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

Athena User Guide—FCFS
by Julie Olmsted Cross 09 Nov '09

09 Nov '09

I have ten copies of the Athena User Guide leftover from the 2009 APS XAFS School. If you want one, send me your mailing address. First come, first served. ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Got Athena data plotted
by abhijeet gaur 27 Oct '09

27 Oct '09

Thanks a lot kicaj, I followed the procedure step by step and I got the data plotted in Excel. Thanks again Kicaj. Abhijeet

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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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Energy Units in phminNN.dat
by Krayzman, Victor 26 Aug '09

26 Aug '09

Who knows what are energy units and energy origin in files phminMM.dat and phaseNN.dat created by FEFF8.2? Are they Rydbergs or atomic units? Thanks. Victor Krayzman

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Athena error reading file
by Christopher Allen 26 Aug '09

26 Aug '09

Hi everyone, I have two scans taken at x19a of the NSLS (attached) recently that won't open in Athena. Scans before and after these two had no problem, but these give the error reading file message. This was true using whatever version of Athena is on their beamline computer and also version 0.8.056. Thank you in advance, Chris ---------------------------- Chris Allen Northeastern University for Renewable Energy Technology 317 Egan Research Center 360 Huntington Avenue Boston, Ma 02115 617-373-5630

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Re: [Ifeffit] Ifeffit Digest, Vol 78, Issue 23
by Liu Lei 25 Aug '09

25 Aug '09

Hello,I will cancel the booking. Best Regards! ifeffit-request(a)millenia.cars.aps.anl.gov 写: > 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: Vanadium pre edge peak contributes to K-space? (Bruce Ravel) > 2. Re: Vanadium pre edge peak contributes to K-space? > (Chris Patridge) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Aug 2009 11:32:41 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Vanadium pre edge peak contributes to K-space? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200908251132.41271.bravel(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > On Tuesday 25 August 2009 11:02:26 am Chris Patridge wrote: >> Hello all, >> >> After calibration, alignment and merging V K edge data, there seems to >> be a large peak in R space below 1 A. From most examples and readings, >> this would seem to be noise since atoms do not reside that close to each >> other. Adding a background addresses this noise but then the number of >> variables becomes too large and meaningless to the first shell R space >> range. I believe the problem lies with the large pre edge feature seen >> with high valence state Vanadium compounds. Any suggestions on how to >> work through this and make realistic EXAFS analysis on these compounds. >> >> Thanks everyone, > > > Didn't Richard Mayes answer this same question from you last month? > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-July/004365.html > > In my experience, Richard's answer was spot on for V K edge data. > > If Richard's good advice didn't help, then you need to be more > explicit about what the problem is, perhaps by posting a small athena > project file that demonstrates the problem. > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > > > ------------------------------ > > Message: 2 > Date: Tue, 25 Aug 2009 11:44:38 -0400 > From: Chris Patridge <patridge(a)buffalo.edu> > Subject: Re: [Ifeffit] Vanadium pre edge peak contributes to K-space? > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <4A9406E6.9070808(a)buffalo.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Bruce Ravel wrote: >> On Tuesday 25 August 2009 11:02:26 am Chris Patridge wrote: >> >>> Hello all, >>> >>> After calibration, alignment and merging V K edge data, there seems to >>> be a large peak in R space below 1 A. From most examples and readings, >>> this would seem to be noise since atoms do not reside that close to each >>> other. Adding a background addresses this noise but then the number of >>> variables becomes too large and meaningless to the first shell R space >>> range. I believe the problem lies with the large pre edge feature seen >>> with high valence state Vanadium compounds. Any suggestions on how to >>> work through this and make realistic EXAFS analysis on these compounds. >>> >>> Thanks everyone, >>> >> >> >> Didn't Richard Mayes answer this same question from you last month? >> >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-July/004365.html >> >> In my experience, Richard's answer was spot on for V K edge data. >> >> If Richard's good advice didn't help, then you need to be more >> explicit about what the problem is, perhaps by posting a small athena >> project file that demonstrates the problem. >> >> B >> >> >> > Yes it is a very similar question. I did make this type of correction > by setting E0 myself. When moving to R space the data shows significant > intensity below 1 A which I thought was noise but it may not be. Are > these low A signals data or noise is my main concern because EXAFS > fitting does not fit all that well which then would point me to my model > as the problem which I think i understand. > > Thank you all for your patience, > > -- > Christopher J. Patridge > Graduate Student > SUNY Buffalo - Dept of Chemistry > 716-645-6800 x 2110 > 315-529-0501 > >

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Vanadium pre edge peak contributes to K-space?
by Chris Patridge 25 Aug '09

25 Aug '09

Hello all, After calibration, alignment and merging V K edge data, there seems to be a large peak in R space below 1 A. From most examples and readings, this would seem to be noise since atoms do not reside that close to each other. Adding a background addresses this noise but then the number of variables becomes too large and meaningless to the first shell R space range. I believe the problem lies with the large pre edge feature seen with high valence state Vanadium compounds. Any suggestions on how to work through this and make realistic EXAFS analysis on these compounds. Thanks everyone, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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a question
by Dr Somaditya Sen 25 Aug '09

25 Aug '09

Hi All I am having problems in comparing the real bond length as obtained from EXAFS data and Reitveld analysis of XRD data of te same sample. The bond lengths as observed from the XAFS data seems to be much smaller that that from XRD. Is there some multiplication factor known in literature to address this issue? S Sen

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R space merged data bitmap
by Chris Patridge 25 Aug '09

25 Aug '09

Sorry I forget to add bitmap for my questions. I will not double post anymore. Thanks again, -- Christopher J. Patridge Graduate Student SUNY Buffalo - Dept of Chemistry 716-645-6800 x 2110 315-529-0501

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