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

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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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 07 Jan '05

07 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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