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

Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19
by Christopher Thomas Chantler 21 Apr '17

21 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 06 Apr '17

06 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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