriate > for the second edge? Then your pre- and post-edge lines will be made > using the second e0 and everything else should just follow normally. > > I understand that Athena does not have a way to specify the second edge in > the column selection dialog, but that seems to me like an inconvenience > more than a real limitation. It is an inconvenience because you then have > to specify the second e0 by hand rather than have Athena's magic find it > for you, but is that really so hard? > > B > [Kelly, Shelly D.] Another feature that I have found useful for data with multiple edges is the truncate function. Once you read the data set into Arthena. Make a copy of the data set. Choose your e-zero for each data set. And then truncate the data sets to the "normal" range. This will help with some of the automatic presets, which use the full data range by default, and can give you a very scary initial background function. SK

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Two edge problem (in the same scan)
by Ashtosh Ganjoo 26 Jan '05

26 Jan '05

Hello everybody, I have a question/problem. Last year during the EXAFS course at NSLS, I had requested Bruce if it is possible to analyze the data with two edges. For example, I have the data for As and Se K-edges, which I collect in the same scan. In WinXAS program, I can section the edges and analyze them separately. At that time, the program was not able to perform these edges or the sectioning. Have we reached this possibility. I tried again using the latest updated Athena, but it seems not to be working. Can you please tell me whether the sectioning or dealing with two edges in the same spectra can be done Ashtosh

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[DATA-REQUEST] Platinum standards
by MauRo 24 Jan '05

24 Jan '05

Hi to all, I'm looking forward for some EXAFS (transmission or fluorescence) spectra of Platinum oxide and Platinum carbide at L_III and/or L_I edge. Is there anyone who has taken this data and is so kind to send them to me? Thanks, Mauro

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Increase NOVP error message meaning
by Paul Fons 23 Jan '05

23 Jan '05

I am trying to run feff on some chalcogenide structures that have rather nearest-neighbor long bond lengths, e.g. > Bond search from target site: Te1 > ...found 6 atoms within 0.00 - 3.20 A of this site > > ------------------------ > dist [Å] atoms > ------------------------ > 1. 3.0488 6 > ------------------------ > Bond search complete When I use this structure in feff82, I get the rather mysterious error INCREASE NOVP: > > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > tell authors to INCREASE NOVP Being an experimentalist, I did increase novp until the previous error message stopped, however this resulted in a core dump: > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) > 0 1.76126E+00 1.74898E+00 1.01667E+00 > 1 1.71891E+00 1.63874E+00 1.12886E+00 > 2 1.35785E+00 8.69242E-01 1.15000E+00 > 3 1.78418E+00 1.76792E+00 1.02193E+00 > mu_old= nan > Done with module 1: potentials. > Calculating LDOS ... > LDOS calculation for specified grid > Calculating energy and space dependent l-DOS. > It takes time ... > potential type 0 > Segmentation fault (core dumped) When running the equivalent file in feff6, I get the > Calculating potentials and phases... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > phase shifts for unique potential 0 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 1 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 2 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > phase shifts for unique potential 3 > Hard tests failed in fovrg. > Muffin-tin radius may be too large; coordination number too small. > Preparing plane wave scattering amplitudes... > nncrit in prcrit 9 This message seems similar to the troubleshooting section in feff8 for which it states: • Non-physical, widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any ‘.dat’ file) and possibly a failure of the phase-shift program to converge. This gives error message hard test fails in fovrg. How to I avoid this problem (obviously the crystal structure is a given!). I tried the INTERSTITIAL card, but to no avail. Any suggestions are welcome. 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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Windows update for athena/artemis
by Matt Newville 18 Jan '05

18 Jan '05

Hi, I've built a Windows update file to upgrade to the latest versions of Athena and Artemis. Since Bruce is off-line for a while and since there is no easy way for us to make these executables, there is not much we'll be able to do if there is a problem with this version. Because of this, I am NOT releasing this as a normal update yet, but would like the braver of you to download and install this update by hand and give the new versions of Athena and Artemis a test drive. The update file is at http://cars9.uchicago.edu/ifeffit/updates/ifup_013.zip which is just a simple zip file that can be unpacked in your Ifeffit folder. (Probably C:/Program Files/Ifeffit). If you're willing to try these versions, please let me know how it goes. I'll wait until I hear some positive responses before I make a general update release that would automatically update everyone to these versions. Thanks, --Matt

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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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How does AUTOBK handle the pre-edge background removal?
by hsnuboy＠ksu.edu 11 Jan '05

11 Jan '05

Dear Ifeffit list, There is one question I don't understand very well. How does AUTOBK algorithm handle the pre-edge background removal? I check the mannual of using ATHENA and the paper, "Near-edge x-ray-absorption fine strructure of Pb: A comparison of theory and experiment", M. Newville, et al., Phys. Rev., B47:21 (1993), 14126. Both of them have no information about dealing pre-edge background removal with AutoBK and how is it work within Athena? Hence, I ask this qustion for all the experts on the list. Thank you for your help. Sincerely, Yu-Chuan Lin Research Assistant Dept. of Chemical Engineering Kansas State University

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new release of Athena and Artemis
by Bruce Ravel 11 Jan '05

11 Jan '05

Happy New Year everyone! To welcome in the new year, I have made a new release of my codes. There are several changes in Athena, some improvement to the development branch of Artemis, and a few bug fixes to the stable branch of Artemis. Source code tarballs are now available at SourceForge and on my website. Complete lists of changes are available at http://leonardo.phys.washington.edu/~ravel/software/exafs/notes/ A Windows updater package will be available soon. The biggest new feature in Athena is a dialog for doing self absorption corrections. I coded up four different algorithms and made it easy to switch between them so you can compare different approaches to the problem. The document page built into Athena has all the details. Among the other new features are linear combination fits of standards to data using chi(k) spectra, an option for using the smoothed derivative to align or calibrate data, and lots of bug fixes and minor improvements to the user interface. The new releases of Artemis are all about bug fixes. Several recently reported problems were fixed in the stable branch and many lingering problems from the previous release of the development branch have been fixed. I wrote a few short web pages introducing all the new features in the development version of Artemis. Here's the link: http://leonardo.phys.washington.edu/~ravel/software/exafs/diana/ It's mostly screenshots and terse descriptions, but hopefully you'll find it useful. For the Windows users out there, I built a Windows executable of the development version for the first time. There is a link to it on that web page along with instructions for how to install it. I am eager to get more feedback from users about the development version so I can start thinking about moving it back down to the stable branch. Special thanks this time to all the people who were at my class at the Canadian Light Source User's Meeting in November. Many of the improvements to this release of Athena were suggested or inspired by Canucks. Thanks! 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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Postdoctoral position
by Matt Newville 07 Jan '05

07 Jan '05

OK, here's another postdoc opening, this from Tom Trainor at University of Alaska, Fairbanks (fftpt(a)uaf.edu) ------------------------------------------------------------ A Postdoctoral Position is available in the Department of Chemistry and Biochemistry, University of Alaska Fairbanks, to study the structure and reactivity of hydrated metal-oxide surfaces. The successful candidate will be part of ongoing studies focused on understanding the structure of metal-oxide surfaces and the relationship between structure and reactivity in aquatic environments using synchrotron based x-ray scattering/spectroscopy (surface diffraction, x-ray absorption fine structure and x-ray standing waves) and complimentary scanning probe microscopy and computational techniques. The position involves close collaboration with members of a diverse research group emphasizing the connection between experimental studies and theoretical simulations. A strong background in mineral/fluid interface chemistry or metal-oxide surface chemistry and previous experience with synchrotron based x-ray methods is desired. Application details can be found at http://www.uaf.edu/uafhr/Employment/Job1204-477.html . Please contact Tom Trainor (fftpt(a)uaf.edu) for additional information. The University of Alaska Fairbanks is an Equal Opportunity /Affirmative Action Employer. ------------------------------------------------------------ --Matt

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Re: postdoc opening
by Matt Newville 07 Jan '05

07 Jan '05

Hi Folks, I get a fair number of questions and notices about jobs and post-doc opportunities related to XAFS. So far, I've been reluctant to use this list for that purpose, but since there are many grad students and post-docs on this list, it seems that posting these to the mailing list could help everyone. So, here's a notice for a post-doc fellowship at LBNL, sent to me from Corwin Booth (chbooth(a)lbl.gov) http://actinide.lbl.gov/gtsc/JobDetails.htm Corwin also wrote: > The final candidate will work closely with one or more group > members on something related to actinide research. The group is > an actinide chemistry group, however there are opportunities to > work in solid state physics. Somebody interested in x-ray > absorption spectroscopy, x-ray scattering and/or magnetism of > f-electron systems would obviously be great for me, and I am > starting to focus on measurements in diamond anvil cells. We > have high-radioactivity labs, as well, so someone interested in > synthesis of actinide intermetallics could also make big > contributions. There are other opportunities, so an interested > person could contact me. If you know of any potential > candidates I would appreciate you forwarding them the ad or this > email. We plan on filling this position ASAP. Good luck!! --Matt PS: if anyone else would like to post job notices here, feel free.

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Fwd: News
by Bruce Ravel 07 Jan '05

07 Jan '05

Hi Folks, Can anyone here help Michel with his problems installing the latest horae on his Mac? Thanks, B ---------- Forwarded Message ---------- Subject: News Date: Friday 07 January 2005 06:11 am From: Michel Jaouen <Michel.Jaouen(a)univ-poitiers.fr> To: ravel(a)phys.washington.edu Previously I have updated all using sudo horea_update. At that date (september 2004) it creates a folder horae-042 with the attached log file. It fixes the problems I have mentionned previously: all run fine (artemis version number 07.013, athena version number 08.035). I have seen your mail concerning a new update (horae-047). So I do as previously: sudo horea_update. I receive in the terminal window a lot of informations related to the instal and at the end all seems OK. But when I run artemis in a terminal X window, I have the same version as previously. Looking in the Ifeffit folder I don't see an horea-047 folder nor a log file. The only change I found are in the bin folder where I have new artemis and athena files that are labelled as executable unix files but I can open by clicing on them as text files! So what happens here: I miss something I guess, but what? Any hints? Cheers Michel PS I don't obtain the new interface as quoted on your web server, so I suspect I have some install to do "by hands", but why it is different from the previous update? ------------------------------------------------------- -- 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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Generating single scattering paths in Artemis
by Carlo U. Segre 06 Jan '05

06 Jan '05

Bruce: Occasionally, I don't know or don't care what the extended crystallographic environment of the absorber. All I want to do is apply single scattering analysis and I need some simple paths from FEFF. At this time, I can't see how to do this within Artemis since the Atoms page requires a space group and more information than I have available. Would it be possible to have the option for a simpler interface which just allows me to generate single scattering paths between two atoms at a specific distance from each other? Perhaps, I could even specify a coordination geometry (tetrahedral, octahedral, etc.)? 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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Re: [Ifeffit] Generating single scattering paths in Artemis
by Frenkel, Anatoly 06 Jan '05

06 Jan '05

<<feff.inp>> Hello Carlo et al, FEFF6 allows to use SS cards that were specifically designed to calculate single-scattering paths in the case the structural details are not known, as in Carlo's case. I am attaching a working example where I used to calculate single scattering FEFF in Cu-O in octahedral coordination in Cu2+[H2O]6 complex. I included hydrogen in the input file since it affects charge on oxygen, but in principle it works. Some details are given in this article: http://pubweb.bnl.gov/people/frenkel/HUMIC-EXAFS/est.pdf You can run FEFF6 using attached file and note that it produces three files, each corresponds to the single shell of Cu-O atoms. Note the use of the OVERLAP card in the attached file, as well as the use of Bohr's radius to work around the bug in FEFF6 that uses distances in OVERLAP as multiples of Bohr's radius instead of Angstrems, while the units in SS card are in Angstrems. Regards, Anatoly Anatoly Frenkel, Ph.D. Associate Professor Department of Physics Yeshiva University 245 Lexington Avenue New York, NY 10016 http://www.yu.edu/faculty/afrenkel Office: tel. (212) 340-7827 fax (212) 340-7788 anatoly.frenkel(a)yu.edu Laboratory: tel. (631) 344-3013 frenkel(a)bnl.gov -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Barton, David (DG) Sent: Wednesday, January 05, 2005 4:46 PM To: 'XAFS Analysis using Ifeffit' Subject: RE: [Ifeffit] Generating single scattering paths in Artemis Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit <<feff.inp>>

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Re: Generating single scattering paths in Artemis
by Webb, Samuel M. 05 Jan '05

05 Jan '05

Hi all... I know that this isn't necessarily an Artemis solution, but there is an option/module in SIXPACK (that other IFEFFIT interface) to do just what you've been asking about -- create simple single scattering paths between two atoms in a variety of coordination environments (tetrahedral, octahedral, etc). It has a nice periodic table interface to boot. I use it occasionally to do some quick and dirty fitting -- I do agree with Scott that its not always the most accurate way to go about things. The resulting FEFF file is placed in a FEFF folder in the sixpack root directory. Hope that helps some. Sam

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RE: [Ifeffit] Generating single scattering paths in Artemis
by Barton, David (DG) 05 Jan '05

05 Jan '05

Scott, > This can be fixed by editing the feff.inp file to remove the > Fe potential 1, but that's not enough--the oxygen scatterers > then have to have their potential renumbered to 1 to make > things work. That's a lot of work to do what should be simple. > > So I vote for changing the way Artemis works in such > circumstances so that less editing is needed: if the > absorbing atom is not present in the scattering list, then it > shouldn't have a second entry in the potential list. > I second this vote, since I also have had this same problem. New users could become quickly disgruntled by the Fatal Error message when attempting to put in simple systems or just by choosing a short cluster distance to only include the first shell in the FEFF calculation. At a minimum, it would be nice if Artemis trapped this error and reported a more friendly popup error message. Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D

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Athena & Artemis in Windows
by Peter Southon 22 Dec '04

22 Dec '04

Hello Windows people A few days ago Shelly suggested that Athena and Artemis don't work when installed in the directory "C:/program files/ifeffit/". This has always worked for me using XP, though I wouldn't be surprised if it caused problems in some earlier versions of Windows. Regarding Poorani's question about TRAP files, I have found it useful to put a shortcut to "C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP" on my desktop or wherever for easy access. Cheers, Peter >Date: Fri, 11 Jun 2004 08:36:32 -0500 >From: "Kelly, Shelly D." <SKelly(a)anl.gov> >Subject: RE: [Ifeffit] Running FEFF >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Message-ID: <1C1577844A0BDF448E14E8CCB2F74424015A1B6D(a)ANLMAIL.anl.gov> >Content-Type: text/plain; charset="us-ascii" > >Hi Poorani, > >I believe that Athena and Artemis do not work properly when installed in >the C:/program files/ifeffit directory. The installation proceedures >say to specify C:/ifeffit instead. To fix if, but all of C:/program >files/ifeffit into the trash and then re-install. > >Shelly Peter Southon Post Doctoral Fellow School of Chemistry University of Sydney NSW 2006, Australia +61 2 9351 4425

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