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

Open postdoc position in the APS Spectroscopy Group
by Sterbinsky, George E. 24 Mar '22

24 Mar '22

Hello all, The Advanced Photon Source Spectroscopy Group currently has an opening for a Postdoctoral Research Associate in the area of x-ray absorption spectroscopy. Interested candidates can view the full position description and apply at https://argonne.wd1.myworkdayjobs.com/Argonne_Careers/job/Argonne-National-…. Best, George George E. Sterbinsky, PhD X-ray Science Division Advanced Photon Source Argonne National Laboratory sterbinsky(a)anl.gov

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Conduction band energy and deltae0
by Melike Babucci 13 Mar '22

13 Mar '22

Dear all, For a reliable comparison of two EXAFS data sets (lets say before and after Cu-doping), which parameters should be kept consant in the first model? I understand that sigma^2 values should be the same in two fittings, and I would see a change in coordination numbers and deltaE0 and deltar after Cu doping. Is that a good approach? Does the new deltaE0 indicate a change in the conduction band energy? Thanks in advance. Best regards, Melike N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Open postdoc position at DESY XAFS beamline
by Edmund Welter 10 Mar '22

10 Mar '22

Dear colleagues, in case you are interested in a post doc position as beamline scientist at a XAFS beamline at DESY in Hamburg (a place with notoriously good weather!) please have a look at the following job offer: https://v22.desy.de/e67416/records155637/index_eng.html If you know of a colleague who might be interested please forward this mail to her/him. For any questions concerning the advertised position please do not hesitate to contact me via e-mail but please take care that you do not send your reply to the mail list. The job offer is open till we hired a suited candidate. Best regards, Edmund Welter

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[ifeffit] Intensity difference in XANES
by Chen, Danting 07 Mar '22

07 Mar '22

Dear All, I have been studied Zn XANES and EXAFS for my environmental samples. Due to the unknow Zn speciation in my samples, called ‘A’, I do not have adequate Zn reference materials. I found some Zn reference materials from others work, called ‘B’, and extracted the data from their paper. I found quite similar features, e.g., the location of each peak and bottom. However, the intensity of these peaks or bottoms does not correspond very well. I am guessing that the features of XANES is mainly decided by the bond lengths, ligands and oxidation states of the core atom. The intensity of these features may be influenced by the multiple scattering from the neighbouring atoms beyond the first coordination. Can I conclude that the Zn speciation in my sample ‘A’ has a similar first coordination as other work ‘B’, but the coordination environment beyond the first coordination may be different. I compare their Fourier Transform ‘B’ with my samples ‘A’, and found each peak location correspond well but the intensity is different. I am guessing that their surrounding atoms are heavier than my samples. I am unsure if my explanation. Would you mind providing some suggestions regarding the factors influencing the intensity and also the references for this explanation? I will appreciate your help and many thanks. Best Wishes, Danting Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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fully funded PhD position at ESRF
by Marius Retegan 24 Feb '22

24 Feb '22

Dear IFEFFIT members, We are looking for a PhD student to develop and apply machine learning techniques to analyse X-ray spectroscopy data. The PhD is funded by the Marie Skłodowska-Curie COFUND project ENGAGE. Additional details about the offer can be found at https://esrf.gestmax.eu/1575/1/phd-student-engage-05/en_US <https://esrf.gestmax.eu/1575/1/phd-student-engage-05/en_US>. Applications should be made via the ENGAGE website (https://engage.cyi.ac.cy/?page_id=36 <https://engage.cyi.ac.cy/?page_id=36>), and the application deadline is 15 March 2022. The applicants must not have resided or carried out their main activity (work, studies, etc.) in France for more than 12 months in the three years immediately before the call deadline. Please feel free to forward this offer to any potentially interested candidates. Thank you in advance! Best regards, Marius -- Dr. Marius Retegan European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38000 Grenoble phone: +33 4 38 88 19 29 email: marius.retegan(a)esrf.fr

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Larch install error on MacOS 12.2
by Mangold, Stefan (IPS) 11 Feb '22

11 Feb '22

Dear all, I upgraded a machine to 12.2 (MacPro), Larch was installed via binary installer. Afterwards Larch didn’t launch. I did a re-install with the binary installer and this didn’t work, because already installed. deleted it, but this also didn’t work tried pip install xraylarch stopped with ERROR: Failed building wheel for fabio Failed to build fabio also no director with XAS viewer created. best regards Stefan Mangold

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Artemis warning after FEFF calculation---can't close GLOB filehandle
by Xinyu Luo 10 Feb '22

10 Feb '22

Dear ifeffit memebers, I received an Artemis warning after importing a CIF file into FEFF calculation as usual, which said, “Can’t close GLOB(…) filehandle at …” I first assumed it might be caused by some system errors. So I tried this CIF file on another PC and received a similar warning---can’t close a GLOB() filehandle. Also, I tried FEFF8 using Webatoms, but this still didn't work... Is that due to the CIF file itself or the software bug on my PC? I never met this situation before because it's always been very smooth to import a CIF file and generate atomic coordinates and paths before fitting... I don’t know how to handle this. The CIF file is attached. I appreciate any suggestions that might be helpful. Thank you for your time! Xinyu Luo

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Re: [Ifeffit] [Ext] Larch install error on MacOS 12.2
by Jeffrey Terry 09 Feb '22

09 Feb '22

Hi Stefan, We recently updated our EXAFS Neo analysis package to work with the new version of Larch. I installed Larch using the detailed instructions on our GitHub site on a number of Macs* running OS X 12.x this weekend. https://github.com/laumiulun/EXAFS-Neo-Public If you want to use the Larch GUIs, you need to take the additional step of: larch -m Which puts links to the GUIs on the desktop. Our code calls uses larch Python routines so we have developed a fairly robust procedure for making sure larch installs correctly on all operating systems. Hope that helps. Jeff *all M1 machines but I don’t expect it will make a difference Jeff Terry 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 Sent from my iPhone > On Feb 9, 2022, at 2:05 AM, Mangold, Stefan (IPS) <stefan.mangold(a)kit.edu> wrote: > Dear all, > > I upgraded a machine to 12.2 (MacPro), Larch was installed via binary installer. Afterwards Larch didn’t launch. I did a re-install with the binary installer and this didn’t work, because already installed. deleted it, but this also didn’t work > > tried > > pip install xraylarch > > stopped > with > ERROR: Failed building wheel for fabio > Failed to build fabio > > also no director with XAS viewer created. > > > best regards > > Stefan Mangold > > _______________________________________________ > 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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Postdoc position in X-ray spectroscopy at NSLS-II
by Stavitski, Eli 08 Feb '22

08 Feb '22

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. See full posting at https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> https://www.bnl.gov/ps/beamlines/beamline.php?r=8-ID

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Research scientist position at DOE-NETL
by Mengling Stuckman 07 Feb '22

07 Feb '22

Dear ifeffit members, We are looking for talented environmental scientist/engineer familiar with soil science and synchrotron application experiences at Leidos working for US Department of Energy - National Energy Technology Laboratory, Pittsburgh, PA: Environmental Scientist / Engineer (myworkdayjobs.com) <https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment…> This is a full-time research scientist position that will help with the following projects: (1) converting oil and gas drilling wastes to soil supplements; (2) synchrotron microprobe and bulk XAS studies on critical mineral characterization in different coal byproducts (e.g., REE in fly ash). If you have any related questions, feel free to let me know at mengling.stuckman(a)netl.doe.gov. Thank you, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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Fwd: Position at USDOE-NETL
by Mengling Stuckman 07 Feb '22

07 Feb '22

Dear ifeffit members, We are looking for talented environmental scientist/engineer familiar with soil science and synchrotron application experiences at Leidos working for US Department of Energy - National Energy Technology Laboratory, Pittsburgh, PA: Environmental Scientist / Engineer (myworkdayjobs.com) <https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment…> This is a full-time research scientist position that will help with the following projects: (1) converting oil and gas drilling wastes to soil supplements; (2) synchrotron microprobe and bulk XAS studies on critical mineral characterization in different coal byproducts (e.g., REE in fly ash). If you have any related questions, feel free to let me know at mengling.stuckman(a)netl.doe.gov. Thank you, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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Re: [Ifeffit] Postdoctoral position for Synchrotron Studies of Molten Salts, Solutes and Interfaces
by Gill, Simerjeet 07 Feb '22

07 Feb '22

Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to postdoctoral Research Associate position within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The position requires a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural and spectroscopic investigation of molten salts, solutes in them, and liquid-solid interfaces. You can find the detailed description of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/> under Job ID 2921(https://jobs.bnl.gov/job/upton/post-doc-synchrotron-studies-of-molten-… The postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with X-ray absorption fine structure along with x-ray scattering techniques. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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Postdoc position available at PAL
by 이국승(에너지환경소재연구팀) 28 Jan '22

28 Jan '22

Dear ifeffit members, I would like to let you know a postdoc position available at 8C Nano-XAFS beamline of PAL. Please refer to the following posting. Postdoctoral Research Associate - Pohang Accelerator Laboratory Post details: Full time / Annual contract Application deadline: until the recruitment is completed Job description - In-situ XAFS analysis of electrocatalysts (experience of XAFS analysis preferred) Requirements - PhD degree in physics, chemistry, materials science, or chemical engineering - Excellent writing and communication skills in english. Offered - USD 30,000 - 40,000 according to career If you are interested in this position, please send your CV (including list of publications) to lks3006(a)postch.ac.kr. * Additional documents can be required, for example, two letters of reference, representative publications, etc. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Google Scholar : ?<https://scholar.google.co.kr/citations?hl=ko&user=CRS8vHkAAAAJ>?Kug-Seung Lee? - ?Google 학술 검색?<https://scholar.google.co.kr/citations?hl=ko&user=CRS8vHkAAAAJ>

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Post-doc in catalysis at the ESRF
by Mauro ROVEZZI 27 Jan '22

27 Jan '22

Dear all, I'd like to advertise for a post-doc position in catalysis at the French CRG spectroscopy beamlines at the ESRF: https://bit.ly/32FaDCQ Please, feel free to diffuse it. Best, Mauro -- Mauro Rovezzi CNRS-OSUG | French CRG @ ESRF Beamlines FAME (BM30) & FAME-UHD (BM16) 71 Avenue des Martyrs, 38043 Grenoble, France Tel: +33(0)47688 2963 | Office: LOB-2-50

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post-doc opportunity
by Matt Newville 24 Jan '22

24 Jan '22

Hi Folks, I'd like to pass on this advertisement for a post-doc position at U Illinois at Urbana Champaign: Post-doctoral researcher, Dept of Geology, University of Illinois Urbana Champaign: XAS study of molecular complexation of PGE sulfides in high temperature and pressure geological fluids Applications are invited for a postdoctoral researcher position in the Department of Geology (School of Earth, Society and the Environment) at the University of Illinois at Urbana Champaign. We seek a person with strong background in high-temperature hydrothermal/magmatic liquids and experimental geochemistry to perform EXAFS and XANES analyses on both glasses and solutions produced in high temperature and pressure laboratory experiments. The goal is to determine the solubilities and understand the molecular complexation of PdS and PtS in hydrous alkali silicate and carbonate liquids. Experience and knowledge of synchrotron XAS analyses are required. Skills in performing experiments at high pressure and temperature as well as advanced knowledge of chemical thermodynamics and computational geochemistry are all preferred qualifications. The postdoc will have opportunities to participate in interdisciplinary research involving aspects of geoscience, chemistry, and material science. Requirements and qualifications include: PhD in mineralogy, chemistry, material science, or closely related field. Prior experience with synchrotron X-ray spectroscopy/scattering/microscopy techniques is required. Familiarity with other analytical techniques such as SEM-EDS, XRD, and ICP-MS is highly favorable. Prior experience with high pressure experimental geochemistry is preferred. Excellent oral and written communication skills This position is part of a new collaborative project between UIUC (PI C. Lundstrom), Johns Hopkins University (Co-PI D. Sverjensky), and University of Chicago (Co-PI G. Gauli). This project is funded by the Department of Energy (DOE) Basic Energy Sciences under the critical minerals and materials program (https://www.energy.gov/articles/doe-awards- 30m-secure-domestic-supply-chain-critical-materials). The selected candidate would start in late Spring 2022 at UIUC. XAS analyses at Argonne/APS would likely start in summer 2022 and occur through April of 2023 when the APS beamline shuts down. For the remainder of 2023 and 2024, XAS work using a pressurized hydrothermal cell is planned to occur at Grenoble/European Union Synchrotron facility. The initial appointment is for one year with possible renewal for another 1.5 years upon mutual satisfaction. Interested individuals should submit a single pdf file that includes: 1) a cover letter that outlines the applicant's research, expertise match to the position, and career goals; 2) curriculum vitae; 3) copies of representative recent research publications; and 4) contact information of three references, electronically to Prof. Craig Lundstrom, lundstro(a)illinois.edu. Review of applications will begin January 25, 2022. UIUC is an Equal Opportunity/Affirmative Action employer, and applications from women and under-represented minorities are particularly encouraged.-- --Matt Newville

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FEFF calculation on ferri-/ferrocyanide materials
by Hu, Yang (HIU) 23 Jan '22

23 Jan '22

Dear IFEFFIT members, I am trying to apply the FEFF calculation on Metal-[Fe(CN)6] type materials (in Larch). The calculations were successful with cif files from (K, Na)x(Cu, Ni) [Fe(CN)6] for both C-coordinated Fe and N-coordinated metals, and their results include higher-order paths. However, the calculation on NaxFe[Fe(CN)6] always gives the warning ".Two atoms very close together. Check input." and takes long time. The calculated results have some collinear 5- and 6-leg paths with several hundred or even thousand importance value. I am wondering if it is possible to limit the multiple scattering to a lower order in the calculation (such as suggested in Artemis user guide). Plus, if I only aim to model the nearest Fe-C and Fe-N for its Fe K-edge spectra, are there any alternative methods for the calculation? - I also would like to ask whether it is meaningful to do this while ignoring those multiple scatterings in this type of materials. Your help and comments are highly appreciated, Best regards, Yang

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Question_Demeter installation on Mac with Apple Silicon M1
by 王茂林 23 Jan '22

23 Jan '22

Dear IFEFFIT members, Here I want to install Demeter in my Mac with M1 pro, I followed the processes in https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… (First, install Xcode and Xcode command tool; Then install Macport). But when I type " sudo port install xorg-server demeter in the terminal and after agreeing to the terms, there came to a warning, shown in the attached figure. What should I do to install it on my mac? And the log file (also attached) seems like Demeter doesn't support the M1 with ARM architecture? I'm looking forward to your helpful reply! Best regards, Maolin Wang 确定

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The possibility of the defect concentration estimation by feff
by Iraida N. Demchenko 17 Jan '22

17 Jan '22

Dear All, Do I understand correctly that using feff calculations it is impossible to calculate the concentration of defects in a sample? I'll try to explain my question with an example. Let us assume that we have a (Ga,Mn)As sample, where Mn is a dopant. Comparing the experimental curve (Mn K edge) with the theoretical spectrum, we see that the experimental one is well described by a linear combination of two theoretical ones, namely, substitutional manganese in the position of gallium (Mn_Ga) and interstitial manganese (Mn_i) in proportions of 65 and 35%, respectively. Is it possible to recalculate these phases weights (I mean Mn_Ga and Mn_i) to the real concentration of the mentioned above defects in the sample? For example, for the Mn_Ga model, ONE manganese atom was considered per cluster of 900 atoms (FMS 7A). Does it make sense to recalculate the stoichiometry (using cluster size) and, subsequently, the weights of this model when compared to the experimental curve, which will eventually give the selected defect concentration at the low level (like ~0.2%). Do I understand it correctly? I will be very grateful for your help in understanding. Best, Iraida.

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Larch 0.9.58
by Matt Newville 16 Jan '22

16 Jan '22

Hi Folks, Larch version 0.9.58 has been released. It should now be installed by default using all installation mechanisms, and you may see a notice to update if running xas_viewer. Coming only 6 weeks after 0.9.57, and with the holidays in between, this is mostly a set of bug fixes, especially surrounding installation and errors associated with our use of deprecated features of silx and numpy. Thanks mostly to Mauro for this, and for updating the documentation for installation, especially for existing Anaconda Python users, and on Linux. FWIW, I checked that a fresh install works on Windows 10, MacOS 12, CentOS 7, CentOS 8 Stream, and that "auto-updates" work with "larch -u" or from XAS Viewer works on MacOS 12 and on Fedora 34. But, of course, let us know if you have suggestions, comments, or problems. There are a few fixes for reading some kinds of data files and with de-glitching XAS spectra. The plans discussed in the previous release message (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-December/010345.ht…) about saving more complex projects and how to think "reference spectra" have not had much work done on them. The request for suggestions and comments on these topics still stands. --Matt

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Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels
by Ming Zhang 14 Jan '22

14 Jan '22

sorry for the trouble, I forgot to register this email. -----原始邮件----- 发件人:"Ming Zhang" <mzhang17(a)zju.edu.cn> 发送时间:2022-01-13 14:41:04 (星期四) 收件人: ifeffit(a)millenia.cars.aps.anl.gov 抄送: 主题: Question--FEFF calclulated atom coordinates and labels Dear IFEFFIT members, I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation. 1)I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images. 2)I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this. FEFF calculation VESTA GUI The CIF file is attached. I would appreciate it very much if you could help me out. Best regards Ming Zhang

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How do I launch Larch GUIs?
by Swanner, Elizabeth S [GE AT] 12 Jan '22

12 Jan '22

I use a Mac recently updated to Big Sur (11.6). I used the Binary Installer File for Larch and am a little stuck on what to do next. I was able to run the installer, and I have an xraylarch folder on my computer. However, I was hoping to use the XAS Viewer and do not see it within the folder. Should it be there? I had an old version of XAS Viewer I got while at APS but needed to replace that as it did not have all the modules. I did not check before removing that whether it was working on this OS. I am also not clear how to use Larch in general (i.e., the Basic Larch GUI). Do I need to install python? I see there is a python application in the folder but when I try to open that nothing happens. I’m not sure if these are issues with my OS or if I am missing something really basic about how to launch Larch. Best, Betsy Swanner

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Issues reinstalling Larch, error creating desktop shortcut for macOS
by Lauren N. Pincus 05 Jan '22

05 Jan '22

Hi Matt, I'm having an issue with reinstalling Larch. I'm using macOS Catalina 10.15.7. I had Larch previously installed and it was working well, but found I was no longer able to open up XAS Viewer. The application would start and then quit. So, I removed Larch from my system and tried to reinstall it. I first used the mac installer but would get an error that the "Installation failed. The installer encountered an error that caused the installation to fail." I then tried the installation using the script in terminal. This appeared successful, but no desktop shortcut was created. I tried to create a desktop shortcut using larch -m but get the following error: (base) laurenpincus@lnp24mbp2020 ~ % larch -m Traceback (most recent call last): File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in <module> from larch.apps import run_larch File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", line 22, in <module> from . import io File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", line 39, in <module> from .specfile_reader import (str2rng_larch, read_specfile, open_specfile, File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", line 26, in <module> from silx.io.convert import write_to_h5, _is_commonh5_group ImportError: cannot import name '_is_commonh5_group' from 'silx.io.convert' (/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py) (base) laurenpincus@lnp24mbp2020 ~ % Thanks, Lauren Lauren Pincus, PhD NSF Earth Sciences Postdoctoral Fellow Princeton University Department of Geosciences

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Re: [Ifeffit] [Ext] Re: Problem in xrayLarch installation
by Jeffrey Terry 20 Dec '21

20 Dec '21

We’ve had to come up with a slightly different install plan for Windows users of our analysis package EXAFS Neo that is built on top of xrayLarch. We recommend a slightly different route using both conda and pip. You can read through out full recommended analysis route for xrayLarch in the Prerequisites section of our readme file at: https://github.com/laumiulun/EXAFS-Neo-Public We are pretty confident that the installation method given there works for xrayLarch installation on Mac, Windows, and Linux. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Dec 15, 2021, at 2:42 AM, Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> wrote: > Dear Latif, > > Thanks for reporting this. Unfortunately `pip` is not able to correctly install all dependencies of Larch. The way to go is to install those dependencies via `conda`. > > Under Windows, this is achieved by running the script `GetLarch.bat` (https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLar…) This script will download and install a minconda distribution, plus install Larch in it. > > Seen you already have Anaconda installed, you could simply run the following commands from your Anaconda prompt: > > conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw > pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch > > If this does not work, please, let me know. I have created a related Github issue in order to avoid such troubles in the future: > > https://github.com/xraypy/xraylarch/issues/333 > > Best, > Mauro > > On 2021-12-15 08:20, Latif Ullah Khan wrote: >> Dear Sir Madam, >> I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using “pip install xraylarch” . However, it is not installing and give me an following error: >> If you kindly help me in this regard, I will be grateful to you. >> Thank you in advance >> Best regards >> Latif >> _______________________________________________ >> 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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Re: [Ifeffit] Ifeffit Digest, Vol 226, Issue 9_Problem in wavelet code
by Latif Ullah Khan 20 Dec '21

20 Dec '21

Dear Matt Newville and Mauro, Many thanks for the kind reply and great support in installation of the XrayLarch through window. Unfortunately, I could not install through Anaconda prompt using command " conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch" as suggested by Mauro. Fortunately I succeeded to install through window command prompt using the source code. Now I am using through VS Studio code. I just adopted the code for wavelet transformation written by Matt Newville, however, I faced some problem in plotting the 2D CCWT image, I am sharing the code with input data and also the code. Its showing some error in following syntax, probably "imopts" has problem: plt.imshow(f.wcauchy_mag, win=1, label='Wavelet Transform: Magnitude', **imopts) plt.imshow(f.wcauchy_re, win=2, label='Wavelet Transform: Real Part', **imopts) If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif -----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, December 15, 2021 6:08 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 226, Issue 9 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: Problem in xrayLarch installation (Matt Newville) 2. Re: Any coorelation about 'white line" in K-edge XAS with oxidation states? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 09:23:47 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Ifeffit-request(a)millenia.cars.aps.anl.gov" <Ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem in xrayLarch installation Message-ID: <CA+7ESbqCSsM+==XmUgzkjzjPHTOJjfLRGw8JRDqN5CGUxzJCuQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Latif, Sorry for the trouble. As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. FWIW, I agree that the needed combination of conda and pip is sort of unfortunate. But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support. Conda is a popular option for many of these. We try to support the simpler / more ubiquitous pip where we can. Anyway, that's basically why we have the binary installers and installation scripts. But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333 --Matt

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Any coorelation about 'white line" in K-edge XAS with oxidation states?
by Marco Wang 16 Dec '21

16 Dec '21

Dear everyone: Ihave some questions about the interpretation of "white line", from anarticle (https://doi.org/10.1038/s41467-021-27116-8) and the figure was attached. In the article, it is said that “the sample was fully reduced to Ni (0) state at ~480 °C judging from the edge position and ‘white-line’ profiles”. First, we assumed that the metal was coordinated with the same anion. We all know that K-edge transition in 3d and 4d metalis' spin forbidden, so it may be inappropriate to conclude that the intensity of the "white line" is correlated with metals' oxidation states. But in other words, the probability for s→d transition may be proportional to thenumber of empty d orbitals, so it seems like if the the intensity of "white line" is higher, the oxidation state is higher. So, how should we correctly interpret the “white line” and edge energy from XAS spectrum of metals’ K-edge and L-edge? Thank you in advance for your time. Marco Wang

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