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

Larch 0.9.80
by Matthew Newville 18 Jul '24

18 Jul '24

Hi Folks, I have released Larch version 0.9.80. It's been a few months since the last announced release, and there have been a few important bug fixes and changes, especially to the Larix GUI. A list of changes is at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… . If you run Larix, you should be prompted to update. The most obvious changes in this GUI are a) the re-organization of the main menus, and b) that the different Analysis Tabs can now be re-arranged or even removed (and added back when needed). This is so that we can add more Analysis Tabs for different kinds of data processing and different kinds of data. At this point, Larix is still heavily focused on XANES and EXAFS, but we would like to be able to expand this, and still use much of the infrastructure of the GUI. I think I have addressed all the issues raised over the past couple of months and found several more in testing myself. Comments, suggestions, or bug reports are always welcome. --Matt

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Modeling a spinel structure with fractional occupancy
by matthew marcus 12 Jul '24

12 Jul '24

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Re: [Ifeffit] Modeling a spinel structure with fractional occupancy
by Robert Gordon 12 Jul '24

12 Jul '24

"Does anyone have a good idea or tool with which to do this? " Ummm...6 different metal shells at once! https://urldefense.us/v3/__https://www.amazon.ca/Generic-Pack-Sided-Dice-Bo… 10-sided happy Friday, folks! cheers, -R. On 2024-07-12 11:10 a.m., matthew marcus wrote: > A colleague want to fit EXAFS on a NiAl2O4-based material (I don't > have the details). As shown in the attached CIF, Ni (the central atom) > is distributed 60-40 between the 1 and 2 sites, and Al 20-80. I > imagine that to model this, I'll need > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > A colleague want to fit EXAFS on a NiAl2O4-based material (I don't have > the details). As shown in the attached CIF, Ni (the central atom) is > distributed 60-40 between the 1 and 2 sites, and Al 20-80. I imagine > that to model this, I'll need to somehow generate feff.inp files, one > centered around Ni1 and one Ni2, each with neighboring atoms randomly > chosen according to the site occupancies. Does anyone have a good idea > or tool with which to do this? I'd rather not have to write a program > to do that, but will if it's necessary. > mam

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problem Generating feffNNNN.dat with Larch in python
by Anis Attiaoui 12 Jul '24

12 Jul '24

Dear All, I am trying to generate the path files of a DFT structure using larch in python. I will briefly describe the methodology I am following in hope it might help shed some light to the problem I am facing. I start from a .cif file of the relaxed DFT structure of 64-atoms GeSn. Then, I try to evaluate all the possible .inp file of the corresponding absorbing atoms (Sn and Ge). I am attaching the .inp file of one site0 for Sn ( tested it through Artemis and it works fine). Then I try to call the FeffRunner module to extract the corresponding feffNNNN.dat path files that will be used to build the EXAFS spectra. It is in this step that I am facing an issue. It seems that FeffRunner is working but it doesn't generate the corresponding feffNNNN.dat path files. (I am attaching an image of what is produced when I run the FeffRunner module). Below is the python script I used to generate the .inp file as well as the paths via Larch. " from larch.xafs import FeffRunner from larch.xrd.struct2xas import Struct2XAS # read .cif DFT data with ase DFT_path = '/home/ml-dell/Documents/Simulation/exafs/DFT/' cif_file = f'{DFT_path}CIF-00010-T300K.xyz' mat_obj = Struct2XAS(file = cif_file, abs_atom="Ge") for site in range(mat_obj.nabs_sites): mat_obj.set_abs_site(site) #to get information on the coordination environment around absorber atom mat_obj.get_coord_envs_info() mat_obj.get_coord_envs() # use feff to generate .inp mytemplate = None mypath = DFT_path mat_obj.make_input_feff(radius=9.0, template=mytemplate, parent_path=mypath) # now we can run feff to generate the paths via larch feff_inp = f"{mat_obj.outdir}/feff.inp" session = Interpreter() sim = FeffRunner(feff_inp,_larch=session) sim.run() " I will be thankful for any suggestions on how to fix this issue. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!c… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

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XAS beamline scientist position open at NSLS II
by Stavitski, Eli 10 Jul '24

10 Jul '24

Dear all, Beamline scientist position is now open at the Inner Shell Spectroscopy beamline at the National Synchrotron Light Source II. ISS beamline is an XAS and high energy resolution spectroscopy beamline with a lot of research opportunities and vibrant user community. Apply at https://urldefense.us/v3/__https://jobs.bnl.gov/job/upton/beamline-scientis… https://urldefense.us/v3/__https://jobs.bnl.gov/job/upton/beamline-scientis… POSITION DESCRIPTION The NSLS-II is seeking am experienced scientist to support the user program, operations and new developments at the Inner Shell Spectroscopy (ISS) beamline, working closely with the ISS team and Hard X-ray Scattering and Spectroscopy program staff. The selected candidate will participate in internal and external scientific and technical collaborations that leverage the unique capabilities of ISS and NSLS-II. 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. Essential Duties and Responsibilities: Supports the user program at the ISS beamline. Develops and operates beamline equipment to enhance the beamline productivity and impact Collaborates with NSLS-II and BNL staff, and external users to advance scientific and technical research and development. Contributes to the design, implementation, and maintenance of in-situ/operando capabilities at the beamline and Operates and develops high energy resolution spectrometers. Supports and develops beamline software infrastructure to enable experiments with real-time data analysis and modeling capabilities. Assists with preparation of funding proposals and beamline progress reports . Required Knowledge, Skills, and Abilities: PhD. in physics, materials science, chemistry or related field, and at least 2 years of postdoctoral experience. Ability to work effectively in a team environment with a diverse group of scientists, engineers, technical staff, and users. Proven track record of using synchrotron X-ray spectroscopy including high energy resolution techniques Demonstrated experience using Python (or similar high-level, general-purpose programming language) for data visualization/reduction/analysis. Experience with XAS data analysis. Excellent written and oral communication skills. Preferred Knowledge, Skills, and Abilities: Demonstrated personal interest in research, methodology and instrumentation development aligned with the scientific mission of the NSLS-II. Experience with collaborative code development using version control platforms. Prior experience in the design, installation, commissioning, and/or operation of synchrotron beamline components. Experience in quantum chemistry-based XAS data analysis Experience in high throughput measurements and data analysis. Experience in supporting users at a user facility. Other Information: Brookhaven Laboratory is committed to providing fair, equitable and competitive compensation. This is a multi-level role and the full salary range for this position is $101200 - $184000 / year. You will be placed at the level and salary commensurate with your experience. Salary offers will be commensurate with the final candidate’s qualification, education and experience and considered with the internal peer group. 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://urldefense.us/v3/__https://www.directives.doe.gov/directives-docume… [Image] Eli Stavitski 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://urldefense.us/v3/__https://www.bnl.gov/nsls2/beamlines/beamline.php… >[Title: LinkedIn - Description: image of LinkedIn icon]<https://urldefense.us/v3/__https://www.linkedin.com/in/eli-stavitski-a033a7… >[Google, scholar Icon in SuperTiny]<https://urldefense.us/v3/__https://scholar.google.com/citations?user=cVxErO… >

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Ni standard spectra
by Qiang 08 Jul '24

08 Jul '24

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Upcoming Q2XAFS, Data Formats, and request for data files
by Matthew Newville 07 Jul '24

07 Jul '24

Hi Folks, As some of you may have heard, there will be a virtual Q2XAFS (Quality and Quantity for X-ray Absorption Fine Structure) symposium series this summer, with presentations from Working Groups defined and formed at the 2023 Q2XAFS meeting in Melbourne last August. Details for this summer’s series are at https://urldefense.us/v3/__https://sites.google.com/view/q2xafs/home__;!!G_… , including a registration form. I will be giving the first of the presentations, on July 26 (0600 Seattle, 1400 London, 2200 Tokyo), describing the work of a Working Group on Data Formats and Metadata. Our Working Group has made good progress on defining a NeXuS/HDF5 definition for XAS data which is compatible with XDI and fits the typical NeXuS/HDF5 requirements. We have started working on tools to convert between XDI, NeXuS/HDF5, and even to help convert “raw” beamline data into this format, to make it easy to convert raw beamline data into these two formats for uploading to databases, data portals, supplemental information, etc. We have a pretty good collection of “real-world, as-collected” XAS data (see https://urldefense.us/v3/__https://github.com/XraySpectroscopy/pynxxas/tree… ) that we are working with as test cases. Please let us know if the data you get from your facility is in some other format (including binary files such as HDF5, or even into some database or “document store”). That is, if Larix or Athena struggles to read your data files, please let us know. If you can, please send an example file (you can send it directly to me or use https://urldefense.us/v3/__https://github.com/XraySpectroscopy/pynxxas__;!!… ). Thanks, --Matt

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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