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

Requesting guidance in understanding results from Athena
by Deepak Varanasi 13 Sep '20

13 Sep '20

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Postdoctoral fellowship in AI - related field
by Anatoly Frenkel 12 Sep '20

12 Sep '20

Please pass this info to anyone interested in this opportunity, particularly, those students who are about to obtain their PhD and looking for postdoctoral fellowships. This one may be suitable for those who plan to use data science approaches for interpreting XANES and EXAFS data and apply them to interdisciplinary research projects. https://www.stonybrook.edu/commcms/iacs/opportunities/fellowships/Postdocto… You are welcome to contact me if you are interested. 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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XAFS short course at BNL: Nov. 18-20, 2020
by Anatoly Frenkel 11 Sep '20

11 Sep '20

Dear mailing list subscribers: Please pass this information along to your group members or others who may be interested in this. As it has done every year since 2005, on* Nov. 18-20, 2020*, Synchrotron Catalysis Consortium (SCC) will run an annual short course on X-ray absorption fine structure techniques and applications. *Date of Event:* November 18-20, 2020 *Official Name of Event: * Short course on X-ray Absorption Fine Structure: Application to Nanomaterials *Description: * Every year Synchrotron Catalysis Consortium, in partnership with NSLS-II, organizes and runs a 3-day short course to those interested in learning about the use of x-ray absorption spectroscopy methods. This year, the course will be offered online from November 18–20, 2020. The course will be useful for those scientists' who already possess basic experience with XANES and EXAFS methods, including experiment and data analysis, and are interested in advanced analysis and modeling methods applicable for nanomaterials research. The course will be run in a flip classroom mode. Participants will study video-presentations of leading experts in XAFS methods and applications in advance of the workshop. The video-lectures will be assembled to follow the workshop agenda. During the workshop, the instructors will divide participants in breakout sections for in-depth problem solving, data analysis and modeling, to best match participants and their research interests. There will be Q&A sessions on the subject of the lectures, and in depth practicums of the EXAFS and XANES analysis software programs. The course will be open to 80 participants, selected based on their application materials. Further info about the course, including the application materials and the deadlines, is available here: https://www.bnl.gov/xafs2020/ Note the application deadline: September 27, 2020. For past XAFS workshops, and information about the SCC-supported beamlines and capabilities, please visit the SCC web sites: https://you.stonybrook.edu/scc2/xafs-workshops/ For any questions, please contact me. 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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Unable to Import Data In Athena
by Angshuman Gupta 04 Sep '20

04 Sep '20

Dear sir, I am new to this mailing list and excuse me if the question had already been asked. I am not able to import data in the Athena software. I tried to import some of the examples data like Fe_lepidocrocite.000 in the Fe standards folder while importing the data I encountered an error (screenshot has been attached along with the log file generated in the terminal). I am using Linux Mint 18.3 Sylvia OS and perl 5, version 22, subversion 1 (v5.22.1). I followed the instruction for installation here " https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… " I will be thankful if you could suggest something to getting rid of this issue. Thank you Angshuman Gupta PhD scholar IIT Bombay

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Co K-edge XAS spectra of Co(OH)2 and CoOOH
by Carlos Triana Estupinan 27 Aug '20

27 Aug '20

Dear mailing list, I am looking for the Co K-edge XAS spectra of Co(OH)2 and CoOOH containing both the XANES and EXAFS regions at room temperature. Thank you in advance. Kind regards, -- *Carlos A. Triana* PHD. - LIC.PHIL. Sciences Physics MSC.*-* BSC. Sciences Physics Postdoctoral research fellow University of Zürich Switzerland TEL: +41 076 814 41 60

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web apps for X-ray data and XAS library
by Matt Newville 14 Aug '20

14 Aug '20

Hi Folks, I was fortunate enough to have a summer student this crazy summer and had them work (from home, of course!) on web applications for X-ray data resources, including absorption calculations for materials. The result is a bit like a web version of Hephaestus and is currently at both https://xraydb.xrayabsorption.org/ and https://millenia.cars.aps.anl.gov/xraydb/ While similar to Hephaestus, there are some differences too. There are pages for absorption and fluorescence lines, absorption length calculations, ion chamber flux calculations, mirror reflectivities, scattering factors, and mono Darwin widths. Many of the calculations will show interactive plots, links to data, and/or a link to a python script to reproduce the calculation. Questions, comments, complaints, or suggestions for making this better are most welcome. We may have missed your favorite Hephaestus feature - is so, please let us know. Also: the X-ray Data Library - a collection of XAS spectra - has moved to https://xaslib.xrayabsorption.org/ <https://xraydb.xrayabsorption.org/> This has also expanded some (well, now with about 270 spectra), and added several features, notably interactive plots. Again, any comments or suggestions for making this better would be most welcome. I will be adding more data to this library, but I also ask that if anyone has data they can and would like to share on this site, please let me know. Thanks for any feedback or suggestions you might have. --Matt

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RE-REGISTRATION Request for SSRL Summer School
by Ritimukta Sarangi 05 Aug '20

05 Aug '20

Hello everyone, This message is going out at *11:23 AM PST on Aug 5, 2020*. Our registration website for the summer school has been overwhelmed by requests and we had to stop registration and fix some of the errors. I request that *if you registered before that time, please go ahead and re-register* for the summer school program. I apologize for the issues and request your continued patience with us in determining the best way to support smooth operations for this unprecedented amount of interest in the school. Thank you, Riti Sarangi p.s -please email me at ritis(a)slac.stanford.edu, if you have any questions.

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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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Jupyter/python question for Larch
by Garret Bland 04 Aug '20

04 Aug '20

Hello! I have a Python/Larch related question. I have been developing some python script via jupyter and incorporating Larch as a module. I was able to read an athena prj file with the following code *import larch as lc* *athena_prj = lc.io.read_athena(prjfilename)* Python stores this object as a 'Group' object with each spectrum being an instance. I would like to go through more processing with all spectra. Example: *for spectrum in athena_prj:* * lc.xafs.find_e0(spectrum.energy, spectrum.mu <http://spectrum.mu>, group = spectrum)* This does not work since the 'Group' object is not iterable. I tried to look up some other built-in functionality with python, but couldn't find an efficient way other than manually typing out each spectrum (athena_prj.spectrum1, athena_prj.spectrum2, .... etc). Is there any built-in functionality in larch that can iterate this 'Group' object? Any help would be appreciated. Thank you for your time! Garret -- Garret Bland PhD Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 201 Pittsburgh, PA, 15213

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Writing a Script for MD Simulations / Scripting Atoms
by David Sprouster 28 Jul '20

28 Jul '20

Dear IFEFFIT Experts, My colleagues and I are working on preparing Python scripts which: 1) run about 20,000 cif files from MD simulations through Atoms, 2) produce feff.inp files, 3) run feff.inp files through Feff (for XANES), 4) average all the XANES spectra. We are having trouble opening the stand alone Atoms program through Python – we can get Athena and Artemis to open, but for some reason Atoms will not. A snipet of our code which includes the file path is attached below. *Code:* ### def openAtoms(): try: subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"]) except: print('Error') openAtoms() ### We have searched the Ifeffit archive for some answers but came up short, and we were wondering if anybody on the list has any suggestions for a potential fix to this problem? Additionally, has anybody prepared a similar series of scripts (in Python) to generate XANES spectra from MD simulations? We note that Marcus Karolewski did discuss something similar in a past post: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html Thanks in advance, Dave -- ---------------------------------------------------------------------------------- David J. Sprouster, Ph.D. Assistant Research Professor Department of Materials Science and Chemical Engineering Stony Brook University 222 Old Engineering Stony Brook, NY 11794 Phone: (631) 294-8983 web: http://stonybrook.edu/emrel ----------------------------------------------------------------------------------

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