January 2005 - Ifeffit - millenia.cars.aps.anl.gov

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 12 Jan '05

12 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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