April 2017 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 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: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > 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/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > 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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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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