September 2009 - Ifeffit - millenia.cars.aps.anl.gov

GAANN Fellowships for Synchrotron Radiation
by Carlo Segre 18 Sep '09

18 Sep '09

Hello All: I apologize in advance for filling your INBOX with this if it is not relevant. We have recently been awarded a number of fellowships from the Department of Education GAANN program. Our fellowships are specifically for synchrotron radiation research in the Physics program. The announcement link is below. If anyone knows of students interested in this opportunity, please let them know. http://www.iit.edu/research/undergraduate_research/news/gaan_award.shtml Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
by Joel Kelly 16 Sep '09

16 Sep '09

Hello, I recently upgraded to OS 10.6 (snow leopard) on my intel Mac. It comes with version 2.3.4 of X11. Now, I can't seem to run any of the Horae GUI applications! I've tried launching Athena from iXAFS or from the stand alone IFEFFIT suite. When I run iXAFS, the normal launch window with Athena, Artemis, Hephaestus and the iXAFS shell appears. Clicking on the Athena, Artemis, and icons Hephaestus causes X11 to launch with an xterm window, but Aquaterm does not load. However, the iXAFS shell seems to load, though I'm not experienced enough with the shell to know if it's fine or not. Upon launching the Athena standalone program from IFEFFIT (downloaded here: http://cars9.uchicago.edu/~ifeffit/src/Ifeffit-1.2.10-Mac10.4_Intel_horae06…) clicking on "X11 graphics" launches xterm but not Aquaterm, and clicking on "Aquaterm" closes the program. Not sure if this is a Snow Leopard related problem or not- there has been a new version of X11 released (2.4) that is unsupported in OS 10.6, and unfortunately it doesn't seem to allow me to install a previous 2.3.2 version. Looks like I'll have to downgrade back to Leopard, these cat names are getting confusing. Has anyone experienced anything similar, or have any insight on how to fix the problem? Best regards, Joel Kelly University of Alberta

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8 coordination crystal
by mohamed sobhy 15 Sep '09

15 Sep '09

Dear I am trying to simulate CeO2 crystal lattice but I found that in Artemis documentations the following Currently the following coordination geomatries are available: * 4-coordinate crystal * 6-coordinate crystal * octahedral molecule * tetrahedral molecule * square-planar molecule CeO2 has coordination no of 8, so what is the meaning of that Also is there any manual or working examples for Artemis Thnaks Mohamed

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simplr question
by yavuz al 08 Sep '09

08 Sep '09

Dear all, I have just started the using athena and artemis but I wanna learn that what does it means: degen ? So2 ? eo ? dr ? ss2 ? plase help to me about this. yavuzal _________________________________________________________________ With Windows Live, you can organize, edit, and share your photos. http://www.windowslive.com/Desktop/PhotoGallery

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Re: [Ifeffit] Linear combination fitting reports
by Jens Kruse 02 Sep '09

02 Sep '09

Thanks for the fast answers. Attached is a screenshot. Maybe I just read the pages incorrectly. cheers, Jens ifeffit-request(a)millenia.cars.aps.anl.gov schrieb: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Linear combination fitting reports (Jens Kruse) > 2. Re: Linear combination fitting reports (Bruce Ravel) > 3. Re: Linear combination fitting reports (Kelly, Shelly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Sep 2009 10:13:55 +0200 > From: Jens Kruse <jens.kruse(a)uni-rostock.de> > Subject: [Ifeffit] Linear combination fitting reports > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <4A9E2943.5020408(a)uni-rostock.de> > Content-Type: text/plain; charset="ISO-8859-15"; format=flowed > > Hi, > > I have only two short questions. Is it possible that values for > chi-square and reduced chi-square given in the "Fit results" and the > "Combinatorics" page are inverted within Athena? > In the CSV report for all fits, which of these both columns ("chisqr", > "chinu" ) is chi-square and which is reduced chi-square? > > thanks, > Jens > > > > > ------------------------------ > > Message: 2 > Date: Wed, 2 Sep 2009 09:40:48 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Linear combination fitting reports > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200909020940.48150.bravel(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Wednesday 02 September 2009 04:13:55 am Jens Kruse wrote: > >> Hi, >> >> I have only two short questions. Is it possible that values for >> chi-square and reduced chi-square given in the "Fit results" and the >> "Combinatorics" page are inverted within Athena? >> > > I tried running a combinatorial LCF series just before writing this > email and I think these numbers are reported correctly. If you think > otherwise, you will need to show me an example. > > Of course, the values for both R-factor and reduced chi-square are > rather peculiar in Athena's LC fitting, as explained in the manual: > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/analysis/lcf.html > > > >> In the CSV report for all fits, which of these both columns ("chisqr", >> "chinu" ) is chi-square and which is reduced chi-square? >> > > I don't think these are reported wrongly. As I discuss in the manual, > it is hard to know how to evaluate chi-nu in a XANES fit. I use > epsilon=1 (for want of a better number) and I use the number of points > in the data as the number of independent measurements. There are > typically of the order of 100 points in a XANES scan, so chi-nu tends > to be about 2 orders of magnitude smaller than chi-square, which > itself is very small due to the value of epsilon. > > All of this just underscores the squishiness of the statistical > parameters in this context. Interpreting LCF results requies the use > of prior knowledge and a very conservative interpretation of what > Athena reports. > > B > > > > -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190

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Linear combination fitting reports
by Jens Kruse 02 Sep '09

02 Sep '09

Hi, I have only two short questions. Is it possible that values for chi-square and reduced chi-square given in the "Fit results" and the "Combinatorics" page are inverted within Athena? In the CSV report for all fits, which of these both columns ("chisqr", "chinu" ) is chi-square and which is reduced chi-square? thanks, Jens

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