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

customized dead-time correction in Larch
by Esmael Balaghi 16 May '23

16 May '23

Dear Matt, Dear All, Is there a way to use our customized dead-time correction function in XAS viewer/Larch? Bests, Esmael

2 3

Re: [Ifeffit] Ifeffit Digest, Vol 242, Issue 18
by Jyoti Pandey 26 Apr '23

26 Apr '23

Thank you! With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-928-265-0599 ..................................... On Tue, Apr 25, 2023 at 9:52 AM <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: (no subject) (Anatoly Frenkel) > 2. Re: (no subject) (Kelly, Shelly Diane) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Apr 2023 13:04:16 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] (no subject) > Message-ID: > < > CAFsMoZZZy_-1G5hnw1UNEbGMA+zB6pRMBZR2OPCpXqd8bBUjCg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Joyti, > > The coordination number of Rh-C bonds is defined as the total number of > Rh-C bonds in the sample divided by the total number of Rh atoms in the > sample. > 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 > ------------------------------------------------------------------- > > > On Mon, Apr 24, 2023 at 12:25?PM Jyoti Pandey <jyotipandey51092(a)gmail.com> > wrote: > > > Hello everyone, > > > > I have a cluster of 13 Rh atoms above the graphene sheet. The first > > coordination number that I am getting is around 1.65 (which is obtained > by > > choosing a Rh-C) path. I am curious to know whether this value is the > > "exact" or the "average" coordination number w.r.t all the Rh atoms. > > > > Thanks > > > > With Best Regards > > > > Dr. Jyoti Pandey, Ph.D. > > Postdoctoral Researcher > > Department of Physics > > Central Michigan University, MI, USA > > Mobile No. +1-928-265-0599 > > ..................................... > > > > _______________________________________________ > > 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 > > >

1 0

White line position shift
by Otal Eugenio 25 Apr '23

25 Apr '23

Hi all, I am dealing with in-situ battery measurements. While I am changing the voltage, the white line of TM is changing its position and intensity. The change in intensity can be related to the order as pointed out here: https://pubs.acs.org/doi/10.1021/acsami.0c13161 But what about energy shifts when there is no change in the oxidation state? Any reference where to dig? 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

1 0

(no subject)
by Jyoti Pandey 25 Apr '23

25 Apr '23

Hello everyone, I have a cluster of 13 Rh atoms above the graphene sheet. The first coordination number that I am getting is around 1.65 (which is obtained by choosing a Rh-C) path. I am curious to know whether this value is the "exact" or the "average" coordination number w.r.t all the Rh atoms. Thanks With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-928-265-0599 .....................................

3 2

XAS Data pre-processing
by Kumar Jena 23 Apr '23

23 Apr '23

Hi Ifeffit community, I am Kumar Jena, a PhD student at the University of Auckland. I have recently collected XAS data from amorphous anatase samples. I have read and seen many resources on performing data preprocessing, such as corrections, energy calibrations, etc. However, my question is, is there a specific order for doing so, or does it vary from data set to data sets? The order in which I have done it is as follows: (I have used Athena) - Import > Align data sets > Choose E0 and apply for all the scans > Merge them > Deglith the merged data > Rebin > Normalize Please advise if it's the right way to start. I appreciate your time and help. Kind regards, Kumar -- [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.

2 2

SO2 for samples with non-planar geometry
by Joel Brugger 22 Apr '23

22 Apr '23

Dear list, We are trying to fit EXAFS from data collected on solutions within a capillary. The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. The beam is 1x2 mm (VxH). Fitting the copper reference foil, we get the expected SO2 value of ~0.7. However, the solution containing the Cu(II) aqua ion gives a coordination of 2, instead of the expected 5-6. So our SO2 for this solution is apparently ~0.25. I couldn’t find a discussion of the effect of geometry (in our case cylindrical rather than planar) on SO2. Is it possible that the low SO2 is a result of the odd geometry? Confused as ever, JOEL Joël Brugger Professor of Synchrotron Geosciences Monash University School of Earth, Atmosphere and Environment Room 257A, Level 2, 9 Rainforest Walk <x-apple-data-detectors://2> Clayton, Victoria 3800 <x-apple-data-detectors://2> Australia <x-apple-data-detectors://2> T: +61 3 9905 4898 <tel:+61%203%209902%209095> E: Joel.Brugger(a)monash.edu <mailto:Andrew.Mackintosh@monash.edu> Twitter: @JoelBrugger

3 7

Argument "h_rmax = 4" isn't numeric in array or hash
by Ryan Parmenter 15 Apr '23

15 Apr '23

Hi all, I have been using the Demeter package for a year now and have recently been experiencing an issue when importing data. The following message pops up when importing data into Athena: 10:23:55: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139. Line 139 contains: coerce Window, from Str, via { ($_ =~ m{[0-5]}) ? $window_list[$_] : $_ }; This usually pertains to line 139, but the following errors appear after the data import window is closed. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 19. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 27. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 35. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 43. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 51. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 59. 10:23:58: Argument "h_rmax = 4" isn't numeric in array or hash lookup at AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/StrTypes.pm line 139, <F> line 67. The programme still runs; however, this pop-up is becoming slightly frustrating, given the amount of data I have. I have tried to use an older version, but the issue persists. This occurs with new and old data files, which were fine in the past. Do you have any ideas on how I can resolve this? I appreciate any help you can give me.

2 1

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 >

1 0

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)

2 1

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

2 1