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

Athena .lcf export file
by Miranda Vu 09 Aug '24

09 Aug '24

Hello, I think I may have found an issue in Athena regarding the LCF file export. I have been analyzing data using the LCF section of Athena. Everything looks good on the plot within Athena, but my exported file has my weighted components incorrectly labelled. For example, I have the weighted components in Athena correctly displayed here: [cid:image002.jpg@01DAEA68.340F5790] And an Excel plot of the .lcf export file here where the 3 standards are incorrectly labelled: [cid:image004.png@01DAEA68.340F5790] Has anybody else noticed this or found a solution? I have tried closing and re-opening the file, starting up new athena files, and re-ordering the standards with no luck. Thanks, Miranda

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Looking for Nb K-edge spectrum of Nb2O5
by Jiyun Hong 09 Aug '24

09 Aug '24

Dear all, I'm looking for a XAS spectrum of Nb2O5 at Nb K-edge to use as a bulk standard in XANES analysis. If possible, would anyone on the mailing list be willing to share their data with me? Thank you for your help, Jiyun

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Problem with XRF mapviewer post-update
by Sarah Bowie 02 Aug '24

02 Aug '24

Hi all, Apologies if this has already been asked elsewhere. I have previously been using XRF mapviewer with no issues on my MacBook pro (fully updated). Larch recently prompted me to update to the newest version, and following this, XRF mapviewer seems to be unable to open (tries and then immediately closes without any window ever opening). Oddly, all other programs in the Larch folder still work as normal. I've tried removing Larch, redownloading and reinstalling, and still have the same issue. Any suggestions would be much appreciated - I'm definitely regretting the update currently! I was also curious if there's somewhere I could just download an older Larch version? Thanks in advance, Sarah Bowie PhD student School of Environment, Geography and Geoscience University of Portsmouth, UK

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Periodic boundary condition when generating .inp file and scattering paths in GeSn_Larch
by Anis Attiaoui 29 Jul '24

29 Jul '24

Dear All, While generating the .inp file (attached) of a GeSn DFT structure from a .cif file (attached), I noticed some anomalies in the feff path calculation. In this specific case, we should expect Sn to have 4 nearest neighbors in the first shell. However, when the absorbing (Sn) atom is located on the edge of the supercell, the number of nearest neighbors is reduced to 2, which is non-physical. The DFT structure was generated with periodic boundary conditions (PBC). My question is the following: Is it possible to incorporate the PBC in the feff calculation process to generate the right scattering paths, especially for atoms absorbers located on the edge of the supercell? I wanted to know if there are any option in larch to deal with this specific case. I am attaching the .cif and the current .inp files that I obtained of GeSn structure. Thank you so much for your help. 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!e… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

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How to model the photoexcited charge transfer on FEFF calculation?
by FAN Dongxiao 27 Jul '24

27 Jul '24

Hello, everyone, I am doing the time-resolved XAFS, pump-pulse technique. Sample is Cu2Ti2O5, the absorber is Cu, the scatter is Ti. With photoexcitation, the one electron is excited from Cu site and transfer to neighbor Ti site. My question is how to model this photoexcited charge transfer on the FEFF software? I have tried as below: First method, To separate the absorber Cu and neighbor scattering Ti with other Cu and Ti ions, I create a cluster and modify the POTENTIALS and ION card: POTENTIALS 0 29 Cu (absorber, charge +1) 1 29 Cu 2 22 Ti 3 8 O 4 22 Ti (neighbor scatter, charge -1) ION 0 -1 ION 4 1 The results shows the chi.dat file is same for with or without ION card. Second method, Use the same cluster as the first method and the use the CONFIG card to model the charge transfer: CONFIG card 2 0 Cu Ar 3d 4 6 4s 0 4p 0 #(lost on electron from 4s) 4 Ti Ar 3d 2 0 4s 2 4p 1 #(receive on electron to 4p) But this method gives error before the run. Can some body tell where I am wrong? Best regards, Fan

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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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