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

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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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 07 Jul '24

07 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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High-r range EXAFS fitting by Larch
by FAN Dongxiao 05 Jul '24

05 Jul '24

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] Creating a structure from EXAFS fitting
by Robert Gordon 27 Jun '24

27 Jun '24

Hi Lisa, Starting from a similar crystal structure could work. Alternatively, building a basic "crystal" structure using symmetry P1 and just putting the atoms where you want them would be feasible - tedious if you have a lot of atoms, easier if you know you have higher symmetry. e.g. Test Symmetry P1 * i.e. no symmetry a = 10 b = 10 c = 10 *Angstroms, easy to scale alpha = 90 beta = 90 gamma = 90 * so metrically cubic Central atom 0.000 0.000 0.000 * at origin, could always displace by 1/2 lattice constants to keep all in the unit cell 1st NNa 0.220 0.000 0.000 * 1st nns at 2.2 Angstroms away 1stNNb 0.000 0.220 0.000 1stNNc 0.000 0.000 0.220 1stNNd -0.220 0.000 0.000 etc... I've used this for modelling molecules, surfaces (with deposited films) as well as 3D crystals. It is a bit of brute force, but should work in any crystal visualization program... cheers, -R. On 2024-06-27 8:47 a.m., Lisa Langlois wrote: > Hello XAFS friends. I would like to know how to create a structure > model for a molecule that was measured with EXAFS, then modeled using > the typical strategies? - So, in the end you have some distances and > bond angles from the central atom > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello XAFS friends. > I would like to know how to create a structure model for a molecule > that was measured with EXAFS, then modeled using the typical > strategies? - So, in the end you have some distances and bond angles > from the central atom to the first, and maybe second neighbor. > I was thinking that you start from a similar crystal structure and > then adapt that model using the numbers you got from EXAFS fitting, > using for example the Vesta program. > Best wishes, > Lisa. > > > > > Lisa Langlois, PhD > Beamline scientist > Rm 144 > Phone: +1 225-578-9341 > LSU-CAMD > 6980 Jefferson Hwy, Baton Rouge, LA 70806 > https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!adSZ4… > <https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…> > >

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Creating a structure from EXAFS fitting
by Lisa Langlois 27 Jun '24

27 Jun '24

Hello XAFS friends. I would like to know how to create a structure model for a molecule that was measured with EXAFS, then modeled using the typical strategies? - So, in the end you have some distances and bond angles from the central atom to the first, and maybe second neighbor. I was thinking that you start from a similar crystal structure and then adapt that model using the numbers you got from EXAFS fitting, using for example the Vesta program. Best wishes, Lisa. Lisa Langlois, PhD Beamline scientist Rm 144 Phone: +1 225-578-9341 LSU-CAMD 6980 Jefferson Hwy, Baton Rouge, LA 70806 https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…

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Al and Si references
by Amine EL MESSBAHI 09 Jun '24

09 Jun '24

Hi, Where can I find some Al and Si K-edge normalized data? Thank you, Amine El Messbahi email: amineelmessbahi(a)outlook.com

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alpha and σ2 values for EXAFS data fitting in Artemis came negative
by Arpita Nandy 04 Jun '24

04 Jun '24

Hello Everyone, During one of the data fittings in Artemis, alpha and σ2 came negative!!! What is/are the reason/s behind it? The corresponding file is attached... Regards, Arpita Nandy, PhD student Saha Institute of Nuclear Physics, India

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Issue about plotting simulated EXAFS in Larix
by AowenLi 24 May '24

24 May '24

Dear Matt, I am trying to simulate a theoretical EXAFS with a DFT calculated CIF file via Larix. I performed a FEFF calculation on the CIF file and imported a path to the FEFF fitting panel. However, I didn't get any results when I clicked on the "Plot Current Model" bottom. I get the following error message: TypeError: unsopported format string passed to NoneType.__format__. Could you please help me? Thank you in advance. Best regards, Aowen

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Request for Assistance with Data Import Error of Athena 0.9.26
by Cai, Rui 19 May '24

19 May '24

To whom it may concern, Here's Rui, a PhD student at Georgia Tech. I am writing this email to seek your assistance regarding an import warning I encountered while importing SSRL XAS data collected by uXAS server into Athena 0.9.26, as the Screenshot_Import Warning shows. According to the response from the Ifeffit mailing list, I clicked on all buttons in "Plugin registry", as the Screenshot_Plugin registry shows, and tried to import the same data again. However, there was still the same import warning with the another Athena warning. The data caused error has been attached. I would greatly appreciate it if you could provide guidance on how to resolve this matter. Thank you for your attention to this matter. I look forward to your prompt response. Best regards, Rui Cai

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Choice of E0 in the presence of a huge pre-peak
by Jan-Benedikt Weiss 14 May '24

14 May '24

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Re: [Ifeffit] Trouble downloading Demeter for mac
by Fowler, Joseph W. (Assoc) 09 May '24

09 May '24

Dear Christopher, I have bad news for you. I’m the official MacPorts maintainer of Demeter, and I have not been able to overcome the problems you’re seeing. I’ve seen them too over the last 1-2 years. The ifeffit package has unaddressed problems that have become fatal. I believe they correspond to small incompatibilities with the latest compilers. Over time, code that used to be allowed eventually became deprecated with a warning, and is now an error. As Matt helpfully explained (thanks, Matt!), ifeffit is basically replaced by Larch, and no one wants to update ifeffit to fix problems of that sort. Unfortunately, Demeter, Artemis, and Athena do still depend on ifeffit, and there’s no clear path to integrate that front end with the physics back end of Larch. Or at least, I discussed this a few years ago with the Demeter and Larch authors, and they didn’t see one. If indeed Larch can replace (99% of) the functionality that used to be in the Demeter and ifeffit ports in the MacPorts project, then I am inclined to remove those ports entirely from MacPorts. Otherwise, they are just sitting there, broken. By the way, I have created a `py-xraylarch` port. You could use it, although I don’t particularly recommend that. I’d suggest you use its usual installation options (such as `pip install xraylarch`). Honestly, the pip-based installation is getting so capable these days that I question why we even need MacPorts to package up any python code at all. (Should I ask that in public?) Why not use the MacPorts port? Because I’m the maintainer but not an actual user—I don’t regularly update upstream versions or make it work with the latest Python because of all its dependencies that first have to be updated. For instance, last summer I tried to make a Python 3.11 version, but I was stymied by the lack of Python 3.11 releases by some dependency. I lost interest and haven’t checked in months whether that was resolved. On the other hand, you (obviously) already installed MacPorts, so it’s at least an option if the pip method gives you trouble. Best wishes, Joe Fowler NIST Boulder Labs p.s. Here’s a politically charged question. Has this mailing list’s name falling out of sync with its range of topics, given that ifeffit is finished? On May 9, 2024, at 10:51 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.us/v3/__https://gcc02.safelinks.protection.outlook.com/?… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… > or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@millenia.cars.aps.anl.gov> When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Trouble downloading Demeter for mac (Christopher Reitwiesner) 2. Re: Trouble downloading Demeter for mac (Matt Newville) From: Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> Subject: [Ifeffit] Trouble downloading Demeter for mac Date: May 8, 2024 at 1:37:46 PM MDT To: ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner From: Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> Subject: Re: [Ifeffit] Trouble downloading Demeter for mac Date: May 9, 2024 at 10:51:01 AM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> This Message Is From an External Sender This message came from outside your organization. Hi Christopher, Installing Demeter on macOS has always been painful. The MacPorts solution can work sometimes, but it does require some expertise to use MacPorts and to think about the software as something that needs to be compiled and built. Some of the packages needed (especially "ifeffit" and "wxPerl") are just not very well supported. At this point, I cannot recommend using the old ifeffit - it has too many known issues that will not be fixed. I know that using a virtual Windows interface like Parallels works for some people. But, if you are just getting started, I highly recommend installing Larch, either using the installer at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…>(you'll have to go into Privacy & Security and allow the installer from "an untrusted source" to run. Also, it might say that it has less than a minute to go for about 5 minutes ;) ), or by downloading and running the GetLarch script at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…> and running that from a Terminal. With this installed, the Larix App (in the Larch folder on your Desktop: also, the first launch might take a minute) will run and do basically everything that Athena and Artemis do. There are some differences, and there may be a missing feature or two, but many things are better. In general, comments, complaints, and suggestions are welcome. We aim for "highly compatible and familiar" with Demeter and "better than" the underlying ifeffit library. And, it does install and run on macOS. It turns out that most of the development and testing happens on macOS. Cheers, --Matt On Wed, May 8, 2024 at 2:54 PM Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf…> Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…> -- --Matt Newville <newville at cars.uchicago.edu<https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!fZTlh9…>> 630-327-7411 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…

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Trouble downloading Demeter for mac
by Christopher Reitwiesner 09 May '24

09 May '24

Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner

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Save the date: SCC short course at BNL, Oct. 29-31, 2024
by Anatoly Frenkel 03 May '24

03 May '24

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… -------------------------------------------------------------------

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Re: [Ifeffit] Origin of noise in Ag K-Edge
by Sebastian Kunze 30 Apr '24

30 Apr '24

Dear Shelly, Robert, Matt, thank you for your kind replies, I think I should give more information about the measurement. The sample is a sealed battery anode consisting of silver particles that should undergo alloying with Lithium during charging. This is done at constant temperature and applied pressure. I repeated this experiment under different conditions several times, and each time there is less noise before a certain time during the charging process, after which is persists even when the battery is at rest (not charging/discharging). I0 also did not fluctuate much, and the integration time for each point is indeed the same. Therefore I think it is not instrumental, but rather something happening in the sample. As you can see from the spectra, the silver particles experience a strong decrease of uniform structure when they lithiate. For me, this at least explains why the noise in the post-edge increases, but can it also explain the noise in the edge and pre-edge? In any case, thank you very much for your answers! Best, Sebastian

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