March 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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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 25 Mar '17

25 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

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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]

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