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

Re: [Ifeffit] Ifeffit Digest, Vol 242, Issue 9
by Jyoti Pandey 14 Apr '23

14 Apr '23

Thank you so much for the information. With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +91-9555347259 ..................................... On Thu, Apr 13, 2023 at 4:31 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: Scattering paths in Artemis (Matt Newville) > 2. Re: Stand Alone Atoms (Matt Newville) > 3. Re: Issue with Larch interacting with other software > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Apr 2023 12:57:16 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Scattering paths in Artemis > Message-ID: > < > CA+7ESbriDraZ4TvE7afH_gFj_Aa9R_Hyw64d9WY+0j22wa4v2Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jyoti, > > The scattering paths are held in the "feffNNNN.dat" files, and do not > necessarily need the feff.inp file that was used to generate them. It is > fine to move those around, rename them, etc. That just means that you are > then taking charge of managing and organizing them instead of letting > Artemis (or, say XAS Viewer) do that for you. > > You can definitely use different scattering paths from multiple > calculations, including those done elsewhere. > > > On Thu, Apr 13, 2023 at 10:30?AM Jyoti Pandey <jyotipandey51092(a)gmail.com> > wrote: > > > 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 > > ..................................... > > > > _______________________________________________ > > 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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Issue with Larch interacting with other software
by Luke Townsend 13 Apr '23

13 Apr '23

Hi All, Apologies if this has been brought up previously but I wanted to see if anyone else has had some issues with other software installed on the computer interacting with Larch (particularly XAS Viewer) and resulting in Larch no longer functioning. A couple of colleagues/students have been running into this issue with the SEM software AZtec. The error code that has been reported is (I'm not sure how helpful this is): 'Entry Point Not Found - The procedure entry point H5Literate could not be located in the dynamic link library C:\Program Files\Oxford Instruments NanoAnalysis\AZtec\x64\HDF5_hl.dll.' If anyone has any suggestions for resolving this (without having to run two separate computers for each software which is our current work around) it'd be thoroughly appreciated. All the best, Luke -- Dr Luke Townsend | Research Associate | MinSoc Environmental Mineralogy Group Early Career Representative & Newsletter Editor | Department of Materials Science & Engineering | The University of Sheffield | S1 3JD | +44(0)7464724397 | Twitter: @LukeTTownsend *I may sometimes send emails outside of standard office hours as this suits my working habits. Please note I do not expect an out of hours response in return.* *Latest research:* Cr2+ solid solution in UO2 evidenced by advanced spectroscopy ( https://doi.org/10.1038/s42004-022-00784-3) Sulfidation and Reoxidation of U(VI)-Incorporated Goethite: Implications for U Retention during Sub-Surface Redox Cycling ( https://doi.org/10.1021/acs.est.2c05314)

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Stand Alone Atoms
by Yasin Deep 13 Apr '23

13 Apr '23

Dear All, I want to calculate bond lengths of the SrFe2As2 parent compound for E//ab and E//c polarization with stand-alone atoms pack of the Demeter. How can I calculate bond lengths for these two different polarizations? There is a panel for polarization vector I guess that panel I should adjust. I should put (0,0,1) for E//c and E//ab (1,1,0) is this correct? What should I put let's say for 30 degrees of polarization? Thank you in advance, Dr. Yasin HACISALIHOGLU

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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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Save the date: XAFS short course at BNL and EXAFS-50 symposium
by Anatoly Frenkel 31 Mar '23

31 Mar '23

Dear subscribers, Please save the date for the two back-to-back, *in-person*, events: EXAFS-50 symposium (Oct. 30-31) and annual EXAFS short course (Nov. 1-3, 2023), both to be run at Brookhaven National Laboratory. While the usual format of our short courses is Wednesday through Friday, this year we will mark the 50th anniversary of discovery of EXAFS by organizing a two-day symposium on Monday-Tuesday to celebrate it. The short course participants will benefit from attending the symposium as well because they will be able to learn from, and interact with, leading experts in the field, credited for developing the foundations of the EXAFS experiments, theory, data analysis and modeling. Brookhaven shares with other synchrotron facilities good memories of developing new techniques and applications of EXAFS, and other labs, as well as the International X-ray Absorption Society (IXAS), are planning their own efforts to commemorate the 50th anniversary in the coming years. Regarding the short course: following up on the feedback we received after the 2022 course, we are planning to teach advanced topics in 2023. They will include but not limited to: Reverse Monte Carlo EXAFS, Molecular Dynamics EXAFS, Machine Learning EXAFS, MCR-ALS and others. More information will soon appear on the web site of the Synchrotron Catalysis Consortium that co-sponsors the short course. The other sponsors are National Laboratory and the Users Executive Committee at the National Synchrotron Light Source-II (to be confirmed). We are grateful to BNL and Stony Brook University, as well as NSLS-II UEC (to be confirmed) for the support of the EXAFS-50 symposium that will enable participants to attend it registration fee-free. Stay tuned for further updates. 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://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Fortran runtime error when running feff on Hydrotalcite cif
by van der Veer, Siebe 30 Mar '23

30 Mar '23

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 |

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