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

Larch 0.9.72
by Matt Newville 03 Oct '23

03 Oct '23

Hi Folks, It's been a few months since the last release, but Larch 0.9.72 is now available. There have been several fixes and a few new features. The XAS analysis GUI application has been renamed from the rather dull name of "XAS Viewer" to "Larix" (the genus of trees for the Larch family). We (well, mostly Mauro Rovezzi and others at ESRF) put in a lot of effort over the summer to generate FDMNES inputs from structural information (CIF files, structural information from the Materials Project). This effort to convert structure information to input files for Feff, FDMNES, etc. has been evolving over the past several months, and there will probably be more done on this in the coming months. If you are interested in getting involved, let us know. There are new binary installer scripts for Windows, MacOS, and even Linux, and the "GetLarch" scripts have been updated too. These all will now install a Python 3.11 environment. Although installation is not fast, it is somewhat faster than it has been in the past due to using the Mamba variation of the Anaconda Python tools. More release notes are at https://github.com/xraypy/xraylarch/releases/tag/0.9.72 If you have a fairly recent version of Larch installed, you should be informed that a new version is available, and be prompted to install or run the Larch Updater script. Let us know if you have any troubles with this version or questions, comments, or suggestions for improvements! --Matt

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TiOx K-edge spectra
by Rebecca Katharina Pittkowski 20 Sep '23

20 Sep '23

Dear community, I am preparing a teaching exercise for a course on nano-structure characterization, and I was hoping that someone has some K-edge spectra of titanium oxide nanoparticles lying around that I could reuse for the course. I have been through the NIMS Material Data Repository and found some useful references but it would be great to have a nano-sized example as well. That could very well be from a published article, which I could include in the teaching. Thanks for any input. Greetings from Copenhagen, Rebecca Rebecca K. Pittkowski Tenure-track Assistant Professor University of Copenhagen Center for High Entropy Alloy Catalysis Department of Chemistry Universitetsparken 5 2100 Copenhagen Ø DENMARK Rebecca.pittkowski(a)chem.ku.dk [/var/folders/gc/lhyz4xy96q77x4sbrrh4l46r0000gn/T/com.microsoft.Outlook/WebArchiveCopyPasteTempFiles/cidimage009.png(a)01D5C49F.F68E4220]

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P K-edge EXAFS
by Marcelo Eduardo Alves 15 Sep '23

15 Sep '23

Hi there, I begin by examining phosphorus adsorption by goethite, hematite, and gibbsite. Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K edge that can be properly used, i.e., spectra with a high signal-to-noise ratio, especially for dilute samples? Would it be possible to use arsenic as a phosphorus proxy to get conclusions from As K-edge EXAFS data that could be extended to P? Thank you.

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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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Re: [Ifeffit] EasyXAFS - any experience with?
by laavakyan 04 Aug '23

04 Aug '23

Dear Michele, thank you very much for your reply! It is very valuable, Best regards, Leon On 8/3/23 20:00, 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 (Michele Piana) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Aug 2023 20:13:13 +0000 > From: Michele Piana<michele.piana(a)tum.de> > 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:<0c838f5f84a14ae5a5b130a8dbeea2cc(a)tum.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Leon, > you can request the publications relative to easyXAFS here (it takes a few minutes to receive them): > https://www.easyxafs.com/copy-of-links > I am currently analyzing XAFS data from that instrument and I can tell that the data in the XANES region look good in terms of signal-to-noise ratio, also collecting them for just 1 hour. > To get sufficiently good data in the EXAFS region would need much longer data collections. > One annoying disadvantage is coming from spurious fluorescence peaks from the standard X-Ray tubes used. > The measurable elements and edges are limited, of course. > > Best regards > Michele Piana > > > -----Original Message----- > From: Ifeffit<ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Ofifeffit-request(a)millenia.cars.aps.anl.gov > Sent: Wednesday, 2 August 2023 19:00 > To:ifeffit@millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 246, Issue 1 > > 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. EasyXAFS - any experience with? (laavakyan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Aug 2023 17:23:48 +0300 > From: laavakyan<laavakyan(a)sfedu.ru> > To:Ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] EasyXAFS - any experience with? > Message-ID:<50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Ifeffit and XAFS society, > > I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). > > Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? > > The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. > > Regards, > Leon Avakyan > > > > > > ------------------------------ > > 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 246, Issue 1 > *************************************** > > > > ------------------------------ > > 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 246, Issue 2 > *************************************** -- Авакян Леон Александрович профессор каф. теор. и выч. физики физический факультет Южный федеральный университет +79185630854 laavakyan(a)sfedu.ru

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1
by Daria Boglaienko 03 Aug '23

03 Aug '23

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 ________________________________ 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: Wednesday, August 2, 2023 10:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 246, Issue 1 Note: This message originated from outside the FIU Faculty/Staff email system. 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. EasyXAFS - any experience with? (laavakyan) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Aug 2023 17:23:48 +0300 From: laavakyan <laavakyan(a)sfedu.ru> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] EasyXAFS - any experience with? Message-ID: <50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan ------------------------------ 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 246, Issue 1 ***************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1
by Michele Piana 02 Aug '23

02 Aug '23

Dear Leon, you can request the publications relative to easyXAFS here (it takes a few minutes to receive them): https://www.easyxafs.com/copy-of-links I am currently analyzing XAFS data from that instrument and I can tell that the data in the XANES region look good in terms of signal-to-noise ratio, also collecting them for just 1 hour. To get sufficiently good data in the EXAFS region would need much longer data collections. One annoying disadvantage is coming from spurious fluorescence peaks from the standard X-Ray tubes used. The measurable elements and edges are limited, of course. Best regards Michele Piana -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, 2 August 2023 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 246, Issue 1 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. EasyXAFS - any experience with? (laavakyan) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Aug 2023 17:23:48 +0300 From: laavakyan <laavakyan(a)sfedu.ru> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] EasyXAFS - any experience with? Message-ID: <50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan ------------------------------ 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 246, Issue 1 ***************************************

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EasyXAFS - any experience with?
by laavakyan 02 Aug '23

02 Aug '23

Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan

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Advanced EXAFS analysis course Nov. 1-3
by Anatoly Frenkel 21 Jul '23

21 Jul '23

Dear colleagues: Please share this info with your students and postdocs. The application deadline is Aug. 31. https://www.bnl.gov/xafscourse/ Remember to state your expertise with EXAFS data analysis and modeling in the application. Regards, Anatoly ------------------------------------------------------------------- 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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Deglitch the data
by Shailendra 16 Jul '23

16 Jul '23

Hi, IFEFFIT community, I am Rachna, a Ph.D. student working on IrO2 based OER catalyst. I am a new XAS user. Recently, we recorded some XAS on amorphous IrO2 electrode samples however some of the samples show a dip in adsorption at high energy. The glitches are similar to the one in the attached photo. I am attaching the Athena file for the measurements too. I was wondering if there is a way to remove such glitches. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thanks, Kavya Rachna

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Re: [Ifeffit] Help installing Demeter on a Mac
by Fowler, Joseph W. (Assoc) 01 Jul '23

01 Jul '23

Hello Kyle, I agree that putting /opt/local/bin in your PATH should be adequate, so this isn’t totally obvious. The executables athena, hephaestus, and artemis should all be in /opt/local/bin/. Are they? What is the result if you execute the following? $ port contents demeter I’m the official maintainer of the Macports version of Demeter. Unfortunately, I’m not a regular user. In fact, it’s not installed on the everyday computer that I’ve had for four years (to give you an idea of what “not regular” means to me). Worse, there’s a chronic problem that I have never worked out how to solve. The Demeter ports depends on many things. One is ifeffit, which is not really still supported, but Demeter can’t just magically start using Matt Newville’s replacement for ifeffit, known as Larch. It feels to me like Mac-Demeter is doomed to break permanently pretty soon, if it has not already. [Bruce, Matt, have I stated that accurately? Please correct me if I’m wrong.] Still, there exists a port for ifeffit and for demeter, and one should be able to install them. I’m trying it right now on a Mac that lacks them. It will take me a while, because I’m not a Perl user either, and there are dozens of dependencies to install first. Let’s see how it goes for me… This install is taking a very long time. I’m going to send this note as-is and report later about whether I can make athena run, and where the executable is located. (But I’m sure it will be /opt/local/bin/ ) Could I suggest that, if you get it to work, and you use it regularly, and you’re an open-source supporter, would you think about helping as a second official maintainer of the Demeter port? Other users could benefit from me teaming up with an actual demeter user, to be sure! Best wishes, Joe Fowler NIST Boulder Labs On Jun 30, 2023, at 11:00 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c…<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<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@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. Help installing Demeter on a Mac (Kluherz, Tk) From: "Kluherz, Tk" <Tk.Kluherz(a)nrel.gov<mailto:Tk.Kluherz@nrel.gov>> Subject: [Ifeffit] Help installing Demeter on a Mac Date: June 30, 2023 at 10:02:03 AM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>" <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@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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Help installing Demeter on a Mac
by Kluherz, Tk 30 Jun '23

30 Jun '23

Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle

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EXAFS course at BNL: Nov. 1-3, 2023
by Anatoly Frenkel 29 Jun '23

29 Jun '23

Dear subscribers: The information about the upcoming XAFS short course is here: https://www.bnl.gov/xafscourse/ The course will be taught in-person. The place in the course is limited, and, due to the emphasis on advanced methods, the preference will be given to those participants who have prior experience with EXAFS data modeling and analysis. The info about the past course topics (2005-2022) is at the SCC website: https://you.stonybrook.edu/scc2/xafs-workshops/ Regards, Anatoly ------------------------------------------------------------------- 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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Postdoc position at BM23 ID24 XAS beamlines
by Kirill LOMACHENKO 28 Jun '23

28 Jun '23

Dear all, we are looking for an excellent postdoc to work with us at BM23 and ID24 XAS beamlines of the ESRF (Grenoble, France) in the field of chemistry (catalysis, electrochemistry, energy materials, etc). Cutting-edge research, state-of-the-art equipment, friendly team, competent users, great location, competitive salary and all other things to make a scientist happy. If you are good at applying XAS for chemistry (or know someone who is), please find the link to the position below (in case the link is not visible, just google "ESRF jobs"). Do not hesitate to contact me for more details. Best regards, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Hello, all. It is a low- to medium- level brain teaser. Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly [image: image.png]

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Re: [Ifeffit] [Ext] Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Thank you, Robert, Matthew, Jeff, Kirill, Terry and Sirine for great suggestions. I initially thought that the explanation for the linearity or the transmission signal is a superposition of two opposite trends: 1) increase of flux with energy due to the mirror effect and 2) similar decrease with energy due to the photon removal by first effect in the I0 detector. But I did not look into the main reason for the curving up of the I0 signal and I agree it is not a result of the reflectivity. I fill follow up on all suggestions, and, if something more definitive transpires, will report back. Thanks again for your time and advice! Anatoly > On Jun 15, 2023, at 2:10 AM, matthew marcus <mamarcus(a)lbl.gov> wrote: > The mirror was set up for a run at the Pd K-edge, according to the problem statement. Therefore, its nominal angle must be such as to put the critical energy >25keV. An angle of 3mrad would do it. At that angle, the reflectivity (assuming no roughness) goes up with energy in the relevant range, but only by a few percent. > > We're not told what the ratio of gains of the current amps is, or whether the ion chambers have the same path length, so we can't tell whether the signals are comparable, as shown on the graph, or orders of magnitude different. > mam > > On 6/14/2023 10:17 PM, Jeffrey Terry wrote: >> Well, I’ll take a shot. Looks like the mirror angle is totally fubared, you are getting Bragg peaks from the coating or substrate that are giving you the peaks in Io. Since you have no idea what angle those are going through Io, they are unlikely to make it into either the sample or It. Since those photons are removed from the beam hitting the sample, they would show up as intensity dips in It. I’d bet that most (all?) of the reflected beam is not going into the sample. I’m kind of surprised It signal is as clean as it is, but then I don’t know the gains on either measurement amplifiers. I couldn’t find a flat mirror angle that would cause the cutoff at 12870? eV but since it is a collimating mirror who knows what range of angles were actually being hit. >> Jeff Terry >> Interim Chair, Department of Biology >> Interim Chair, Department of Social Sciences >> Professor of Physics >> Professor of Mechanical, Materials, and Aerospace Engineering >> Editor, Applied Surface Science >> Illinois Institute of Technology >> 3101 S. Dearborn St. >> Chicago IL 60616 >> 630-252-9708 >>> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu <mailto:anatoly.frenkel@stonybrook.edu>> wrote: >>> Hello, all. It is a low- to medium- level brain teaser. >>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >>> Anatoly >>> <image.png> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> _______________________________________________ >> 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 > _______________________________________________ > 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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