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

Open position at BioXAS sector
by Morgane Desmau 28 Mar '24

28 Mar '24

Dear colleagues, We have a permanent position opening in the BioXAS sector (XAS/XRF) at CLS: https://urldefense.us/v3/__https://www.northstarats.com/Canadian-Light-Sour… Here are our websites: - spectroscopy: https://urldefense.us/v3/__https://bioxas-spectroscopy.lightsource.ca/__;!!… - imaging: https://urldefense.us/v3/__https://bioxas-imaging.lightsource.ca/__;!!G_uCf… with our contact information if you have any questions. If you know of a colleague who might be interested, please forward this email to her/him. Best regards, Morgane Desmau

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Re: [Ifeffit] Using Larix from Jupyter notebook
by Ryuichi Shimogawa 25 Mar '24

25 Mar '24

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Using Larix from Jupyter notebook
by Yohei Uemura 25 Mar '24

25 Mar '24

Hi all I read the documentation of Larch and Larix can generate a feff input file from a xyz file. https://urldefense.us/v3/__https://cars.uchicago.edu/xraylarch/xasviewer/ov… Does anyone have a python script to generate a feff input file from a xyz file using Larix? Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Instrument scientist FXE beamline, European XFEL GmbH Address : Holzkoppel 4, 22869 Schenefeld, Germany Phone: +49-40-8998-6006 上村洋平所属 : FXE beamline, European XFEL GmbH, 住所 : Holzkoppel 4, 22869 Schenefeld, Germany 電話 : +49-40-8998-6006 ================================================

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Larch 0.9.75
by Matthew Newville 22 Mar '24

22 Mar '24

Hi Folks, Larch 0.9.75 has been released and is now available. You may see a prompt to install this the next time you launch the Larix GUI. It's been several months since the last release of Larch, and there have been many updates, especially for the Larix GUI, and for using Larch for XAS analysis and visualization with Jupyter notebooks. More complete release notes are at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases__;!… There have been a lot of people who helped with this release, either with code or very detailed discussions and bug reports. There are still several things on the near-term to-do list, including (in no particular order): better customizability and remembering user settings of detailed plotting preferences (themes, colors, etc) in Larix and Jupyter/plotly. Larix automatically generating Jupyter notebooks from analyses. getting a good implementation of MCR-ALS creating a self-contained set of packages so that installation can include exactly one (maybe large) download, but simplifying installation, especially on machines with poor or no internet connection. If you have any questions, trouble, or suggestions, please let us know. --Matt

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[IFEFFIT] Polarized FEFF calculation
by Soyoung Kim 11 Mar '24

11 Mar '24

Dear XAFS community, I have a series of Ru K-edge data on a single-crystal RuO2 sample measured at different incident X-ray angles. Because of the linear polarization of X-rays, the EXAFS of this single-crystal sample depends on the X-ray angle. I am trying to fit the four EXAFS spectra simultaneously with one set of parameters to extract the deltaR and MSRD parameters of this sample. For oriented samples, N for a certain single scattering path is supposed to be proportional to 3*cos^2(θ), where θ is the angle btwn the X-ray's e-vector and the absorber-scatterer vector. Instead of manually calculating the 3cos^2(θ) for all of the scattering paths in RuO2 (there are 7 single and 3 multiple scattering paths that need to be included to achieve a good fit with a reference RuO2 powder sample), I decided to use the polarization card in my FEFF input. For example, for one of the X-ray angles, the e-field vector would be (1, 0, 0), so I added the line "POLARIZATION 1 0 0" in the FEFF input file. Running this input file gave me a list of paths that had different importance values for each path compared to the non-polarized (isotropic) calculation. *Since "importance" is the relative magnitude of each path's scattering contribution (integration of the chi(k)), I thought that it would be proportional to 3cos^2(θ).* That is, for path i from a FEFF calculation for angle a, the "importance" (abbreviated as "Imp") of that path would be: Imp(a)_i = C(a) * Imp(iso)_i * 3cos^2(θ_i) where C(a) is a constant for each angle that accounts for the fact that importance values are relative (because it is scaled so that the first path in the list has an importance of 100). Now, I wanted to check whether the polarized FEFF calculations really follow this relationship underlined above. So, I tried manually calculating the values of 3cos^2(θ) for two of the paths from the same polarized FEFF calculation, then plug them into the above equation to get C(a). But, as the table below shows, the C(a) values are not the same. FEFF 1 has a disagreement that is small enough to ignore, but the disgareement of C(a) values for The disagreement is small enough to ignore for FEFF 1, but for FEFF 2 and 3 the disagreements are quite large. [image: image.png] *FEFF 1, 2, 3 designate individual polarized FEFF calculations. FEFF 1 was with polarization vector = (1, 0, 0). FEFF 2 and 3 were with polarization vector = (0.85, 1.13, 0). For this polarization, the two Ru sites gave different lists of paths. I do think the qualitative trend of the "importance" values in the polarized FEFF calculations is correct, and I can get a bad but not-disastrous fit from simultaneously fitting the data from different angles. However, the above analysis makes me wonder whether the "importance" values from polarized FEFF are truly proportional to 3cos^2(θ), and whether my fitting models for different angles, which I derived from the polarized FEFF calculations, are correct. An alternative would be to manually calculate 3cos^2(θ) for all the paths, but I'm not sure how to calculate it for multiple scattering paths. One note, I am running the FEFF calculation with Larix to get the importance values (labeled as "amp ratio" in the list.dat file, in the FEFF output folder). I wonder if the default settings for getting these amp ratios are not accurate enough for my purposes. It would be nice if I could just pull out the 3cos^2(θ) terms from the FEFF calculations... Anyways, thank you very much for reading this rather lengthy question. Hope it makes sense, and I would appreciate any help regarding this. Best, Soyoung

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Meaning of ldosNN
by jaskirat brar 05 Mar '24

05 Mar '24

Dear list I have a question regarding DOS calculations using feff. (I am using feff8.2) I have calculated the DOS of V-doped Ni, with Ni as the central atom and Ni and V as neighboring atoms. The potential indexes are 0 - Ni 1 - Ni 2 - V I have obtained ldos00.dat, ldos01.dat, and ldos02.dat files corresponding to the l-projected DOS for the NNth potential index. I am not clear about the meaning of ldosNN. Does it correspond to the DOS of the central atom modified by the presence of the potential index NN? If yes, does ldos02 contain the effect of both potentials 01 and 02 or that of just 02? If this is not the case, what does ldosNN mean? Kindly provide your comments to clarify this. Thanks in advance. Jaskirat Brar FMP Lab, South Campus IIT Mandi, H.P., India

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Re: [Ifeffit] Ifeffit Digest, Vol 252, Issue 21
by Ryuichi Shimogawa 21 Feb '24

21 Feb '24

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test/validation sample for air-sensitive sample cells?
by Gerald T. Seidler 21 Feb '24

21 Feb '24

Dear XAFS community, We've been developing air-sensitive sample cells for several of our XAFS experiments, but we don't have a good way of characterizing how well they actually reject air and water. Does anyone have recommendations for easily available 3d transition metal compounds that have a 'reasonable' amount of air sensitivity for purposes of sample call validation? Any suggestions for other methods to validate performance? We would grind the sample and form a pellet with a degassed binder, in a glovebox or glovebag. With thanks, Jerry -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *https://urldefense.us/v3/__http://faculty.washington.edu/seidler/index.html__;!!G_uCfscf7eWS!bc8I7gtiYjYV5xc8tbm1xHCOWp8emLi4nZo7rvTjsDdGw3JMBVgas9avdYSiT995CKzLi-eu2GCc0RfkE-Cz2uX2VeU-3A$ <https://urldefense.us/v3/__http://faculty.washington.edu/seidler/index.html… >* *seidler(a)uw.edu <seidler(a)uw.edu>*

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Larix.desktop on Arch Linux AttributeError: 'list' object has no attribute 'shape'
by Chris Vijeu 19 Feb '24

19 Feb '24

Hello, So I recently installed Larch on two different machines running two different distributions of Arch (Manjaro and EndeavourOS). When I am starting Larix.desktop from the terminal and open a .xlsx data file with two columns (energy and intensity), I get the following error: Traceback (most recent call last): File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1162, in onReadDialog self.onRead(path) File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1187, in onRead self.show_subframe('readfile', ColumnDataFileFrame, filename=path, File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1114, in show_subframe self.subframes[name] = frameclass(self, **opts) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxlib/columnframe.py", line 870, in __init__ self.set_energy_units() File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxlib/columnframe.py", line 1208, in set_energy_units ncol, npts = workgroup.data.shape ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' I haven't modified any of the respective files at all. This is what the programme came as. Chris Cristian Vijeu, Postgraduate PhD Student, Materials for Energy and Electronics Division of Natural Sciences

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Fe K-edge maghemite (gamma-Fe2O3)
by Christian Wittee Lopes 17 Feb '24

17 Feb '24

Dear XAFS community, Does anyone have a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3) sample or standard? Thank you in advance. Best, Christian Wittee Lopes -- Christian Wittee Lopes Professor Adjunto *Departamento de Química - Setor de Ciências Exatas* Universidade Federal do Paraná (UFPR) *Curitiba - Paraná* *LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>*

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