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

Save the date: SCC short course at BNL, Nov. 6-8, 2024
by Anatoly Frenkel 21 Aug '24

21 Aug '24

Hello, As a follow up on my previous "save the date" message, the dates of the Synchrotron Catalysis Consortium short course have been finalized (they changed from the previous dates in an attempt to resolve the conflict with other meetings). The final dates are: Nov. 6 (Wed) through Nov. 8 (Fri), 2024. The course will be held at Brookhaven National Laboratory. The course is in the final stage of approvals - after we have it officially approved I will send another update with the course agenda and registration details. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) *Stony Brook University* Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… ------------------------------------------------------------------- On Fri, May 3, 2024 at 10:58 AM Anatoly Frenkel < anatoly.frenkel(a)stonybrook.edu> wrote: > Dear subscribers: > > Please pass it along to your group members who may be interested in this > opportunity. > In continuation of the annual tradition at the Synchrotron Catalysis > Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS > short courses there since 2005, we are planning a first specialized course > targeting catalysis and electrocatalysis researchers. The course will > follow a successful model of our XAFS courses: the lectures (on the topics > ranging from in situ/operando characterization and multimodal > instrumentation to data analysis) and software demonstrations on the first > two days, followed by the hands-on data analysis session on the last day. > The program is being finalized, and we are in the process of getting the > necessary approvals from BNL and DOE. In the meantime, please, mark your > calendars and contact me if you have any questions. > > Anatoly > ******** > On sabbatical leave at Weizmann Institute of Science, Israel > ******** > ------------------------------------------------------------------- > Anatoly I. Frenkel > Professor > Department of Materials Science and Chemical Engineering (primary > appointment) > Department of Chemistry (affiliate appointment) > *Stony Brook University* > Stony Brook, NY 11794 > Email: anatoly.frenkel(a)stonybrook.edu > <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… > Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL > https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… > > Joint Appointment: > Senior Chemist > Chemistry Division, *Brookhaven National Laboratory* > Upton, NY 11973 > Email: frenkel(a)bnl.gov > https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… > ------------------------------------------------------------------- > Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

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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 08 Aug '24

08 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 01 Aug '24

01 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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