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

Re: [Ifeffit] Ifeffit Digest, Vol 79, Issue 8
by abhijeet gaur 19 Sep '09

19 Sep '09

Hi Abhijeet: The FEFF6L distributed with Ifeffit is only set up to calculate EXAFS. If you want the near edge structure, you will have to use FEFF8 separately. Cheers, Carlo Hello Carlo Sir, Thanks for your quick response. But if you can tell me, from where I can get FEFF8 to calculate the near edge structure, it will be very helpful to me. with regards Abhijeet

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XANES spectrum of cobalt carbide
by Xiaoming Wang 19 Sep '09

19 Sep '09

Dear All, I am doing the analysis of some unknown cobalt-containing samples, and I suspect that there might be cobalt carbide there. Thus I am wondering if anybody has a cobalt K edge XANES spectrum of cobalt carbide to share. Your help will be greatly appreciated! Many thanks! Xiaoming Wang Yale University

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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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Re: [Ifeffit] Ifeffit Digest, Vol 78, Issue 27
by Kevin McPeak 31 Aug '09

31 Aug '09

Andreas, Thanks for your input. We did you use a Zn foil reference and I had aligned the scans in Athena using the auto align feature (to the smoothed derivative). But do to your and Carlo Segre's suggestions I re-checked the alignment, this time zooming very closely. I noticed that a few of the reference scans were +/-0.1 eV misaligned from the reference standard. After the re-alignment the IND value now reaches a minimum at 2 components. Thanks so much for the suggestion! You really can't be too careful with the alignment. Kevin On Fri, Aug 28, 2009 at 1:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: Determining the correct number of components from PCA > (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Aug 2009 23:12:12 +0200 > From: "Voegelin, Andreas" <Andreas.Voegelin(a)eawag.ch> > Subject: Re: [Ifeffit] Determining the correct number of components > from PCA > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <9B57B672CD2140498D728E4524354F4264D5BF(a)EA-MAIL.eawag.wroot.emp-eaw.ch> > > Content-Type: text/plain; charset="us-ascii" > > Hi Kevin > > Maybe the 3rd component is not due to noise but accounts for very small > shifts in energy calibration between scans (considering that the > reconstructed white-line is shifted to higher energies in the > 2-component reconstruction). Do you have a reference foil measured with > each scan to exactly align the spectra or some other way to check for > small shifts in energy calibration? > > Best regards, > > Andreas > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Kevin > McPeak > Sent: Donnerstag, 27. August 2009 07:23 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Determining the correct number of components from PCA > > Hi all, > > I have a question about the "best" method to use to decide the correct > number of components in a system based on a PCA. Myself and a > collaborator took in-situ XANES scans of the formation of ZnO in > aqueous solution. We have a series of scans from this experiment and I > have done a PCA on them using SIXPack. After doing the PCA I unchecked > the components until I could no longer visually reconstruct the series > of scans accurately (by visual determination). Using this visual > method I only need 2 components. But if I go by the minimum of the IND > function (what the SIXPack user guide recommends) I should use three > components. > > I have posted the sample/reconstruction plots for 2 and 3 component > reconstructions here (the scan I chose to reconstruct is > representative of the data series): > > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_2comp. > html > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_3comp. > html > > The main difference between the two plots is that the 3 component > reconstruction fits the edge region better. Zoom in (hold down the > right mouse button) and you'll see what I'm talking about. That said I > really have my doubts about 3 components being necessary, the visual > differences are so slight that I can't help but think that these > differences are just part of the noise. As for 2 or 3 components being > physically possible, both are feasible give the chemistry involved. > > SIXPack does not provide IE or F test, so I plotted the IND results > vs. number of components for all the reactions. Except for the lowest > concentration the IND value reached a minimum at 3 components for all > the reactions. You can see the plot of IND value vs. number of > components here: > > http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_ind_results.html > > The IND minimum is rather broad. Are there other techniques that I > should be using to determine the number of components from the PCA? I > look forward to your feedback. > > Kevin McPeak > kmm333(a)drexel.edu > -- > PhD Candidate > Chemical Engineering > Drexel University > > P.S If you use Firefox or Safari you can zoom in on these plots by > holding down the right mouse button and making a box. Release the > right mouse button to zoom in on that box. Press the left arrow button > to the left of the plot to un-zoom. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 78, Issue 27 > *************************************** >

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Determining the correct number of components from PCA
by Kevin McPeak 27 Aug '09

27 Aug '09

Hi all, I have a question about the "best" method to use to decide the correct number of components in a system based on a PCA. Myself and a collaborator took in-situ XANES scans of the formation of ZnO in aqueous solution. We have a series of scans from this experiment and I have done a PCA on them using SIXPack. After doing the PCA I unchecked the components until I could no longer visually reconstruct the series of scans accurately (by visual determination). Using this visual method I only need 2 components. But if I go by the minimum of the IND function (what the SIXPack user guide recommends) I should use three components. I have posted the sample/reconstruction plots for 2 and 3 component reconstructions here (the scan I chose to reconstruct is representative of the data series): http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_2comp.html http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_3comp.html The main difference between the two plots is that the 3 component reconstruction fits the edge region better. Zoom in (hold down the right mouse button) and you'll see what I'm talking about. That said I really have my doubts about 3 components being necessary, the visual differences are so slight that I can't help but think that these differences are just part of the noise. As for 2 or 3 components being physically possible, both are feasible give the chemistry involved. SIXPack does not provide IE or F test, so I plotted the IND results vs. number of components for all the reactions. Except for the lowest concentration the IND value reached a minimum at 3 components for all the reactions. You can see the plot of IND value vs. number of components here: http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_ind_results.html The IND minimum is rather broad. Are there other techniques that I should be using to determine the number of components from the PCA? I look forward to your feedback. Kevin McPeak kmm333(a)drexel.edu -- PhD Candidate Chemical Engineering Drexel University P.S If you use Firefox or Safari you can zoom in on these plots by holding down the right mouse button and making a box. Release the right mouse button to zoom in on that box. Press the left arrow button to the left of the plot to un-zoom.

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