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

(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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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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Information content from Athena for Hamilton test?
by Will Bennett 11 Apr '17

11 Apr '17

Hi everyone, Just a quick question regarding the "Information Content" output in Athena's LCF window. I've recently been playing around with using the Hamilton test (as outlined in Scott Calvin's book "XAFS for Everyone") to interrogate my combinatorics results. As many of you will know, this requires an estimate of the number of independent measurements in the data, in order to determine the degrees of freedom and subsequently the "a" value for computing the Lower Incomplete Beta Function. Would Athena's value for "Information Content" be appropriate to use as an estimate of the number of independent measurements in this case? How is this value of "Information Content" determined in Athena? Thanks in advance. Will

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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 7
by Christopher Thomas Chantler 10 Apr '17

10 Apr '17

You really need to know the number of actual data points, which must come from the actual data. You should also know the experimental uncertainties of each point. Most standard procedures map the actual data to a uniform grid, sometimes with smoothing of the original data. Then the information content is lost. We are doing final testing on some general routines to address this and will make them available soon. -------------------------------------------------------------------------------------- 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: Tuesday, 11 April 2017 3:00:02 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 170, Issue 7 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. Information content from Athena for Hamilton test? (Will Bennett) 2. Re: Information content from Athena for Hamilton test? (Wayne Lukens) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Apr 2017 13:59:36 +1000 From: Will Bennett <w.bennett(a)griffith.edu.au> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Information content from Athena for Hamilton test? Message-ID: <CAA5p-7P__WKyB6Hzf4bUkd6=+mYEEvGc967p+3hdcsqAvY8ENw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi everyone, Just a quick question regarding the "Information Content" output in Athena's LCF window. I've recently been playing around with using the Hamilton test (as outlined in Scott Calvin's book "XAFS for Everyone") to interrogate my combinatorics results. As many of you will know, this requires an estimate of the number of independent measurements in the data, in order to determine the degrees of freedom and subsequently the "a" value for computing the Lower Incomplete Beta Function. Would Athena's value for "Information Content" be appropriate to use as an estimate of the number of independent measurements in this case? How is this value of "Information Content" determined in Athena? Thanks in advance. Will

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SSRL EXAFS Summer School
by Ritimukta Sarangi 10 Apr '17

10 Apr '17

Hello folks, This is a reminder that today is the last day to apply for the summer school in April. I encourage you to visit the site at: http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2017/index.html>. Best Wishes, -Riti Sarangi

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Larch 0.9.33
by Matt Newville 05 Apr '17

05 Apr '17

Hi Folks, We've released and uploaded Larch 0.9.33. This have been many small fixes and improvements over the past year or so, including significant progress on handling X-ray diffraction data from X-ray micro-probes. There have also been improvements in Python 3 support,so that almost everything now works in both Python 2.7 and 3.6. The "server mode" for Athena and Artemis now works on all platforms and I strongly encourage everyone to use this over the ifeffit back end. Progress has been made on the xyfit app, a peak fitting GUI. It's not complete, but any feedback on functionality or usability at this point would be greatly appreciated. To install, please see http://cars.uchicago.edu/xraylarch/installation.html --Matt Newville

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Conflicting FEFF calculation
by Ashis Biswas 04 Apr '17

04 Apr '17

Dear All, I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter. I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated. With regards, Ashis -- Dr. Ashis Biswas Alexander von Humboldt Postdoctoral Fellow Environmental Geochemistry Group University of Bayreuth Room: 211, Geo III Universitätsstraße 30, 95447 Bayreuth, Germany Ph. No.: +49 921 553991; Fax:+49 921 552334

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number of independent points
by dcnguyen 31 Mar '17

31 Mar '17

Dear Seniors, I have an issue of a discrepancy between values of independent points calculated by Demeter 0.9.25, on Windows 7, shown on the path page and the one presented on the log file after a fit to data. For an example, I use the file named FeS2_final.fpj that you have in your computer, and choose an R-range 1.2-4.2 A, and a k-range 3.00-14.80. Then the N value is calculated by Artemis and shown as 22.54 after clicking "shown Nidp" from the "Data" tab on the path page. The value is consistent with the formula N=(2/pi)*delta_K*delta_R. However, after I click the "Fit" button and look at the Log file, the Nidp is shown as 22.0312500. My question is what causes this discrepancy. When publishing data, which number shoud be reported? Thank you. Bokky Duc-Chau Nguyen IoP, Academia Sinica, Taiwan

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APS/IIT XAFS Summer School - Final announcement
by Carlo Segre 27 Mar '17

27 Mar '17

Hello All: The APS/IIT XAFS Summer School will be held from July 9-13, 2017 in Chicago Please see the attached flyer for details. We only have 10 slots left so if you are interested, please send your application to Grant Bunker <bunker(a)iit.edu> soon. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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Multiple data set fit limit
by Victor Streltsov 24 Mar '17

24 Mar '17

Hello Bruce, The Linux latest version of Artemis limits multiple data set fit to 2 data sets. The input takes any number of data sets but 2 sets is used in the fit only. I've tried latest available windows version it uses more than 2 in fit (e.g. I used 3). Thanks, Victor Streltsov

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Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 20
by Abhinav Prabhakar 23 Mar '17

23 Mar '17

Hello Robert, Thanks for your help. We do not have access to ICSD at the moment, but should get it soon. I can't see the pdf that you attached. Could you send it again? Thank you very much. Regards, Abhinav On Tue, Mar 21, 2017 at 3:02 AM, <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: Ifeffit Digest, Vol 169, Issue 9 (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Mar 2017 12:02:41 -0700 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9 > Message-ID: > <CA+FiM0HUOwyvK-=pU7Xa0UC-U=PKqeHYyu2gZ-VQgfYsxQt+7Q@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Abhinav, > > As I mentioned previously, it is often helpful to check a database (i.e. > the ICSD) for a standardised form of the crystal structure. > As a courtesy, I have done that for you for this structure and attached a > pdf. You would need to enter the structural > information manually in ATOMS rather than by importing a cif file. > > Looking at the notes, the transformation from B11b to Cc is not so > straightforward. > > You should check with your institution to see if they have access to this > (ICSD) resource. > > regards, > Robert > > > On Wed, Mar 15, 2017 at 9:05 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 03/14/2017 06:15 AM, Abhinav Prabhakar wrote: > > > >> Attached is the CIF file in question. The crystal is Tobermorite 14A, > >> taken from COD website. > >> > >> > > Abhinav, > > > > I don't understand the contents of the CIF file in the context of the > copy > > of the International Tables that I have in front of me. The list of > > equivalent positions given in the CIF file just doesn't seem to be right > > for space group 9. > > > > The CIF file is clearly using the C axis as the unique axis since the z > > coordinate is the negated coordinate. But the list of positions does not > > correspond to any of the three cell choices. > > > > While this could be a problem in Artemis, I am inclined to think that the > > authors of the paper cited in the CIF file made some kind of non-standard > > choice for the setting of their crystal. > > > > As I said before, Artemis does what the International Tables tell it to > > do. If the author of a crystallography paper makes some non-standard > > choice, Artemis won't know how to deal with it. > > > > B > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 743, Room 114 > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > >

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Re: [Ifeffit] Strange EXAFS oscillations, never seen before
by Rana, Jatinkumar Kantilal 22 Mar '17

22 Mar '17

Dear Carlo and Lorenzo, Many thanks for sharing your feedback. I agree, the only option is to remeasure the system. Best regards Jatin ________________________________________ 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: Monday, March 20, 2017 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 169, 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: Strange EXAFS oscillations, never seen before (Carlo Segre) ---------------------------------------------------------------------- Message: 1 Date: Sun, 19 Mar 2017 12:00:14 -0500 (CDT) From: Carlo Segre <segre(a)iit.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Strange EXAFS oscillations, never seen before Message-ID: <alpine.DEB.2.20.1703191154500.17810(a)hydride.segre.home> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Rana: I agree. The data is basically unusable as it is. You clearly have issues in the background (look at the oscillations in the pre-edge area) and the three data sets are different from each other which is another clue. It looks like you have transmission data with a very samll edge jump (0.09) which is sort of marginal for XANES much less EXAFS at 5BM). In addition, your sample probably has pinholes and is not uniform. You should be taking this data in fluorescence with such a small amount of sample unless you have an absolutely uniform sample. Carlo On Sun, 19 Mar 2017, Lorenzo Stievano wrote: > > Dear Rana, > > you seem to have real EXAFS oscillations up to k=9, then there are surely > some artefacts in your spectra, which are unusable from that point on. In > fact, if you limit your spline range to 9 in Athena, you get oscillations > that look real and seem to have some sense. > > These artefacts are probably of experimental origin (shit happens), I do not > think you can do much about them,with the exception of remesuring your > spectra. > > Yours sincerely, > > Lorenzo > > Le 19/03/2017 ? 17:13, Rana, Jatinkumar Kantilal a ?crit?: > > Dear all, > I observed strange EXAFS oscillations in my data up to about 1000 eV > beyond the K-edge, I would like to share this situation with you and > hope to get some feedback. Please find attached the athena project > file of the data. > > The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS > sample was prepared by taking the material equal to 2 absorption > lengths at the Cu K-edge, mixing it with graphite and pressing into > the pellet, which was sealed between the Kapton tape. > > The measurements were carried out at the Cu K-edge of the material in > the transmission mode at the beamline 5BM of APS. > > Here are my concerns: > > (1) In the athena project file, the data files "Cu_S1_scan003" > and?"Cu_S1_scan004" are the two scans of the same sample measured one > after the other. As can be seen, there are strong oscillations even at > 1000 eV from the Cu K-edge, which is strange because generally EXAFS > oscillations "wash out" as we go higher in energy. Nevertheless, the > two scans appear reproducible. > > (2) Once I removed the sample and remeasured it after some time > (because?I did not believe the previous 2 scans), I found completely > different data (i.e., data "Cu_S1_scan005").? > > (3) The Cu reference foil measured simultaneously along with the > sample for each of these scans appear quite reproducible. > > I am puzzled as to what can contribute to such effects. I have never > seen such effects before.? > > We can rule out the possibility of beam damage, since I have measured > up to 3 scans (25 min per scan) and they all look reproducible. > However, once I remove the sample and remeasure it after some time to > reproduce the previous 3 scans, the scan looks totally different. > > Also, we can rule out the chemical instability of the material, since > the material is quite air-stable. > > I have measured a series of samples with this composition and all of > them have the same effect.? > > I would very much appreciate your feedback! > > Best regards > Jatin > > > > ____________________________________________________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende > Dr. Jutta Koch-Unterseher > Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas > Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > -- > [IMAGE] > > Lorenzo Stievano > Professeur > Tel : +33(0) 4 67 14 33 46 > aime.icgm.fr/spip.php?article102 > > [IMAGE] > > Institut Charles Gerhardt Montpellier > UMR 5253 CNRS-UM-ENSCM > Universit? de Montpellier, Place E. Bataillon, B?t 15, cc 1502 > 34095 Montpellier cedex 5 - France > > > -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ End of Ifeffit Digest, Vol 169, Issue 19 **************************************** ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Strange EXAFS oscillations, never seen before
by Rana, Jatinkumar Kantilal 19 Mar '17

19 Mar '17

Dear all, I observed strange EXAFS oscillations in my data up to about 1000 eV beyond the K-edge, I would like to share this situation with you and hope to get some feedback. Please find attached the athena project file of the data. The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS sample was prepared by taking the material equal to 2 absorption lengths at the Cu K-edge, mixing it with graphite and pressing into the pellet, which was sealed between the Kapton tape. The measurements were carried out at the Cu K-edge of the material in the transmission mode at the beamline 5BM of APS. Here are my concerns: (1) In the athena project file, the data files "Cu_S1_scan003" and "Cu_S1_scan004" are the two scans of the same sample measured one after the other. As can be seen, there are strong oscillations even at 1000 eV from the Cu K-edge, which is strange because generally EXAFS oscillations "wash out" as we go higher in energy. Nevertheless, the two scans appear reproducible. (2) Once I removed the sample and remeasured it after some time (because I did not believe the previous 2 scans), I found completely different data (i.e., data "Cu_S1_scan005"). (3) The Cu reference foil measured simultaneously along with the sample for each of these scans appear quite reproducible. I am puzzled as to what can contribute to such effects. I have never seen such effects before. We can rule out the possibility of beam damage, since I have measured up to 3 scans (25 min per scan) and they all look reproducible. However, once I remove the sample and remeasure it after some time to reproduce the previous 3 scans, the scan looks totally different. Also, we can rule out the chemical instability of the material, since the material is quite air-stable. I have measured a series of samples with this composition and all of them have the same effect. I would very much appreciate your feedback! Best regards Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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[Question about XANES] Hello I'm a graduate student in Korea
by 김도엽(신소재공학과) 17 Mar '17

17 Mar '17

Hello I'm a graduate student at POSTECH in Korea. Currently, I obtained XANES spectra over a narrow energy range and looked through the Athena manual But, I'm kind of lost as to how exactly I'm supposed to normalize raw data which only has XANES spectra. It would be very generous of you if you help me figure this out Thank you Best wishes Doyoub Kim

3 2

question mark in xanes plot athena
by Anna Smith 16 Mar '17

16 Mar '17

Hello, I am struggling with the normalization in Athena. When I plot u(E) and pre-ede and normalization ranges, I get a question mark on the plot instead of the normal cross (see below). Can you please help me solve this problem? Thanks in advance [cid:image001.jpg@01D29E50.91B6E320]

2 2

Data export and coordination number
by Abhinav Prabhakar 13 Mar '17

13 Mar '17

Hello, As a new user, I have some questions related to the use of Athena and Artemis: i) Is it possible to extract the normalized/background corrected data from Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' parameters (Artemis allows only numerical values for N)? Thank you. Regards, Abhinav Prabhakar (Mr.)

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