April 2023 - Ifeffit - millenia.cars.aps.anl.gov

Scattering paths in Artemis
by Jyoti Pandey 13 Apr '23

13 Apr '23

Hello everyone, I have a question regarding the scattering paths. Can we manually feed the scattering paths in artemis or it will only read from the feff input file. Thank you. With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-9282650599 .....................................

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Exporting XANES data as a .csv file
by Kumar Jena 13 Apr '23

13 Apr '23

Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k) Is it possible to do so in Athena? Any help would be appreciated. Kind regards, Kumar [image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email.

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Q2XAFS, Aug 17 and 18, Melbourne, Australia
by Matt Newville 05 Apr '23

05 Apr '23

Hi Folks, As a reminder to all interested, there Q2XAFS meeting will be August 17 and 18, 2023. See the attached flyer for details, and hope to see some of you there. --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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developer Zoom meeting
by Matt Newville 05 Apr '23

05 Apr '23

Hi Folks, As I mentioned a few weeks ago ( https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2023-March/010594.html) we are trying to start a monthly Zoom meeting to talk about the development of Larch and related tools. The first of these meetings will be this Friday, April 7 at 9 AM Chicago (1400 UTC, I believe). I'm reluctant to publish the Zoom link on this forum, but if anyone is interested, send me a direct email. I know this time is not convenient for many of you. If you would like to participate but cannot make this meeting, please let me know. I think the first order of business will be to work on a better day/time and organization. Thanks, --Matt Newville <newville at cars.uchicago.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 241, Issue 13
by van der Veer, Siebe 04 Apr '23

04 Apr '23

Dear Matt and Robert, Thanks for the feedback and information. I'll play around with the file and indeed think about what it means for what I'm trying to achieve. Best, Siebe On Fri, Mar 31, 2023 at 7:02 PM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Fortran runtime error when running feff on Hydrotalcite > cif (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Mar 2023 14:50:26 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Fortran runtime error when running feff on > Hydrotalcite cif > Message-ID: > < > CA+7ESbr_33qqQo4midvNcO3rQdrCu00KB9nNGY6WyeZhsc-NpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Siebe, > > Sorry for the trouble. I agree with Robert's suggestion to check whether > "Wat" might be causing the problem. > > The CIF Browser and Feff runner in XAS Viewer does actually support > fractional occupancies, by randomly assigning atoms to match the partial > occupancy (but of course, not with great precision -- each X, Y, Z position > has exactly one actual atom of a determinant Z). That allows a lot CIF > files to "just work" that would otherwise need manual intervention. At the > moment (and possibly for the foreseeable future), the CIF Browser does not > support editing the CIF directly, but does support editing the result > Feff.inp file, but one can export a CIF, edit that elsewhere, and then > import it. > > What I see trying to run a calculation from that CIF file is that there are > many oxygen atoms that are too close together. Like Robert suggested, I > suspected these come from the "Wat", but when I removed those and the H > atoms, the prolem still happened. As Robert listed the atomic positions > for this structure, I think it might actually be the "C", "O2", as well as > the "Wat" with the low occupancy of "0.0833" that might be the problem. > > If I remove CO groups and Waters, these to generate the attached CIF (I > changed the ID number) that seems to run, though I don't know if it is then > the structure you actually are trying to model ;). > > --Matt > > > On Thu, Mar 30, 2023 at 6:51?AM van der Veer, Siebe <s.van.der.veer(a)rug.nl > > > wrote: > > > Dear all, > > > > I'm trying to run feff on the Hydrotalcite cif file as can be found in > the > > Larch Am Min CIF browser and I get the following error: > > > > > > *At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran > runtime > > error: Bad real number in item 2 of list input* > > > > I've been able to gather that this means there is some unreadable input > in > > the file that is been used, but I don't know what file this is so I don't > > know what the actual bad input is and what has caused it. > > > > Any help is greatly appreciated! > > > > Kind regards, > > > > > > -- > > *Siebe van der Veer* | *PhD student* > > Nanostructures of Functional Oxides | Zernike Institute for Advanced > > Materials > > University of Groningen | Nijenborgh 4, 9747 AG Groningen | The > Netherlands > > Email: s.van.der.veer(a)rug.nl | > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 >

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