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

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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Problem with cif file in larch
by Otal Eugenio 25 Mar '23

25 Mar '23

Hi all, In November I was generating the feff-path in Larch using the .cif file I attached. Now I am generating additional paths from another absorbing atom and I am getting the error message "Error opening .cif file" using the same .cif file. Any ideas? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

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monthly xraylarch developer zoom meeting
by Matt Newville 17 Mar '23

17 Mar '23

Hi All, A few of us would like to start having regular (or somewhat regular) Zoom meetings to discuss planning and development goals for the xraylarch project. We would like to eventually settle on a stable-ish time for the monthly meeting. A doodle poll for the time of the initial meeting is at: https://doodle.com/meeting/participate/id/e99lKPze I will send out an announcement by March 27th of when the first meeting will be. There are many potential topics to discuss. A few that are on my mind as topics for the next months/year might include: a) supporting (and perhaps working on design) of an XAS schema for NeXuS/HDF5 b) better support for using xraylarch from Jupyter, especially plotting routines. c) creating inputs, launching, and reading of outputs for XANES calculations with Feff and/or FDMNES. d) MCR-ALS or related additional linear algebra methods. e) improvement to XRF / XRF mapping schemas, formats, and analysis. These discussions will sort of focus on what these codes and programs should do, so anyone interested in working with Larch from Python or other tools is definitely most welcome. Having input from knowledgeable "power users" or experts in the field would be great. I think we don't want this to be a support forum, but if people would also like to see "virtual office hours" (say, 1 hour per month for support questions), please let me know. Thanks, --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Looking for candidates for a PhD Thesis on the application of XAS to radioecology at the University of Nice (France)
by Lorenzo Stievano 16 Mar '23

16 Mar '23

Hi everybody, my colleague Christophe Den Auwer from the university of Nice is currently looking for candidates for a PhD Thesis on the application of XAS to radioecology. If anybody is interested, please do not hesitate to contact him. A description of the PhD project (in French and English) is joined. Have a nice day, Lorenzo Lorenzo STIEVANO Professeur Tél : +33 (0)4 48 79 21 00 <tel:+33 (0)4 48 79 21 00> Lorenzo.Stievano(a)umontpellier.fr <http://www.umontpellier.fr/> <http://www.umontpellier.fr> Institut Charles Gerhardt Montpellier UMR 5253 CNRS-UM-ENSCM D4 - Pôle Chimie Balard Recherche - 1919, route de Mende 34293 Montpellier cedex 5 - France www.icgm.fr <http://www.aime.icgm.fr> www.umontpellier.fr <http://www.umontpellier.fr>

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Re: [Ifeffit] Looking for XANES Cr(II) carbide standard (Anna Wade)
by Paktunc, Dogan 03 Mar '23

03 Mar '23

Please check Ifeffit archives. I'd posted a spectrum of Cr3C2 several months ago. Dogan Dogan Paktunc, PhD Senior Research Scientist - CanmetMINING Natural Resources Canada / Government of Canada 555 Booth Street Ottawa, Ontario, K1A 0G1 Canada Chercheur principal - MINESCanmet Ressources naturelles Canada / Gouvernement du Canada 555 Rue, rue Booth Ottawa, Ontario, K1A 0G1 Canada Cell: (343) 543-9864 dogan.paktunc(a)nrcan-rncan.gc.ca -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 2, 2023 8:43 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 241, Issue 5 ***Caution - email originated from outside of NRCan. Read the warning below / Attention- Ce courriel provient de l'extérieur des RNCan. Voir la mise en garde ci-dessous*** Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c… 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. Looking for XANES Cr(II) carbide standard (Anna Wade) 2. Re: [External] Re: XAS viewer unit detection during data reading (Edmund Welter) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Mar 2023 16:33:32 -0500 From: Anna Wade <awade91(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Looking for XANES Cr(II) carbide standard Message-ID: <CAL9RWR4oO_+1yQbUDtBZYjpbTX4En9t+FeNr2rXq3m-jdXA8Xw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Good afternoon, Does anyone have a Cr2C3 standard scan they could share? I'm looking at stainless steel powder and know that Cr carbide can be used as an additive to combat corrosion. Thanks! Anna Wade

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XAS viewer unit detection during data reading
by van der Veer, Siebe 02 Mar '23

02 Mar '23

Dear all, I am not sure if this mailing list is the correct medium for this question. Apologies, if not. I am looking to import files in XAS viewer, which worked fine in ATHENA, but in XAS viewer the correct units of the data are not detected and I cannot manually change them. I can get a plot of the data, but the data is not recognized by the software as XAS data, i.e. a lot of plotting/conversion options do not show. I hope the following screenshots provide sufficient information to illustrate my issue. Reading in a .dat file of fluorescence data. I can't change the units in the marked area. [image: image.png] The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. [image: image.png] Any advice would be much 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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