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

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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