November 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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XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: 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 is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced 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 methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). 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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Introduction to Synchrotron Radiation Course Online for Spring 2018
by Carlo Segre 29 Nov '17

29 Nov '17

Hello All: Illinois Tech's PHYS 570 (Introduction to Synchrotron Radiation) Course will be offered in the Spring semester of 2018 starting January 8, 2018. This is a graduate level course suitable for students in all science and engineering disciplines interested in learning more about synchrotron radiation production, instrumentation and experimental techniques. This is a for credit course which has both a live and online section. Lectures will be presented live on Tuesdays and Thursdays and will be posted for the online section within 12 hours through Illinois Institute of Technology's Blackboard system. A short description of the course is below. If you have an interest in this course, please contact me (Carlo Segre <segre(a)iit.edu>) for more details. PHYS 570 - Introduction to Synchrotron Radiation Term: Spring 2018, January 8, 2018 – May 5, 2018 Time: Tuesday & Thursday 13:50-15:05 Location: Live & Internet Instructor: Carlo U. Segre Description: This is a graduate course which introduces students to the production, manipulation and use of synchrotron radiation in research. The course will include visits to, and possibly hands-on experience with, beamlines at the Advanced Photon Source (APS) at Argonne National Laboratory but is not specific to the APS. Students will be expected to give presentations and write a General User Proposal to the APS as their final projects. Graduate students in any science or engineering program are welcome to register as are undergraduates with senior standing and permission of instructor. It is particularly recommended for students wishing to make use of synchrotron radiation in their research. The class meets Tuesdays and Thursdays 17:00-18:15 and the lectures are available online as an Internet section for students not on the IIT campus or outside the United States. Textbook: Elements of Modern X-Ray Physics, 2nd ed., Jen Als-Nielsen and Des McMorrow, (John Wiley & Sons, Ltd. 2011). Topics Covered: • X-rays and their interaction with matter • Sources of x-rays • Refraction and reflection from interfaces • Kinematical Diffraction • Diffraction by perfect crystals • Photoelectric absorption • Resonant scattering • Small angle scattering • Other topics as appropriate Course Organization: The grade will be based equally on homework assignments, student presentations and a draft General User Proposal to the Advanced Photon Source. There will be at least one field trip to the Advanced Photon Source for experiment demonstrations. -- 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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Athena: Data cannot be imported by using plugin PFBL12C
by 平岡　裕治 16 Nov '17

16 Nov '17

Dear all, I tried to import a data of multi-element detector at SPring-8 by using plugin PFBL12C to Athena, but it was not successful. if the number of rows in the file is about 2000[success.dat], it can be successfully imported. But for the data over about 4000 rows[fail.dat], it seems that several data at first of both converted energy and intensity are substituted by 0. column6.png shows intensity of ch6 vs energy_attained and I0.png shows intensity of I0 vs energy_attained. you can see this behavior. As a result, intensity cannot divide by I0, and data cannot be imported. if someone knows approach to solve this, could you teach me. Best regards, Yuji Hiraoka

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current-amp recommendation
by Matthew Marcus 14 Nov '17

14 Nov '17

I've gotten involved with a project in which stabilization of the position of a monochromatic, soft X-ray beam is needed. The offending frequencies seem to be vibration frequencies like 57 and 116Hz. We have in mind to use a thin Au film with a gap in the middle, measuring the drain current from the films, much as people normally use the jaws of slits. Now, I'd like to find a couple of current amplifiers which are small enough so that they can be connected with very short cables to the BNC connectors on the air-side of this detector, and which would have decent frequency response and low noise with inputs of the order of 0.1-1nA. Although this topic is outside the realm of XAFS analysis with IFEFFIT, I figure that people on this group might have some good experience. mam

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Re: [Ifeffit] Consult a few questions about XAS data analysis
by fred.mosselmans＠diamond.ac.uk 14 Nov '17

14 Nov '17

Hi Jun, Two points so Bruce doesn't get two upset. If you included the Athena project you used for the lcf and maybe an excel file of the results you got, then someone could Check what you did, as it is there is almost no way to offer an opinion on that. Bruce gave a course at Dimaond several years ago now, but most of what he shows is relatively as true as it was the day he said it. The videos can be found here. http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html The VLC media player works well with them. Regards Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Consult a few questions about XAS data analysis
by Jun Ge 14 Nov '17

14 Nov '17

Hi Bruce I'm a learner for XAS data analysis because of the need of scientific research. I have been to SLAC in San Francisco three times last year and collected some XAS data of samples and models in Beamline 7-3. This summer, I began to learn how to analyze these XAS data. My professor used to use WinXAS to analyze data. But this time he asked me to learn Athena. He thinks use two different softwares can double check the result. After the data pro-processing, including background remove and data normalization, etc., I save each spectrum in the form .txt. However, *in the same energy range and same file of sample and models, the result of LCF performed by WinXAS and Athena was totally different!* I try to solve this problem for a long time but no progress was made. So I turn to you and Ressler (the author of WinXAS) for help. I guess may be the algorithm is different between your Athena with WinXAS, but I'm not sure. With great experience in XAS data analysis, I think it's easy for you to solve this problem, isn't it? By the way,* I don't know how to fit the Coordination Number in another software called Artemis* in the software package of Demeter. I was told by Artemis that the coordination number can only be a number not alphabet. So I have no idea how to do this (yeah, I'm really a noob orz). And I don't know how to set the parameter more correctly to run a excellent Feff fit. So could you please help me? Finally,* I want to learn XAS data analysis systematically. So could you please recommend me some references like books or papers?* Anyway, thanks a lot for your help and your precious time! Sincerely, Jun Ge

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Re: [Ifeffit] Hephaestus: Absorption Data Source
by fred.mosselmans＠diamond.ac.uk 14 Nov '17

14 Nov '17

Hi Apologies for turning this into a social network, but Robert scanning Krause and Oliver, reminded me of when several decades ago, as a PhD student I typed all the K and L shell values from that paper into a table for Norman Binsted to use in his latest version of Excurve , probably Excurv88. Regards Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Hephaestus: Absorption Data Source
by Daniel Przyrembel 13 Nov '17

13 Nov '17

Dear All This might be a stupid question, but I have not been able to track this down myself: What is the data source of the "core-hole lifetimes" (i.e. the energy widths "gamma(ch)" in eV) of the "Absorption edges" in the "Absorption" panel of Hephaestus? As far as I could see these lifetimes/widths are not given in the 'Elam database'. Other XAS data tools based on the Elam database (like e.g. 'XrayDB') claim to be using values from 'O. Keski-Rahkonen and M. O. Krause, Atomic Data and Nuclear Data Tables 14, pp139-146 (1974) (http://dx.doi.org/10.1016/S0092-640X(74)80020-3)' for this. Because that reference does not give tabulated values but rough data plots only, it is difficult to compare those with the values in Hephaestus. If someone knows the respective data source used in Hephaestus, the answer/information is deeply appreciated! Best regards Daniel

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