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

EXAFS-50 symposium and short course, Oct. 30-Nov. 3 at BNL
by Anatoly Frenkel 08 Sep '23

08 Sep '23

Dear subscribers: Sharing here my Linkedin post: I am excited to share that Brookhaven National Laboratory will be hosting the Symposium ("EXAFS-50") that will mark the 50th anniversary of Stern-Sayers-Lytle team's introduction of the Extended X-ray Absorption Fine Structure (EXAFS) technique in early 1970s. The Symposium will open the week of events, hosted by Brookhaven National Laboratory, that will include the talks of the experts in the field on the past, present and future of the EXAFS technique on Oct. 30 and 31, and culminate by the three-day long short course on advanced data analysis methods of EXAFS, from Nov. 1 to 3. Both events will be in-person. The web sites below have all the information for registration for the symposium (registration begins on Aug. 21) and for application/registration for the short course (application deadline is Aug. 31). Although the Symposium and the Short course are organized and run as separate events, attending both of them will be ideal for graduate students and postdocs. No registration fee is charged for attending these events but registration is required. EXAFS-50: https://www.bnl.gov/exafs-50/ XAFS short course: https://www.bnl.gov/xafscourse/ ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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CatMASS - XAS "Catalyst" Sample Mass Calculator
by Hoffman, Adam S 07 Sep '23

07 Sep '23

Hi All, We would like to announce the release of CatMASS - a XAS (and X-ray scattering) sample mass calculator for complex sample compositions most commonly found in catalysis science. This software builds off of codes found in Hephaestus and XAFSMass allowing for more complex sample descriptors (multiple metals/supported organometallics) and allows for the inclusion of diluents. The absorption can be visualized in E- or k-space highlighting potentially competing edges in the sample that may limit the range of your EXAFS data collection. The documentation can be found in the recent publication: https://onlinelibrary.wiley.com/iucr/doi/10.1107/S160057752300615X To download the executable file (windows only) please see the link here: https://web.slac.stanford.edu/coaccess/resources/software To download the python-based version or collaborate on the GitHub project please go to: https://github.com/ahoffm02/catMass If you have any questions please reach out to Jorge Perez-Aguilar (jperezag(a)slac.stanford.edu<mailto:jperezag@slac.stanford.edu>) or myself, Adam Hoffman (ashoff(a)slac.stanford.edu<mailto:ashoff@slac.stanford.edu>). Cheers, Adam Hoffman, Jorge Perez-Aguilar, and the Co-ACCESS team

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Shift in Eo when fitting PtO2 and similar samples
by Zi Qi Chen 07 Sep '23

07 Sep '23

Dear all, I am looking at EXAFS of PtO2 powders and Pt particles supported on TiO2. I used a beta-PtO2 crystal structure data for the PtO2 EXAFS and after the first shell fit, I observed a large shift in Eo (delta Eo of ~14 eV) in my fit parameters. When I tried to fit the Pt foil to obtain the So2, the energy shift also seemed high (delta Eo of ~7 eV). I am wondering if there could be a problem in the selection of Eo prior to EXAFS analysis? I left the Eo as the energy at the first peak of first derivative (ifeffit default). All of the data were also aligned using the reference foil in Athena before looking at EXAFS. I am wondering what would have caused this shift? Any help is appreciated, thank you. Best regards, Yanny

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Shift in Eo when fitting PtO2 and similar samples
by Clément Laskar 23 Aug '23

23 Aug '23

Dear Yanny Chen, You can find recorded and fitted EXAFS and HR-EXAFS spectra of PtO2 in our following paper: Laskar, C., Bazarkina, E. F., Kokh, M. A., Hazemann, J. L., Foulon, S., Leynaud, O., ... & Pokrovski, G. S. (2022). Exploring Platinum Speciation with X-ray Absorption Spectroscopy under High-Energy Resolution Fluorescence Detection Mode. *Minerals*, *12*(12), 1602. The spectra can be directly downloaded at the following link on the sshade database: https://www.sshade.eu/data/experiment/EXPERIMENT_GP_20181107_001 https://www.sshade.eu/data/experiment/EXPERIMENT_CL_20210211_001 Maybe it could help you to deal with your fitting problem to compare your spectra and your fit with ours, Regards, Clément LASKAR -------------------------------------------------------- Dear all, I am looking at EXAFS of PtO2 powders and Pt particles supported on TiO2. I used a beta-PtO2 crystal structure data for the PtO2 EXAFS and after the first shell fit, I observed a large shift in Eo (delta Eo of ~14 eV) in my fit parameters. When I tried to fit the Pt foil to obtain the So2, the energy shift also seemed high (delta Eo of ~7 eV). I am wondering if there could be a problem in the selection of Eo prior to EXAFS analysis? I left the Eo as the energy at the first peak of first derivative (ifeffit default). All of the data were also aligned using the reference foil in Athena before looking at EXAFS. I am wondering what would have caused this shift? Any help is appreciated, thank you. Best regards, Yanny

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Postdoc position in XAS and catalysis is open at BNL
by Stavitski, Eli 21 Aug '23

21 Aug '23

Postdoctoral Research Associate Catalysis and X-ray Spectroscopy https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an… Postdoctoral Research Associate Catalysis and X-ray Spectroscopy Description at Brookhaven National Laboratory<https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an…> Learn more about applying for Postdoctoral Research Associate Catalysis and X-ray Spectroscopy at Brookhaven National Laboratory jobs.bnl.gov Job ID 3913Date posted 08/11/2023 Brookhaven National Laboratory (www.bnl.gov) delivers discovery science and transformative technology to power and secure the nation’s future. Brookhaven Lab is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and more than 70 years of pioneering research. The Lab is primarily supported by the U.S. Department of Energy’s (DOE) Office of Science. Brookhaven Science Associates (BSA) operates and manages the Laboratory for DOE. BSA is a partnership between Battelle and The Research Foundation for the State University of New York on behalf of Stony Brook University. Organizational Overview The Hard X-ray Scattering & Spectroscopy (HXSS) program at BNL’s National Synchrotron Light Source II (NSLS-II) offers world-class capabilities for studying complex and heterogeneous materials under in situ and operando conditions. The program provides advanced spectroscopy, diffraction, and imaging x-ray tools, supported by computational resources for high-throughput analysis and modeling. One of the leading research directions in the HXSS science program is heterogeneous catalysis with emphasis on in situ and operando characterization. The Inner Shell Spectroscopy (ISS) beamline is a frontier X-ray spectroscopy instrument allowing high throughput and high energy resolution studies of a variety of catalysts. ISS is aimed at establishing structure-function relationships under relevant reaction conditions. Position Description NSLS-II is seeking exceptional candidates for a research associate position in the Hard X-ray Scattering and Spectroscopy program. The successful candidate will work collaboratively with the ISS team and supporting technical, engineering and controls staff. They will be involved in developing, commissioning, and testing custom sample environments for catalysis experiments, including high pressure gas and integration of the high energy resolution spectrometers in the ISS operando catalysis research infrastructure. They will also be involved in the support of the users at the beamline, including industrial partners. Leveraging the technical developments, the successful candidate will conduct mechanistic studies of catalytic carbon dioxide hydrogenation at high pressures in collaboration with ISS scientists. Essential Duties and Responsibilities: * Develop, commission, and test new catalysis infrastructure at the ISS beamline. * Take part in the logistic work required for successful beamline user operation * Participate in experiment planning, execution, translation of results into new scientific knowledge. * Disseminate scientific results as manuscripts, conference presentations, progress reports etc. * Develop and maintain safe practices and working conditions. Position Requirements * A PhD in chemistry, chemical engineering, or materials science * Understanding of heterogeneous catalytic reaction mechanisms, demonstrated by a publication record * Knowledge of in-situ/operando characterization applied to heterogeneous catalysis, relevant instrumentation and data analysis methods * Experience with synchrotron X-ray characterization techniques * Excellent written and oral communication and presentation skills * Demonstrated organizational and planning skills and methodical record-keeping * Ability to work in a collaborative team environment Preferred Knowledge, Skills, and Abilities: * Demonstrated record of applying X-ray absorption spectroscopy to solve problems in heterogenous catalysis * Knowledge of X-ray absorption spectroscopy data modelling including advanced quantum methods * Expertise with sample environment development and applications * Proficiency in programming using Python or equivalent languages OTHER INFORMATION: * BNL policy requires that after obtaining their PhD, eligible candidates for research associate appointments may not exceed a combined total of 5 years of relevant work experience as a post-doc and/or in an R&D position, excluding time associated with family planning, military service, illness or other life-changing events. At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes, but is not limited to: * Medical, Dental, and Vision Care Plans * Flexible Spending Accounts * Paid Time-off and Leave Programs (vacation, holidays, sick leave, paid parental leave) * 401(k) Plan * Flexible Work Arrangements * Tuition Assistance, Training and Professional Development Programs * Employee Fitness/Wellness & Recreation: Gym/Basketball Courts, Weight Room, Fitness Classes, Indoor Pool, Tennis Courts, Sports Clubs/Activities (Basketball, Table Tennis Pong, Softball, Tennis) Brookhaven National Laboratory and the Energy and Photon Sciences Directorate are committed to your success. We offer a supportive work environment and the resources necessary for you to succeed. Brookhaven National Laboratory (BNL) is an equal opportunity employer that values inclusion and diversity at our Lab. We are committed to ensuring that all qualified applicants receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, status as a veteran, disability or any other federal, state or local protected class. BNL takes affirmative action in support of its policy and to advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities. We ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. *VEVRAA Federal Contractor Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1A. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at: https://www.directives.doe.gov/directives-documents/400-series/0486.1-BOrde…<https://www.directives.doe.gov/directives-documents/400-series/0486.1-BOrde…> [cid:7661b08b-12f2-48e3-8920-20aae481d8b3] Eli Stavitski Sr. Scientist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist. Phone: 631-344-8641 Email: istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 [NSLS-II ISS]<https://www.bnl.gov/nsls2/beamlines/beamline.php?r=8-ID>[Title: LinkedIn - Description: image of LinkedIn icon]<https://www.linkedin.com/in/eli-stavitski-a033a713/>[Google, scholar Icon in SuperTiny]<https://scholar.google.com/citations?user=cVxErOsAAAAJ&hl=en>

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sulfur XAS for Li2SO3
by Enyuan Hu 20 Aug '23

20 Aug '23

Hi all, I am wondering if anyone has sulfur XAS for Li2SO3. Data/help is much appreciated and relevant reference will be cited. Thank you. Enyuan

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Larch and calculation of theoretical EXAFS via cif -files part 2
by Mangold, Stefan (IPS) 14 Aug '23

14 Aug '23

Dear all, i have another set of cif files, which also don't work on larch. They work with Artemis, except that they hit the 500 atoms limit per cluster. This won't be a problem in larch, because of the option to exclude the H-atoms. One problem seems to occur on the line _chemical_formula_moiety ; 2(C18 H36 K1 N2 O6 1+),Bi2 2- ; which I rewrote to _chemical_formula_moiety '2(C18 H36 K1 N2 O6 1+),Bi2 2-' but still I got the message Error reading CIF File: /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif Traceback (most recent calls last): File "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/wxlib/cif_browser.py", line 618, in onImportCIF cif_data = parse_cif_file(path) File "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/xrd/amcsd.py", line 142, in parse_cif_file raise ValueError(f'Cannot read symmetries from file {filename:s}') ValueError: Cannot read symmetries from file /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif Anybody an idea, I attached the unchanged file (Bi2-crypt-222.cif) and the edited file (Bi2-crypt-222_e.cif). Any idea what’s wrong? best regards Stefan

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Larch and calculation of theoretical EXAFS via cif -files
by Mangold, Stefan (IPS) 10 Aug '23

10 Aug '23

Dear all, i have some cif files, which doesn’t work on larch. One example is KBi2, which works well on Artmenis with feff6. The same file (and also the cifs found in the database) won't work on larch (not with feff 6 nor feff8). There is no error message displayed -> just, that feff is started. ######## ### # Run Feff in folder: /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13 ### ####### no result even after hours. Any ideas? Best regards Stefan

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request for comments on XDI and NeXuS data formatting
by Matt Newville 08 Aug '23

08 Aug '23

Hi Folks, As some of you are aware, there is a Q2XAFS meeting in a few weeks. I will be presenting some work on using NeXuS and HDF5 to store and distribute XAS data. This builds on and closely follows the XDI format from Bruce Ravel. While XDI is a great way to represent a single XAS spectrum, it is not able to contain multiple spectra. It also is not very specific about how to deal with data files with a large number (say, > 20) columns as might be found coming from many beamlines with multi-element detectors. I think that many of us are starting to see the need to regularly provide "raw" or "nearly raw" data as supplementary data for published articles or as part of datasets made available under FAIR data principles. While XDI could be one way to do that, I think it is also reasonable to reconsider formats other than plaintext files holding one spectrum. As I am preparing to present this, I've put together something like a blog post on a proof-of-concept for a NeXuS file format based on XDI at https://millenia.cars.aps.anl.gov/nxxas/. There are a few example data files using the proposed layout at https://millenia.cars.aps.anl.gov/nxxas/nexus_xas.html. There is also a Pull Request in with the NeXuS developers for this. If you are interested and have time over the next week or two, please read the pages above and let me know your thoughts on this. I know that not everyone is interested in this, but I also know that some who might be interested are not able to attend Q2XAFS. I think the discussion on this topic should be as wide as possible, which is why I am posting this here and before the meeting. Thanks, --Matt Newville <newville at cars.uchicago.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 3
by laavakyan 05 Aug '23

05 Aug '23

Dear Daria, thank you very much for your reply, supplied reference and hint about data processing Best regards, Leon On 8/4/23 09:32, 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 246, Issue 1 (Daria Boglaienko) > 2. Re: EasyXAFS - any experience with? (laavakyan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Aug 2023 17:18:35 +0000 > From: Daria Boglaienko<dbogl003(a)fiu.edu> > To:"ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1 > Message-ID: > <DM6PR05MB60587A50DD443C31FFD2EAF08B08A(a)DM6PR05MB6058.namprd05.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hello Leon, > > I frequently use the easyXAFS instruments in Pacific Northwest National Laboratory. If samples are well made, then even the troublesome fluorescence lines can be managed and cancelled out during the data processing once you collect both It and I0 at the same power making the dead time and count rate to match. > This is a paper I published where we collected XAS data both in the lab and APS: Boglaienko D, Andersen A et al X-ray absorption spectroscopy of trivalent Eu, Gd, Tb, and Dy chlorides and oxychlorides. J. Allows Compounds. 2022. > > Also, easyXAFS company has an excellent customer support. > > Daria -- Авакян Леон Александрович профессор каф. теор. и выч. физики физический факультет Южный федеральный университет +79185630854 laavakyan(a)sfedu.ru

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