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

question concerning the limitations of the webatoms program
by I. D. 30 Apr '24

30 Apr '24

Dear All, We are studying the gallium oxide polymorph (gamma phase). The *.cif file used is in the appendix. After testing this file with the webatoms program, I believe that there is a limitation of the number of atoms in the list between between 256 and 299. As can be seen in the *.cif file considered structure contains 426 atoms. If we try to use the webatoms program to generate the feff.inp file, error like that appears: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." Also there is no possibility to change the cluster size and select the desired absorption atom for generating feff.inp file. Can anyone help and explain how to solve the existing problem? Best regards, Iraida.

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Origin of noise in Ag K-Edge
by Sebastian Kunze 29 Apr '24

29 Apr '24

Greetings, I recently did in-situ QEXAFS at Ag K-edge, expecting to see structure loss starting from crystalline (metallic) state. While we can see that, in addition we also see an increase in noise(?) in the xanes region (compare start and end in the attached image). I am confused by this because the amount of material did not change, so I did not expect a difference in the signal/noise ratio at the absorption edge. And it is reproducible across several samples, so not instrument related. Could anyone point me in the right direction as to what I am missing? Thank you! Best, Sebastian Kunze

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Difficulty in generating XANES for Ni.
by jaskirat brar 22 Apr '24

22 Apr '24

Dear list I am using feff8.2 to generate the XANES for Ni and compare it with the experimental spectra collected on pure Ni. To include the contribution from different scattering paths, I have increased the value of *r_fms* in steps. I find that the intensity ratios of the generated spectra match with that of the experimental spectra when* r_fms* is around 5 angstroms (figure below). Further increasing the* r_fms* produces a mismatch in the intensity ratios of the calculated and the experimental spectra, as shown in the figure. [image: fig.jpg] As per my understanding, increasing the *r_fms* should include more scattering paths and give a better match with the experimental spectra. Please comment on what might be the problem here. Thanks in advance. Jaskirat Brar FMP Lab, South Campus IIT Mandi, H.P., India

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Difficulty with normalization of XAS spectra
by jesse walters 15 Apr '24

15 Apr '24

Hi all, I have some spectra collected by a collaborator, Francesco Ressico, a PhD student at Uni Bologna, (see attached .h5 file below) and we are having trouble normalizing the Fe K edge spectra. The data are for serpentine group minerals and were collected in fluorescence mode. In the attached file, the correct X array value is 'energy_enc', the data type is 'xas', and the y array should be 'mu_fluo_det0'. The spectra are already normalized for the incoming beam energy (although this can also be done using 'flou_det0/i0'). There are multiple spectra in the file, any one of them can be chosen to test the procedure. After loading the spectra, I am able to plot the raw spectra correctly (see attached). But when I try to normalize the pre and post edge regions and plot the normalized spectra, the software only gives a blank plot. I have tried changing the normalization type, polynomial type, range, etc for both the pre and post edge, but nothing seems to work. I also tested different spectra, but with similar results. Does anyone have suggestions for how these data can be normalized? The h5 file is too large, so here is a dropbox link https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac… Sincerely, Jesse Walters -- Jesse B. Walters Ambizione Fellow Institut für Geologie Universität Bern

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Re: [Ifeffit] Ifeffit Digest, Vol 254, Issue 4
by Ryan Parmenter 08 Apr '24

08 Apr '24

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Peak-Fitting Process in Larix
by Ryan Parmenter 07 Apr '24

07 Apr '24

Hi All, I have some questions regarding different aspects of the peak-fitting process in Larix. I wish to repeat the process reported in similar studies, but I'm facing challenges in adapting it effectively to my dataset. * Farges 2005: 'One should model the pre-edge feature with either two or three peaks of fixed width and shape pseudo-Voigt functions of 1.3 eV 2σ width and 45% Gaussian'. * Chalmin 2009: 'The pre-edge region was extracted from the normalised XANES spectra and modelled using a series of pseudo-Voigt functions of fixed width (1.3 eV) and fixed Gaussian percent to minimise the number of variable parameters. Two contributions were modelled for Mn2+ and three for Mn3+.' Using Mn2+ as an example, after normalisation, the baseline is fitted within the pre-peak region, followed by fitting an arctangent background function to the data. The parameters for the arctangent function are initially estimated using the 'pick values from plot' feature. However, modifying these parameters doesn't result in corresponding changes in the graph, making it difficult to ascertain if it aligns with the data points. Considering this, would it be acceptable to set the arctangent's amplitude to 1 (normalised edge jump) and position its centre a couple of eV below E0? Following this, two pseudo-Voigt functions are introduced, with their parameters initially estimated. Then, to replicate the conditions of '1.3 eV 2σ width and 45% Gaussian,' do I set the pseud_fraction to 0.45 and pseud_sigma to 2? I'm uncertain about where to input the 1.3 eV width and whether this choice is optimal, especially considering that the natural width of the atomic K level at the Mn edge is 1.16 eV (Krause, 1979). Finally, I couldn't find the specific paper, but the authors stated that due to the significant processing times required for Voigt functions, they opted for pseudo-Voigt functions to model instrumental and core-hole broadening factors. With improvements in processing times, are Voigt functions now the preferred choice, or does the pseudo-Voigt function still hold advantages over both? Any insights and suggestions would be immensely valuable and greatly appreciated. Ryan

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Imidazole multiple scattering in Artemis
by Chris Pollock 02 Apr '24

02 Apr '24

Hi everyone, I've been using Artremis for quite a while, but have only recently come across a case where the inclusion of multiple scattering seems to be important for fitting some data and wanted to ask what is probably a super basic question to make sure I don't mess anything up. I've recently collected some data on a metalloenzyme with a quite histidine-rich active site and, since it's been shown previously that multiple scattering is important for fitting the longer range scattering for these types of systems, I wanted to make sure I capture this in my Artemis fits. The data appear to show scattering contributions from N3, C2, and N1 in the imidazole ring, and FEFF seems to agree that those paths are the most important, though it calculates the MS intensity to be significantly greater than the single scattering for the farther N (N1). So, my super naive question is: To include multiple scattering paths in the fits--say, the Fe-N3-N1 triangle--is it correct to include the Fe-N3-N1 multiple scattering path in addition to the Fe-N3 and Fe-N1 single scattering paths, or would that effectively be double counting the farther nitrogen (N1)? Thanks in advance!

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lithium scattering paths
by Hu, Yang (HIU) 30 Mar '24

30 Mar '24

Dear ifeffit members, I would like to ask a few questions about the FEFF calculation and fitting of scattering paths between the light lithium (scatters) and transition metals (central abs.). For materials containing Li, there are Li scattering paths in FEFF calculations, but usually with low "rank" or low "importance". Through my limited experience, I often ignored those paths when treating cations-disordered materials, where Li share the same crystallographic site with other TMs. For the pristine materials, if I include the Li paths, the fitting got unstable especially for the paths degeneracy. Things became more complicated with Li extraction/insertion in cycled cathode materials. Recently I am rechecking previous data (same cif, before XASViewer and now Larix), and I could "fit" some spectra with Li paths (the fitted parameters were not so crazy), which I never managed before (I tried a lot). I am wondering if there have been developments in FEFF or software that would allow better treats of Li scattering paths in shell fitting? The behaviour of Li and their influence on the TM local structure are quite interesting and important for our works, but I rarely see literature involving Li scattering paths. I just don't know if it is worth continuing to invest time and efforts on this...... I really appreciate if you can provide some suggestions and opinions J Thanks very much, Best regards, Yang

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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 04 Mar '24

04 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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XAS data on U-oxychloride standards
by Nirmalendu Patra 15 Feb '24

15 Feb '24

Dear All, Can anyone share the XAS data collected at U L3-edge on various Uranium Oxychloride standards. ? Thank you. Kind regards, *Nirmalendu Patra*

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Problem with cif files using Larch
by Otal Eugenio 15 Feb '24

15 Feb '24

Dear all. I am trying to generate the path for fitting Mn and Ni K edge at LiMn1.5Ni0.5O2 using cif files from ICSD. I receive this error: *Elements: ['Li', 'Mn', 'Ni', 'O']Sites: [2.08337619 6.16682619 6.08352381] Li:0.980Traceback (most recent calls last): File "C:\Users\Me\xraylarch_2023_10\Lib\site-packages\larch\wxlib\cif_browser.py", line 447, in onShowCIF sites = ['%d' % (i+1) for i in range(len(sites))] ^^^^^^^^^^TypeError: object of type 'PeriodicSite' has no len()* I also attached the cif. Any hint to go forward? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

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Ir standards
by Ольга Филимонова 12 Feb '24

12 Feb '24

Hello! Does everyone have standards of metallic Ir, IrO2 etc.? (L3-edge, both XANES and EXAFS would work). Thank you! Sincerely, Olga -- Olga Filimonova Post-doc researcher - BM28 - XMaS Office: 30-1-24 Extension: 2436 European Synchrotron Radiation Facility (ESRF), Grenoble, France

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weak scattering from second-nearest neighbors for single atom catalysts
by Qiang 08 Feb '24

08 Feb '24

Hi everyone, I would like to have a discussion about the common EXAFS for single atom catalysts. It is usually observed that there is only one strong peak around 1.5A in EXAFS, and it is attributed to the nearest neighbors of O or N. Take an example of Pt1/CeO2 catalyst. Pt single atom is coordinated with a few oxygens, i.e., PtOx. These oxygens constitute the first shell of Pt. It is supposed that these O should also attach to the metal element of the support (Ce here). So there is also Pt-O-Ce structure. Why it doesnot have strong scattering peak in EXAFS? Is it that because the Pt-O-Ce formed is not ordered, or it is actually not a bond just some weak contact? Thank you very much. Qiang

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Larch version up problem
by 정은석 07 Feb '24

07 Feb '24

Hello~ I used Larch 0.9.71. until now. However, I would like to update larch and I reinstall anaconda and larch. I installed Larch 0.9.74. as following installation guide I didn't have any problems during the installation process. However, I faced problems during feffit fitting. Before, I used feffit fitting in larch 0.9.71., and then I hadn't had any problems. I only changed larch as new version. What am I doing? When I run feffit fitting, I have debugs as the below: ------------------------------------------------------------------------------------------------------------------------- File "c:\Users\Administrator\Desktop\RL\feffit_error_test\test-feffit.py", line 51, in <module> out = feffit(pars, dset) ^^^^^^^^^^^^^^^^^^ File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 645, in feffit ds.prepare_fit(params=params, other_hashkeys=dset_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 374, in prepare_fit self._generate_hashkey(other_hashkeys=other_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 291, in _generate_hashkey dat = [self.data.ek0, self.data.e0, self.data.rbkg] ^^^^^^^^^^^^^ AttributeError: 'Group' object has no attribute 'ek0' ---------------------------------------------------------------------------------------------------------------------- -- Best regards, Ph. D. Eun-Suk Jeong X-ray absorption fine structure(EXAFS+XANES) Mobile:+82-10-4628-9896

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Larch version up problem in Python, Window 10
by 정은석 02 Feb '24

02 Feb '24

Hello~ I have used Larch 0.9.71. until now. However, I would like to update larch and I reinstall anaconda and larch. I installed Larch 0.9.74. as following installation guide I didn't have any problems during the installation process. However, I faced problems during feffit fitting. Before, I used feffit fitting in larch 0.9.71., and then I hadn't had any problems. I changed larch as new version. What am I doing? When I run feffit fitting in python, I have debugs as the below: ------------------------------------------------------------------------------------------------------------------------- File "c:\Users\Administrator\Desktop\RL\feffit_error_test\test-feffit.py", line 51, in <module> out = feffit(pars, dset) ^^^^^^^^^^^^^^^^^^ File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 645, in feffit ds.prepare_fit(params=params, other_hashkeys=dset_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 374, in prepare_fit self._generate_hashkey(other_hashkeys=other_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 291, in _generate_hashkey dat = [self.data.ek0, self.data.e0, self.data.rbkg] ^^^^^^^^^^^^^ AttributeError: 'Group' object has no attribute 'ek0' ---------------------------------------------------------------------------------------------------------------------- The data(EXAFS(k)), which are inputted for feffit, have two column, k and chi. As you know, it doesn't have ek0. -- Best regards, Ph. D. Eun-Suk Jeong X-ray absorption fine structure(EXAFS+XANES) Mobile:+82-10-4628-9896

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Query: abnormal FT-EXAFS peak at ~1.1A
by Huaming 29 Jan '24

29 Jan '24

Hello! I faced an issue with fitting of FT-EXAFS data (Rh@zeolite) with Artemis. There is one distinct peak located at ~1.1 angstron. The intensity is comparable to the nearby peak of Rh-O scattering. I wonder the peak (~1.1A) is a real peak or just noise. Raw data is enclosed. Another question is why S02 can be negative in data fitting with Artemis. Cheers, Huaming

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