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

Calculating Ce oxidation state at the L3 edge
by Stephanie Laga 16 May '17

16 May '17

Dear all, I have a (hopefully) quick question about calculating oxidation state of CeO2 at the L3 edge. When calculating ox state by taking the ratio of peak areas, is the pre-edge feature for Ce included in this calculation? This point isn't clear to me from looking at various papers. I've attached an image from Bernardi 2015, which shows that the %Ce III calculation doesn't include the fitted pre-edge feature A. I'm not sure why this would not be included? Is this because we only consider 2p > 5d transitions and the pre-edge is 2p > 4f (forbidden) transition? Thanks! Stephanie

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Calculation of NSS and R-factor
by Marine Albertelli 16 May '17

16 May '17

Good afternoon, Could you please tell me what is the difference between the calculation of the R-factor and the NSS ? I found that R-factor is equal to : sum((data - fit)^2)/sum(data^2) and NSS = sum((data - fit)^2)/sum(data^2)*100 But when I compare the R-factor obtained by Athena and the NSS divided by 100 (calculated by myself) I didn't find the same results. Did I make a mistake somewhere. Thank you for your answer. Kind regards Marine Albertelli PhD student IPREM 2 av du Président Pierre Angot 64000 Pau FRANCE --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Cobalamin XANES: experiments and simulations do not match
by Ganesh Subramanian 15 May '17

15 May '17

Dear all, I have been working on simulating for the K-edge XANES spectra of methylcobalamin (MeCbl) and cyanocobalamin (CNCbl). The only change in the two materials is one bond (the upper axial bond in an octahedral coordination at the Cobalt site) from CH3 to CN. The molecule consists of about 180 atoms in total. We, however, use a truncated (50 atom) structure and more recently, an extended (90 atom) structure. But neither of them seem to predict the relative changes in peak positions and edge chemical shifts accurately. As a quick summary: Experimental XANES spectra show: 1. CNCbl has a 1 eV blue-shifted absorption edge as compared to MeCbl. 2. The shoulder peak in CNCbl (about 6-7 eV lower than the main-peak) is much stronger (than MeCbl) and comparable in intensity to the main (strongest) peak. We use Gaussian to identify the optimized structure and then feed it to FEFF 8.4 to simulate for the XANES. When we do the simulations we note - 1. CNCbl has an approx. 0.1-0.2 eV red-shifted absorption edge as compared to MeCbl. 2. The shoulder peak intensity is comparable to the main peak intensity in CNCbl. However, in comparing with MeCbl, the shoulder peak intensity is still lower. Incidentally, we see the exact same problem repeat with hydroxocobalamin OHCbl as we see with CNCbl as well ! (I do not present that here, since I assume the origin of the problem is same). I thought, maybe truncation is affecting the the optimized geometry when we perform DFT and hence increased the cluster size to about 90 atoms but noticed no significant change. (We did this quite sometime back just with MeCbl to actually justify the use of a truncated structure. But now we are not sure where the error is). Now I wonder if I am performing the FEFF accurately and not missing something here. I attach the input feff files for the truncated and the more elongated structures of both MeCbl and CNCbl. I also attach the (ATHENA deglitched, merged and normalized) experimental XAFS for MeCbl and CNCbl. Any help in identifying the issue is greatly appreciated ! (Sorry for the long email). Thanks, Ganesh Subramanian Post Doctoral Research Scholar, Spence Group, Arizona State University

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E0 on linear combination fitting: fit or not?
by Carrillo Sanchez, Pamela 13 May '17

13 May '17

Hi all, I have gone through the mail archives as well as following the instructions of Athena user's manual as well as Scott Calvin's book but still I find myself with the doubt of how correctly "choose E0". I have aligned the data and standards with the merge of reference foils measurements of the metal (Mn). We did not have a reference foil placed while measuring the data so I used the merge of the references scans when the standards were measured and they showed a consistent energy shift. I have set the same E0 for all the data and standard to the same E0, I chose the first peak of the derivative in the data (6MnRh_RED). When I do the LCF analysis without 'fitting E0' , I get a worse fitting than when I choose the fit E0 on Athena as well as different types of components on the fitting. Which one is the best choice for it ? From what I have read I think that without fitting E0 would be the proper one regardless of the "worse fit". Also, I would like to know which fit range would be appropriate for this, I have chosen -20 to +30 eV due to the features of my data and ranges for XANES. Any recommendation. I have attached the files for the project and screenshots of both fittings. Any help is highly appreciated! Pamela

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(no subject)
by Carrillo Sanchez, Pamela 11 May '17

11 May '17

Hi all, I have gone through the mail archives as well as following the instructions of Athena user's manual as well as Scott Calvin's book but still I find myself with the doubt of how correctly "choose E0". I have aligned the data and standards with the merge of reference foils measurements of the metal (Mn). We did not have a reference foil placed while measuring the data so I used the merge of the references scans when the standards were measured and they showed a consistent energy shift. I have set the same E0 for all the data and standard to the same E0, I chose the first peak of the derivative in the data (6MnRh_RED). When I do the LCF analysis without 'fitting E0' , I get a worse fitting than when I choose the fit E0 on Athena as well as different types of components on the fitting. Which one is the best choice for it ? From what I have read I think that without fitting E0 would be the proper one regardless of the "worse fit". Also, I would like to know which fit range would be appropriate for this, I have chosen -20 to +30 eV due to the features of my data and ranges for XANES. Any recommendation. I have attached the files for the project and screenshots of both fittings. Any help is highly appreciated! Pamela

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Save the date: Nov 1-3, 2017, XAFS short course at BNL
by Anatoly Frenkel 09 May '17

09 May '17

Dear Colleagues: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course will continue the annual tradition of gathering a group of scientists, active in the field, to share their expertise with those interested in learning about the use of x-ray spectroscopy methods in their research. *The course will be useful for those scientists who are already familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced analysis and modeling methods*. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis techniques. Course instructors will use examples from their research during presentations. Topics covered will include theory of XANES and EXAFS, direct modeling methods using Molecular Dynamics simulations and Reverse Monte Carlo, multiple data set modeling and multiple-scattering analyses. Other topics will include, but not limited to: chemometrics, bonding dynamics and transformation kinetics. During the data analysis practicum on Nov. 3 the course participants will get an opportunity to work with demonstration examples and/or their research projects with the help of the course instructors. The course will be open to 30 participants, selected based on their application materials. The course web page will appear on BNL web site in near future, with instructions how to apply. For any inquiries please contact me. Best Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Error importing data into Athena
by Bone, Sharon Elizabeth 03 May '17

03 May '17

Hi, I’m running the current version of Athena on a windows 10 machine. It had been working fine, but now I get an error whenever I try to import new data (.dat file from SSRL). The error tells me the program can’t read the file and asks whether I need a plugin. Do I need a plugin? How do I uninstall and reinstall the program? I’m guessing this might be the best fix? Thanks! Sharon

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Need FEFF9 for Z> 95: how to use in Demeter?
by Bone, Sharon Elizabeth 01 May '17

01 May '17

Hello, I have a problem with demeter that I am hoping to get some help with: My understanding is that the current version of demeter does not support versions of FEFF greater than 6. Usually this isn’t a problem for me, but I recently started working with elements with Z > 95 and FEFF6 can’t handle these elements. I recently tried to download an old version of demeter (ixafs through http://cars9.uchicago.edu/ifeffit/Downloads) but the link was no longer valid. Is there a way to access an old version? I’d far prefer to use the new vesion of demeter. Is there any chance that the capability to run higher versions of FEFF will be incorporated soon? Thanks for your help! Best, Sharon

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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 21
by Christopher Thomas Chantler 21 Apr '17

21 Apr '17

[?] I'm just agreeing with Matt's comment. Too fine a spacing does not help you due to typical broadening from imfp or thermal sources [or structural disorder]. And the difference between operation of ifeffit and larch in this context is pretty interesting. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Friday, 21 April 2017 11:01:11 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 170, Issue 21 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: Ifeffit Digest, Vol 170, Issue 19 (Matt Newville) 2. Fwd: Ifeffit Digest, Vol 170, Issue 19 (Matt Newville) 3. Looking for EXAFS data of Ni2+ ion in aqueous solution (Van Vu) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Apr 2017 21:18:39 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19 Message-ID: <CA+7ESbpEWenMLpspnYAXT4j2T1LkjAaYua59XcGebLpteKTyWg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Chris, On Thu, Apr 20, 2017 at 5:02 PM, Christopher Thomas Chantler < chantler(a)unimelb.edu.au> wrote: > Note that in general any and every smoothing operation reduces the > information content of the data and its ability to reveal structure. > Well, maybe. If one has mu(E) measured every 0.01 eV over an 600 eV EXAFS scan to k=12A^-1, one does not really 60,000 independent measures of the structure. Yuji's data wasn't that absurd, but it did have close to 4000 measurements for the full EXAFS spectrum out to k=18^-1. And to be clear, there is not anything wrong with that, it's just a matter of how you decide to treat it. As the plots attached in Yuji's original message and my replies show, the resulting chi(k) definitely has is amplitude suppressed when doing a simple boxcar average of data onto the 0.05 Ang^-1 grid (Athena with Ifeffit). But when using cubic spline interpolation (Larch), the amplitude of the EXAFS oscillations are not noticeably suppressed, though the high frequency noise is also much higher. Applying a Savitzky-Golay filter prior to the cubic spline interpolation did not appreciably suppress the EXAFS oscillations though the high frequency noise was reduced. Very finely-spaced energy data might reveal is at much higher R than we can hope to model with EXAFS. A k-grid of 0.05 Ang^-1 can give frequencies to 31Ang, and so is probably accurate to 16Ang without significant signal loss. That is, out to k=18Ang^-1, you really only need 360 samples, but you'd like these as noise-free as possible. Having 3600 measurements on a grid of 0.005 Ang^-1 might give you data out to 160Ang in principle, but the photo-electron tends to not cooperate. --Matt

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Looking for EXAFS data of Ni2+ ion in aqueous solution
by Van Vu 21 Apr '17

21 Apr '17

Dear everyone, I am looking for XAS data of Ni2+ ion in aqueous solution that contains EXAFS data in the k range of 0-12 (Angstrom-1) or so for an undergraduate student project. I was wondering if anyone would be willing to share the data with me? Many thanks in advance. Best, Van On Fri, Apr 21, 2017 at 5:02 AM, Christopher Thomas Chantler < chantler(a)unimelb.edu.au> wrote: > Note that in general any and every smoothing operation reduces the > information content of the data and its ability to reveal structure. Also, > many of the smoothing algorithms change the data point values at vertices, > so change the data prior to analysis. > > > Hence in general avoid unless you know exactly the physical cause > requiring smoothing. > > > Best wishes > > > ------------------------------------------------------------ > -------------------------- > Christopher Chantler, Professor, FAIP, Fellow American Physical Society > Editor-in-Chief, Radiation Physics and Chemistry > Chair, International IUCr Commission on XAFS > President, International Radiation Physics Society > School of Physics, University of Melbourne > Parkville Victoria 3010 Australia > +61-3-83445437 FAX +61-3-93474783 > chantler(a)unimelb.edu.au > <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> > chantler(a)me.com > <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> > http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html > <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> > http://optics.ph.unimelb.edu.au/~chantler/home.html > <https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> > > ------------------------------ > *From:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of > ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request@millenia. > cars.aps.anl.gov> > *Sent:* Friday, 21 April 2017 3:00:01 AM > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* Ifeffit Digest, Vol 170, Issue 19 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://protect-au.mimecast.com/s/2mpEBkUbb8ExSZ?domain= > millenia.cars.aps.anl.gov > <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: The difference of EXAFS oscillation when using Athena and > when using Larch (Yuji Mahara) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Apr 2017 19:47:20 +0900 > From: "Yuji Mahara" <mahara.yuji(a)e.mbox.nagoya-u.ac.jp> > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using > Athena and when using Larch > Message-ID: <003501d2b9c3$7c75c560$75615020$(a)e.mbox.nagoya-u.ac.jp> > Content-Type: text/plain; charset="utf-8" > > Dear Matt > > > > Thank you for your reply. > > I confirmed that chi (k) becomes smooth by the Savitzky-Goley method by > doing the attached lar file. > > > > I will try on various conditions from now. > > I may also ask if there is something I do not understand. > > Thank you for your help again! > > > > Bests, > > Yuji Mahara > > > > > > From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov > <ifeffit-bounces(a)millenia.cars.aps.anl.gov>] On Behalf Of Matt Newville > Sent: Thursday, April 20, 2017 5:26 AM > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] The difference of EXAFS oscillation when using > Athena and when using Larch > > > > Hi Yuji, > > The attached larch script (a modification of your script but note: not > python, so you may have to add a bunch of '_larch=mylarch' arguments) to > show the effects of smoothing with Savitzky-Golay and of interpolating onto > a "classic XAFS energy grid". You might want to play around with this > different options. It definitely seems that none of these methods are > systematically over-smoothing the data and reducing the amplitudes of the > oscillations -- one more reason to use Larch instead of Ifeffit. But it > also seems like smoothing this data with a Savitzky-Golay fitler is helpful. > > Also attached are plots showing k- and R-space generated from the attached > script. > > > > --Matt > >

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