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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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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19
by Christopher Thomas Chantler 20 Apr '17

20 Apr '17

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(a)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 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] 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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The difference of EXAFS oscillation when using Athena and when using Larch
by Yuji Mahara 20 Apr '17

20 Apr '17

Dear All, I am Yuji Mahara at Nagoya University, Japan. I am using Athena in Demeter 0.9.24 package and Larch 0.9.33 on windows 10. At that time, I am worrying about the difference of EXAFS oscillation when using Athena and when using Larch. k3-weighted Pd K-edge EXAFS and Fourier transform EXAFS spectrum for PdO bulk are shown in attached file(PdO.png). When XAFS raw data is read using Athena and EXAFS oscillation is obtained, EXAFS spectrum is smooth and noise is small. On the other hand, using Larch, noise is noticeable in k space. This phenomenon occurred when analyzing other XAFS data as well. I tried to analyze XAFS data by Athena and Larch with the almost same conditions. Does this difference of EXAFS results arise from the difference in autobk's algorithm between Athena and Larch? The analysis conditions are shown below. If someone knows this reason, please let me know. Best regards, Yuji Mahara ****************************************** ■ Yuji Mahara Nagoya University(Japan) D3 Graduate School of Engineering Furo-cho, Chikusa-ku, Nagoya-shi, Aichi, 466-8603, Japan ・Phone : <tel:%2B81-52-789-3192> +81-52-789-3192 ・E-mail : <mailto:mahara.yuji@e.mbox.nagoya-u.ac.jp> mahara.yuji(a)e.mbox.nagoya-u.ac.jp ****************************************** #####Analysis condition of Athena ##### e0 -->[ set e0 to a fraction of the edge step] --> 24355.9037323484 Normalization order: 3 Pre-edge range: from -150 to -60 eV Normalization range: from 150 to 1100 eV Rbkg: 1 k-weight used by spline: 2 Spline clamp: low=None, high=Strong Spline range in k: from 0 to 17 Fourier transform k-range: from 3 to 15, dk=0.5, window=’hanning’ #####Analysis condition of Larch ##### dat.e0 = 24355.9037323484 <-- e0 was estimated by Athena pre_edge(dat.e, dat.mu, group=dat, e0=dat.e0, pre1=-150, pre2=-60, norm1=150, norm2=1100, nnorm=2, _larch=mylarch) autobk(dat.e, dat.mu, group=dat, e0=dat.e0, rbkg=1, nclamp=5, clamp_lo=0, clamp_hi=24, kstep=0.05, kmin=0, kmax=17, kweight=2, win='hanning', _larch=mylarch) xftf(dat.k, dat.chi, group=dat, kmin=3, kmax=15, dk=0.5, window='hanning', kweight=3, _larch=mylarch) #########################

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Silent Oxygen
by Fuxiang Zhang 19 Apr '17

19 Apr '17

Hi, all, I am in studying the EXAFS of perovskite and clearly see the split of the first peak after ion irradiation. It should come from a symmetry change, so I use a tetragonal model (instead the original cubic) which contains two independent O sites. However, after running Atoms and Feff, all paths are contributed by only one O atom and nothing related to another Oxygen atoms (see attached file). As a result it may be difficult to get a good fit of the first split Ta-O peaks. I am not sure if it is true or something wrong. Thank you very much Fuxiang Zhang

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the shortest possible K-range ,
by Al Humaidi, Mahmoud 18 Apr '17

18 Apr '17

Hi , I want to ask please what is the shortest k-range one can use for "Forward Fourier transform" in my projects I used: Spline range k 0.0 - 9.0 k range in Forward Fourier transform 1.0 - 9.0 A^-1 I am trying to reduce the contribution of noise in FT .. the attached project shows nice fit ,,,but high phase shift toward lower R value ,, any recommendation please I will appreciate .. and thank you in advance , best regards Mahmoud AL Humaidi --------------------------------------------------------------------------------- Mahmoud Al Humaidi Department of Physics, University of Siegen Emmy-Noether-Campus Walter-Flex-Str. 3, 57072 Siegen Room : B-015 Tel : +49 (0) 271 740 3727 ---------------------------------------------------------------------------------

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Installation to mac OS/ Hephaestus crash in Perl 6.00
by Acevedo-Esteves, Raul 12 Apr '17

12 Apr '17

I was able to install Demeter on a mac (OS X el capitan 10.11.6). Athena runs well, Hephaestus work intermittently. After a while, it crashes when using the periodic table. · After installation, I have this message in terminal: “Some of the ports you installed have notes: p5.24-libwww-perl has the following notes: As of version 6.00, libwww-perl has been split into multiple packages. If you were using p5.24-libwww-perl for just one or two of its modules before, you may be able to pare down your installation to just those modules now. Other important changes have been made that may affect your code; for details, please see: /opt/local/share/doc/p5.24-libwww-perl/Changes” · The log in Hephaestus displays the following message: 11:31:46: Missing argument in sprintf at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Wx/PeriodicTable.pm line 183. Regards, Raul Acevedo, PhD Post Doctoral Research Associate – ISS beamline NSLS-II, Bldg 743 C08U Brookhaven National Laboratory Upton, NY 11973-5000 631 344 4181<tel:631%20344%204181> racevedo(a)bnl.gov<mailto:racevedo@bnl.gov>

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