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

Open postdoc position in the APS Spectroscopy Group
by Sterbinsky, George E. 04 Oct '21

04 Oct '21

Hello all, The Advanced Photon Source Spectroscopy Group currently has an opening for a Postdoctoral Research Associate in the area of x-ray absorption spectroscopy. Interested candidates can view the full position description and apply at https://argonne.wd1.myworkdayjobs.com/en-US/Argonne_Careers/job/Argonne-Nat…. Best, George George E. Sterbinsky, PhD X-ray Science Division Advanced Photon Source Argonne National Laboratory sterbinsky(a)anl.gov

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S02 selection from reviewer
by Peng Liu 03 Oct '21

03 Oct '21

Dear IFEFFIT members, I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. " 1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples. At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. " We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great. -- Best Regards, Peng Liu

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Open postdoc position at SSRL for theorist (DFT)
by Bone, Sharon 17 Sep '21

17 Sep '21

Hello Everyone, SSRL has an open postdoc position for a researcher with expertise in DFT, especially in application of DFT to X-ray absorption spectroscopy analysis. Please see the listing here if you are interested: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/SSR… Thanks! Sharon Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

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SSRL User Meeting Sept 20-24: Session on XAS +Theory for Environmental Systems
by Bone, Sharon 17 Sep '21

17 Sep '21

Hi All, The annual SSR:/LCLS User Meeting is coming up Sept 20-24th. I am advertising a session on Thursday, Sept. 23rd, titled: "Enhancing X-ray Spectroscopy with ab initio and classical computational tools to understand environmental processes" Agenda: https://events.bizzabo.com/SLAC-UsersMeeting-2021/agenda/session/565625 In this workshop, we will examine how theoretical tools, such as DFT and MD, can be used to aid interpretation of XAS data and enhance understanding of chemical structure and reactivity in environmental systems (e.g., for biogeochemical and geochemical applications). The User Meeting will be held virtually this year and registration is free. You can find the registration link here: https://events.bizzabo.com/SLAC-UsersMeeting-2021/home We hope to see you there! Best, Sharon Bone, Ritimukta Sarangi and Jocelyn Richardson Sharon Bone, PhD Beamline Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory (650) 926-3104

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EXAFS Fitting with 2 CIF files
by Zihao Yan 13 Sep '21

13 Sep '21

Dear Ifeffit members: I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS fitting, I imported 2 CIF files on Artemis and generated the following 3 paths: >From PtO2: Pt-O @ 2.07 nm >From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm Then, I used these 3 bonds to do the fitting as in the online tutorial (which used 1 CIF file). The fitting result is good in terms of R^2 but it is not scientifically correct. I think I didn't set up a parameter which determines the ratio between CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how much each CIF contributes to the fitting or the molar ratio between PtO2 and Pt3Fe in my system. Could someone please give me some suggestions on how to do EXAFS fitting with 2 CIF files? Is there anywhere I can set up the molar ratio between PtO2 and Pt3Fe? Yours sincerely, Zihao Yan

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Re: [Ifeffit] Ifeffit Digest, Vol 223, Issue 9
by Moreau, Liane Michelle 08 Sep '21

08 Sep '21

Dear Matts, Thank you for helping Shinhyo sort out his saving problem. Now we can do science! I appreciate your help (as someone who is less technologically inclined I was pretty lost as to suggestions). It was kind of you to take the time to work with him. Thank you, Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073 ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Tuesday, September 7, 2021 7:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 223, Issue 9 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… 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: IFEFFIT file saving issue (Bang, Shinhyo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Sep 2021 02:25:50 +0000 From: "Bang, Shinhyo" <shinhyo.bang(a)wsu.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] IFEFFIT file saving issue Message-ID: <DM6PR01MB48596919474C38ED6664E81F97D49(a)DM6PR01MB4859.prod.exchangelabs.com> Content-Type: text/plain; charset="euc-kr" Dear Matthew, I can certainly save the files onto a folder directly under the C: (although I have to point out that I had/have only English alphabets in the folder names). Thank you very much. I appreciate your support. Best, Shinhyo ________________________________ ?? ??: Matthew Marcus <mamarcus(a)lbl.gov> ?? Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> ?? ??: 2021? 9? 7? ??? ?? 7:14 ?? ??: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> ??: Re: [Ifeffit] IFEFFIT file saving issue This probably isn't relevant, but Desktop is actually a folder under c:. On my computer, it's C:\Users\MAMarcus. I see that 'other Matt' concurs with this and seems to be suggesting that your username may have non-ASCII characters. I'm guessing Korean. Try making a new folder under C:\ with only ASCII characters in the name. mam On 9/7/2021 6:25 PM, Bang, Shinhyo wrote: > Dear Matthew, > > I tried to save a project to "Desktop" which had no parent folder, but > the same problem occurred. I think the non-ASCII character is not the > only problem. > Still, I can save onto a usb from now on. Thank you very much. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matt Newville <newville(a)cars.uchicago.edu> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov> > *?? ??:* 2021? 9? 7? ??? ?? 6:06 > *?? ??:* XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > Hi Shinhyo, > > Again, I would ask to check that the folder you are having trouble > saving to has any non-ASCII characters. For sure, ifeffit and demeter > are not going to be able to handle folder or file names with non-ASCII > characters. > > Larch is slightly better at this - it can work with files with names in > non-ASCII text encodings. To be clear, the situation with Larch is > still not ideal, especially on Windows, because > a) the base installation folder can contain only ASCII characters, > and cannot contain any spaces (apparently this is some problem > with other libraries or possibly some other variation on point b). > b) the concept of "localization" on Windows machines is sort of a > mess and many libraries (at least, from Python) don't handle this very > well. For Larch, we recently had to explicitly set locale to be "simple > C / ASCII". That sort (or should!?) mean that you can read/write files > and folders with non-ASCII characters, though I'm not certain that will > work for all character encoding sets. It's possible this will get > better with time, but it's not something that we can solve. > > For ifeffit / demeter there is simply no hope for non-ASCII text to ever > be handled. > > > On Tue, Sep 7, 2021 at 7:45 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu > <mailto:shinhyo.bang@wsu.edu>> wrote: > > Dear Matthew, > > I tried to save the project onto a usb, and it WORKed! Thank you so > much for your help. > > Best, > Shinhyo > ------------------------------------------------------------------------ > *?? ??:* Matthew Marcus <mamarcus(a)lbl.gov > <mailto:mamarcus@lbl.gov>> ?? Ifeffit > <ifeffit-bounces(a)millenia.cars.aps.anl.gov > <mailto:ifeffit-bounces@millenia.cars.aps.anl.gov>> > *?? ??:* 2021? 9? 7? ??? ?? 4:11 > *?? ??:* ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov> > <ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > *??:* Re: [Ifeffit] IFEFFIT file saving issue > There are other characters that Windoze doesn't like in filenames: > |\/*":<>? > mam > > On 9/7/2021 3:58 PM, Matt Newville wrote: > > Hi Shinhyo, Liane, > > > > On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo <shinhyo.bang(a)wsu.edu <mailto:shinhyo.bang@wsu.edu> > > <mailto:shinhyo.bang@wsu.edu <mailto:shinhyo.bang@wsu.edu>>> wrote: > > > > Thank you for the response. > > The OS is Windows 10. > > In addition to the symptom that was described aforehand, Athena > > freezes when I try to save the file. > > > > > > Is it possible that the folder or file you are saving to has a space or > > other non-ASCII character in it? I believe that non-ASCII characters > > are known to cause problems. > > Can you check whether you can save a file anywhere (maybe even the > > top-level "C:\" folder)? > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > <mailto:Ifeffit@millenia.cars.aps.anl.gov> > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin…> > Unsubscribe: > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > <https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…> > > > > -- > --Matt Newville <newville at cars.uchicago.edu > <https://urldefense.com/v3/__http://cars.uchicago.edu__;!!JmPEgBY0HMszNaDT!9…>> > 630-327-7411 > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… > Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option… > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/listin… Unsubscribe: https://urldefense.com/v3/__http://millenia.cars.aps.anl.gov/mailman/option…

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IFEFFIT file saving issue
by Moreau, Liane Michelle 08 Sep '21

08 Sep '21

Dear fellow XAFS enthusiasts, My student is running into some trouble in that he can't seem to get any files from IFEFFIT (be it project or exported data files) to save on his computer. When he saves, no files show up in the folder he has saved to. I watched him do this myself to confirm this is indeed the case. I have never run into this issue, nor have I heard of anyone else having this issue previously, but has anyone else run into this issue, and, if so, how did they solve it? I imagine there might be something incompatible with the student's computer settings somehow, although he is able to use the software just fine, it is just that nothing will save. He tried uninstalling and reinstalling Demeter, but unfortunately that did not fix the problem. I appreciate any experience anyone can share that might be helpful. Thank you! Liane Liane Moreau, PhD Assistant Professor Department of Chemistry Washington State University 509-335-6073

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EXAFS fitting - noisy data
by Hu, Yang (HIU) 01 Sep '21

01 Sep '21

Dear Ifeffit members, I have some fundamental questions regarding noisy data, and I am wondering how to tell whether the data quality worth doing Fourier transformation/EXAFS fitting or not. For example, the attached MnO chi(k) data becomes noisy from 7 Å-1 when it was measured up to 12 Å-1. The deglitching (left: red -> blue) mitigated the strong dips but the high-k end still has too much noise. I practiced the FT and fitting the 1st and 2nd shells by using the lower part. But My questions here are: 1) How noisy would be too noisy? Like the data between 8 and 10 Å-1 in the attached file, can they still be included for the FT? 2) We can choose the high-k end based on the signal-to-noise ratio, but to what extend? With data being noisy from even 5 or 6 Å-1, can they still be used? 3) For fitting the 1st and 2nd shells, I still lack of clear understanding how the high-k portion can influence. If I measure a set of samples, and one of them has much noisy data so a shorter k-range is picked up for background subtraction and FT. In this case, can I still consider the change or evolution in the fitted parameters systematic? Thank you in advance, Best regards, Yang

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Manuscript comments regarding EXAFS modeling
by Peng Liu 30 Aug '21

30 Aug '21

Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (σ²) and coordination number (CN), so any chosen value will be compensated by CN and σ². As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (σ²). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

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Re: [Ifeffit] [EXT] Ifeffit Digest, Vol 222, Issue 6
by Christopher Chantler 28 Aug '21

28 Aug '21

Just a little comment. If you propagate uncertainties, there is mathematically no difference between the weightings and expected fits for k powers times chi, so differences will mainly be in correlated parameters. Without propagating uncertainties you can get different answers in different regions of k fitting but the differences do not reflect physical parameters. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Sunday, 29 August 2021 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [EXT] Ifeffit Digest, Vol 222, Issue 6 External email: Please exercise caution 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. Manuscript comments regarding EXAFS modeling (Peng Liu) 2. Re: Manuscript comments regarding EXAFS modeling (Matthew Marcus) ---------------------------------------------------------------------- Message: 1 Date: Sat, 28 Aug 2021 10:40:37 +0800 From: Peng Liu <liupeng5182(a)gmail.com> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Manuscript comments regarding EXAFS modeling Message-ID: <CAJniE5J7VBPfTkKjU01fWUUzYoFR-DqarJmwNuLuDfK5GO2Niw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Ifeffit members, I received the following two comments. " Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a fixed value (0.85). This factor is specific to particular chemical compound and sample preparation and quality (mostly homogeneity), measurement method (e.g. absorption, fluorescence). Authors can find in literature [e.g. Rehr2000] that SO2 for ideal samples (having no other effects) represent multielectron effects, which by definition depend on valence and ligands. Even more, SO2 is correlated with Debye-Waller factor (??) and coordination number (CN), so any chosen value will be compensated by CN and ??. As coordination numbers are used as quantitative indicators in discussion and following conclusions. I would request to clarify the selection criteria for SO2 values and advise to revise this approach (i.e. not to fix SO2 as the same value for all samples). I do not expect drastic changes in obtained CN values, but this should be tested. Comment 2: As I mentioned previously, coordination number (CN) is correlated with Debye-Waller factor (??). My question is: how this correlation is managed (eliminated)? Most probably (in FEFFIT) this is done by using 3 separate values for n (1,2,3), where n is a power in expression chi(k)*(k^n). " I used Artemis for the calculation. 1) Because S02 and CN are multiplication relations in the EXAFS equation, as we usually do, we fixed S02 to obtain CN for unknown samples. 2) there are outputs regarding the correlation between different fitting parameters from Artemis. Is there a way to manage or eliminate the correlation as the reviewer mentioned using Artemis or Larch? If you also could give me some suggestions to answer the comments, that would also be greatly appreciated. -- Best Regards, Peng Liu School of Environmental Studies China University of Geosciences, Wuhan, Hubei Province, PR China https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en http://grzy.cug.edu.cn/049121/zh_CN/index.htm

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Global XAS seminar on Thursday: Ultrafast x-rays...
by Gerald T. Seidler 23 Aug '21

23 Aug '21

Dear ifeffit mailing list recipients, See seminar details below, and please send recommendations for speakers. Jerry Seidler (seidler(a)uw.edu) ------------------------------------ *Deciphering the Dynamics of the Ferrous Cytochrome c Photodissociative State Using Ultrafast X-ray Spectroscopy and Scattering Methods* Prof. Michael Mara (Northwestern University) Thursday August 26: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/92742942089 password: EXAFS *Abstract*: The femtosecond X-ray pulses provided by X-ray free electron lasers enable tracking of electronic and structural dynamics in metalloprotein active sites immediately following photoexcitation. Here, we decipher the evolution of the photodissociated state of ferrous cytochrome c using Fe K-edge X-ray absorption and emission spectroscopies, as well as X-ray solution scattering. By absorption and emission methods, we track the rebinding of the cleaved ligand and identify an electronic intermediate state involved in ligand dissociation. X-ray scattering further defines the early-time active site structure while following heat dissipation from the hot ground state of the active site into the solvent. By relating the active site temperature to the kinetics of ligand recombination, we quantify the protein bulk contribution to stabilizing the protein iron-methionine bond; this is the first direct measurement of the protein entatic state, whereby the protein regulates activity through modest tuning of the energetics of the active site. *Suggested reading:* [1] Mara, M. W. et al., Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy, Science, 2017, 356, 1276-1280. https://science.sciencemag.org/content/356/6344/1276.full [2] Reinhard, M. E. et al, Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c, Nature Communications, 2021, 12, 1086. https://doi.org/10.1038/s41467-021-21423-w -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

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XAS/MEX workshop at the Australian Synchrotron 26-27 August - Registrations closing soon! [SEC=OFFICIAL]
by MITCHELL, Valerie 23 Aug '21

23 Aug '21

[https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/3527f043-2633-a6…] Registrations closing soon! XAS & MEX Workshop [https://cdn-images.mailchimp.com/template_images/gallery/ribbon_bottom.png] [https://cdn-images.mailchimp.com/template_images/gallery/icon_clock2.gif] Thursday 26 & Friday 27 August, 2021 [https://cdn-images.mailchimp.com/template_images/gallery/icon_info2.gif] [https://mcusercontent.com/50e44d7c99f0bcbe3f66cb4e9/images/da939b82-7a45-84…] The Australian Synchrotron will be hosting a two day workshop designed for new XAS users and those interested in the capabilities of the soon-to-come MEX beamline. Registrations close at 24:00 AEST, 24 August, 2021. Program: Day 1 On the first day, talks from beamline scientists and experts in the field will highlight the capabilities of the XAS and MEX beamlines, discuss how to get the most out of beamtime, and present case studies illustrating how these techniques can help solve questions in earth, biological and chemical sciences. Day 2 Day two will feature a hands-on tutorial in XANES data analysis led by Dr. Ryo Sekine of the University of the Sunshine Coast. Opportunities will be available to discuss common data issues with beamline scientists. Presenters Dr. Niloofar Karimian, Southern Cross University Assoc. Prof. Neeraj Sharma, University of New South Wales Prof. Peter Kopittke, University of Queensland Dr. Mark Hackett, Curtin University Dr. Rosalie Hocking, Swinburne University of Technology Dr. Ryo Sekine, University of the Sunshine Coast XAS Beamline Scientists: Dr. Bernt Johannessen, Dr. Valerie Mitchell, Dr. Jessica Hamilton MEX Beamline Scientists: Dr. Chris Glover, Dr. Jeremy Wykes, Dr. Simon James, Dr. Emily Finch, Dr. Krystina Lamb Program<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_locator2.gif] Free Virtual Event [https://cdn-images.mailchimp.com/template_images/gallery/icon_share2.png] Registration is essential Click to register <https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Facebook]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Facebook<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Twitter]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Twitter<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [Website]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> Website<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> [YouTube]<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> YouTube<https://ansto.us17.list-manage.com/track/click?u=50e44d7c99f0bcbe3f66cb4e9&…> You are receiving this email because you are an ANSTO User. Edit Subscription Preferences<https://ansto.us17.list-manage.com/profile?u=50e44d7c99f0bcbe3f66cb4e9&id=0…> Unsubscribe<https://ansto.us17.list-manage.com/unsubscribe?u=50e44d7c99f0bcbe3f66cb4e9&…> [https://cdn-images.mailchimp.com/template_images/gallery/icon_contact2.gif] ANSTO New Illawarra Rd LUCAS HEIGHTS, NSW 2234 Australia [Email Marketing Powered by Mailchimp]<http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…> OFFICIAL

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Re: [Ifeffit] Ifeffit Digest, Vol 222, Issue 2
by Vitova, Tonya (INE) 17 Aug '21

17 Aug '21

Hi everybody, I would like to draw your attention to the following postdoc position: https://www.pse.kit.edu/karriere/joboffer.php?id=85889&language=en It will be great if you forward it to suitable candidates. Thank you in advance and best from me, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Montag, 16. August 2021 23:46 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 222, Issue 2 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: Problem Importing CIF files into Larch (Matt Newville) 2. Re: Problem Importing CIF files into Larch (Vincent Wu) 3. Re: Problem Importing CIF files into Larch (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Aug 2021 15:21:13 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem Importing CIF files into Larch Message-ID: <CA+7ESbrWMTGYTa+T+2u+++Qz92JQyTJFDqsFkhVZCCqMQfiXhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Amol, Sorry for the delay, I was offline most of last week. Thanks for posting these CIF files. I think these should be usable -- the basic "cif2feffinp()" function works on these to generate a valid Feff.inp, but the GUI CIF Browser is currently expecting additional fields such as publication information. I guess those fields should be optional. I think there is another issue with using multi-site CIF structures that I want to look into. So, I hope to get this fixed soon, but I also want to tackle a few other issues before posting a completely new version. --Matt On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2025(a)u.northwestern.edu> wrote: > Hi, > > I hope you are doing well. I am writing regarding some issues that I > am having with opening my CIF files in Larch. I have used these same > CIF files in the past in Artemis to run feff calculations. When I open > these files in the Larch open feff tab, it shows a dialog box saying > that there is an error opening the CIF file. This is happening with > all my CIF files and I am not sure why. I am attaching a couple of > these CIF files. I would really appreciate some help on this. > > > > Amol Agarwal > > PhD Student > > Materials Science & Engineering | Northwestern University > > > _______________________________________________ > 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 >

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Problem Importing CIF files into Larch
by amolagarwal2025＠u.northwestern.edu 16 Aug '21

16 Aug '21

Hi, I hope you are doing well. I am writing regarding some issues that I am having with opening my CIF files in Larch. I have used these same CIF files in the past in Artemis to run feff calculations. When I open these files in the Larch open feff tab, it shows a dialog box saying that there is an error opening the CIF file. This is happening with all my CIF files and I am not sure why. I am attaching a couple of these CIF files. I would really appreciate some help on this. Amol Agarwal PhD Student Materials Science & Engineering | Northwestern University

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XAFS short course at BNL: Nov. 17-19
by Anatoly Frenkel 30 Jul '21

30 Jul '21

Dear subscribers: As it does every year in the Fall, Synchrotron Catalysis Consortium at Brookhaven National Laboratory will run a short course from November 17 to 19 at BNL. As in the last year, when it gathered 80 participants, it will be virtual, and the course will be limited to 80 registered participants again. The course application deadline is August 15. It will be an introductory course, gearing at the beginner level. The link with the course information and application instructions is here: https://www.bnl.gov/xafs2021/ Please share this information with your group members and anyone else who may be interested. Thank you very much, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, 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 Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Larch 0.9.55
by Matt Newville 18 Jul '21

18 Jul '21

Hi Folks, Larch 0.9.55 is now available for download. This comes only two weeks after the announcement for 0.9.53, but there have been several important improvements especially for Windows users outside of the US, and based on bugs found or features requested during the Larch for XAFS Analysis Workshop at the Virtual XAFS 2021 conference (there was a 0.9.54, but a few things were fixed since then too!). If you have installed a recent version of Larch and are on a machine connected to the internet, you should see a notice that version 0.9.55 is available, and can use that notice to automatically install the update. That will be much faster than installing from the full installer. A series of instructional videos made for this workshop on using Larch's XAS Viewer application for various aspects of XANES and EXAFS analysis are now publicly available at https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be. Comments, questions, suggestions on these are most welcome, either on youtube or here. For folks without access to youtube.com, these videos are also at https://millenia.cars.aps.anl.gov/videos/XrayLarch/ The changes here are relatively minor compared to the changes made in 0.9.53 (see https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2021-July/010251.html) The most important changes and fixes since 0.9.53 are: - Larch's GUI applications should again work without problems on non-US Windows 10 machines. There was a serious bug (possibly since Larch 0.9.52) for using wxPython applications with Python>=3.8 and wxPython>=4.1.0. I believe we have a workaround, at least for now. - Fixes for turning CIF structures into Feff inputs and running Feff: -- more external CIF files from Crystallography Open Database and Materials Project can be converted to Feff.inp. -- external Feff.inp files can be loaded and run. -- the name of the folder created for any Feff calculation can be renamed before running Feff. - the plot selection choice in the XAS normalization panel for "one group" and "selected groups" are no longer reset each time a data set is selected. - A reference spectrum can now be set for any XAFS spectrum. When aligning or energy-shifting XAFS data, you can now easily select all of the spectra that share a reference and apply the same energy shift to those spectra. You can also easily select a reference group for one XAS spectrum and copy that to a set of other "selected spectra". There is not (yet?) a way to select a reference channel from a file when importing data, so these must be read separately and assigned. - a bug was fixed on the EXAFS / background subtraction panel on "copied groups" to ensure that processing parameters (kweight, rbkg, etc) are kept separate. - For linear combination fitting, a single energy shift can be varied during the fit, shifting the unknown data to match the combination of a (presumably aligned) set of standards. - For pre-edge peak fitting and Feff Path fitting, entries in the "fit history" can have user-specified labels which can be more meaningful than the default "Fit #1", "Fit #2", etc. - testing is now done only with Github Actions, not with the appveyor service. I want to thank all the people who took part in the workshop and gave feedback -- XAS Viewer is a lot better than it was a week ago. Thanks to Monica Bairagi and Nengchuan Tian for help, and special thanks to Klemen Bucar for helping track down and solving the Locale issue and working on the testing tools. And also thanks to Mauro Rovezzi for continued suggestions and fixes. If you have any questions, problems, or suggestions, please let me know. --Matt

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Position available: Postdoc (f/m/d) specialization in chemistry or physics
by Zimina, Anna (IKFT) 15 Jul '21

15 Jul '21

Dear all, we are looking for a chemist or physicist with a doctorate and several years of experience in the fields of catalysis, laboratory support, synchrotron radiation source, commissioning of in situ cells for X-ray absorption spectroscopy, material characterization, modelling of spectra and detailed EXAFS analysis. The main tasks include the scientific supervision of a beamline for X-ray absorption spectroscopy at the Karlsruhe synchrotron (CAT-ACT) and structural investigations of mono- and bimetallic nanoparticles for various catalytic processes. Further information can be found here: https://www.pse.kit.edu/karriere/joboffer.php?id=86224&language=en ______________________________________________________________________________________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Beamline scientist Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

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Position available: NSLS-II Quick Absorption and Scattering (QAS) Lead Beamline Scientist
by Stavitski, Eli 14 Jul '21

14 Jul '21

Dear all, NSLS-II is seeking high-profile candidates for the lead scientist position of the QAS beamline. The lead beamline scientist has a vision, defines the strategy to advance the science program, enhances the beamline capabilities and proposes facility improvements and upgrades. The lead beamline scientist develops, monitors, and maintains safe operating conditions at the beamline and provides oversight of all staff and users of the beamline. The lead beamline scientist is responsible for the operation of the beamline in support of the NSLS-II facility users, supervises a group of scientific and technical staff, reaches out effectively to the relevant scientific and industrial user communities, develops collaborative programs, and liaises with vendors. The lead beamline scientist works closely with users, oversees the design, implementation, maintenance and upgrade of the beamline equipment, provides guidance and oversees progress in advanced data management and analysis. https://jobs.bnl.gov/job/upton/lead-beamline-scientist-quick-x-ray-absorpti… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov>

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July 15 seminar: X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics
by Gerald T. Seidler 12 Jul '21

12 Jul '21

Dear Colleagues, The Global XAS Journal club is an ongoing virtual seminar series. The seminar for this week in the Americas/Europe time window is below -- you can forward this to interested persons in the XAS community but *please do not make any public posting *(we've had problems with zoom-bombing). Please email me seidler(a)uw.edu to be added to the direct mailing list, where you would get this information for both the Americas/Europe and also Asia-Oceania/Europe timed seminars. About 70 prior lectures are available at the youtube channel https://www.youtube.com/channel/UCwtkyiTV4BltKTQ7tS0CltQ/videos Looking to August and the autumn term I am particularly interested in finding: (1) XAS speakers who are early career scientists, such as postdocs, assistant professors, or new staff scientists at facilities and national labs, and (2) beamline scientists to speak about capabilities and science outcomes/goals at their beamlines. Please send suggestions! Cheers, Jerry Seidler (seidler(a)uw.edu) ---------------------------------------------------------------------------------- *X-ray Spectroscopy of Light-induced Chemical Reactions -- A New Universal Probe of Photoexcited Molecular Dynamics * Prof. Aditi Bhattacherjee (University of Iowa) Thursday July 15: 9 am Seattle (PDT), 12 noon NY, 5 pm London, 6 pm Berlin, 7 pm Moscow link: https://washington.zoom.us/j/96246359168 password: EXAFS *Abstract*: Photochemical reactions of small organic molecules are prevalent in the atmosphere, in biological machineries and photocatalytic materials. Recent laboratory breakthroughs have enabled access to ultrafast X-ray spectroscopy at the carbon K-edge (1s absorption edge of carbon, at 284 electron volts). This has opened new avenues to explore ultrafast reaction mechanisms in a host of photochemical reactions in small molecules with high temporal resolution.[1] In this talk, I will discuss experiments that show how the excitation of 1s-core electrons of the constituent carbon atoms in organic molecules is a key spectroscopic probe of photoinduced molecular dynamics. First, I will present the mechanistic details that emerge in the ultrafast ring-opening reactions of hydrocarbon as well as heteronuclear organic molecules from the direct orbital sensitivity of time-resolved X-ray absorption spectroscopy at the near edge.[2,3] Second, I will also show that in favorable cases, ultrafast intersystem crossing in molecules can be identified even though X-ray absorption spectroscopy is not directly sensitive to spin states.[4] Our work reveals that future chemical applications of this method at multiple absorption edges may provide new universal spectroscopic probes of photoinduced molecular dynamics. *Suggested reading*: [1] Bhattacherjee and Leone AccChemRes 21, 3203, 2018. https://pubs.acs.org/doi/10.1021/acs.accounts.8b00462 [2] Attar, Bhattacherjee, Das, Schnorr, Closser, Prendergast, and Leone Science 356, 54, 2017. https://science.sciencemag.org/content/356/6333/54 [3] Bhattacherjee, Schnorr, Oesterling, Yang, Xue, Vivie-Riedle and Leone JAmChemSoc 140, 39, 12538, 2018. https://pubs.acs.org/doi/10.1021/jacs.8b07155 [4] Bhattacherjee, Das, Schnorr, Attar and Leone JAmChemSoc 139, 46, 2017. https://pubs.acs.org/doi/abs/10.1021/jacs.7b07532 -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *http://faculty.washington.edu/seidler/index.html <http://faculty.washington.edu/seidler/index.html>* *seidler(a)uw.edu <seidler(a)uw.edu>*

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Another Mac OS install question
by Jilbert, Tom 07 Jul '21

07 Jul '21

Hi Ifeffit folks, I am attempting installation via macports on Mac OS Big Sur, and there are problems to build demeter. Before I send around a log file, I wanted to check if anyone is still maintaining/solving macports issues (Joe Fowler?). ie is it worth it to keep trying. From the archive it seems that installing a virtual machine is a recommended alternative. Cheers, Tom

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Farrel Lytle database
by Monica Bairagi 06 Jul '21

06 Jul '21

Hello all: I am looking forward to standard metal foil data of titanium. I downloaded the data from the Farrel Lytle database but I can not import it into Athena. I looked into the data, it looked wired for me. As Athena expects data to be in columns of energy but this data is not recorded by energy but by steps of the monochromator rotation stage. I am wondering if anyone has any idea how to import or transfer the data. I am attached herewith the data file. Thanks Monica Bairagi Ph.D. Student, Ujjain, India

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Larch 0.9.53
by Matt Newville 03 Jul '21

03 Jul '21

Hi Folks, Larch 0.9.53 is now available for download and use. Although the last announcement here was in April for version 0.9.51, there have been several improvements especially to the XAS Viewer application since the last release, mostly in anticipation of upcoming workshops and short courses. - There are important fixes for reading Spec/Bliss HDF5 files from ESRF - thanks to Mauro Rovezzi for this. You can now import multiple XAS spectra from Spec/HDF5 files. - XAS Viewer now supports doing Feff6l or Feff8l calculations and has a GUI interface for doing a Feffit fit to a sum of Feff paths. In the current GUI frame, this is limited to analyzing one dataset at a time. This brings up a related feature: - A database (sqlite3) of CIF structures from the American Mineralogist Crystal Structure Database (http://rruff.geo.arizona.edu/AMS/amcsd.php) is included. The version of this database in the source code contains about 9000 structures. If your machine is well-connected to the internet and can reach https:/millenia.cars.aps.anl.gov, a more complete version (~30 Mb) with 20,000 structures will be downloaded and used. To be clear, the 9000 structures in the smaller set are probably sufficient -- what is removed is some CIFs from publications with many similar structures (T or P dependence) or structures so large and complex that they will be hard to make into single Feff files. - The CIF files from this DB or other CIF files (well, CIF is notoriously variable!) can be automatically converted to Feff input files (using python tools from the Materials Project, modified a bit). Because many of these CIF structures contain fractional occupancy, that is handled (probably poorly, but at least not failing) by randomly selecting atoms based on the site occupancy. - XAS Viewer has a CIF Browser (from the Feff menu) where you can browse by mineral name, included atoms, etc. From that you can generate a Feff6l or Feff8l input file, potentially edit that input file, and run Feff to generate path files. These will be organized in your home folder (C:\Users\Name\larch\feff for most Windows users, $HOME/.larch/feff for Linux/MacOS). There is also a Feff browser to select Feffnnnn.dat files from your previous Feff runs and bring them into the "Feffit" tab in XAS Viewer to use in the sum of paths fitting of EXAFS spectra. Of course, all of this Feff and Feff fitting interface should be viewed as "initial release" and comments, suggestions, and bug reports are welcome. The notes above are approximately the extent of the documentation, though some videos of using this will be publicly available in a few weeks. There are updated binary installers for Windows, MacOSX, and Linux. There are also updated "GetLarch.sh" and "GetLarch.bat" scripts that also hopefully fix any earlier problems. If you have any questions, problems, or suggestions, please let me know. --Matt

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Beamline Scientist position
by Kelly, Shelly D. 01 Jul '21

01 Jul '21

Hello XAFS community: I'm excited to let you know that we have an opening for beamline scientist within the Spectroscopy group at the Advanced Photon Source. Please help spread the word. https://bit.ly/3iN7Ehe Kind Regards, Shelly Kelly Spectroscopy Group Leader Advanced Photon Source

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Question about CsNO3 L3 edge
by 田能全 01 Jul '21

01 Jul '21

Hi everyone, My colleague sent me data of liquid CsNO3 sample measured using fluorescence model. According to the attached figure, I don't understand why mu(E) increased with increasing energy before and after the L3 edge. Does it make sense for cesium? Thanks. Nengchuan [image: image.png]

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Postdoc position for XAFS analysis
by 이국승(에너지환경소재연구팀) 30 Jun '21

30 Jun '21

Dear Ifeffit members, We are looking for a postdoc candidate for XAFS analysis in PAL. Tasks will be 1. XAFS analysis of electrochemical energy materials 2. Beamline management at Nano-probe XAFS beamline (BL8C) 3. One's own research The position requires PhD degree in Electrochemistry, Chemistry, Materials science or Physics, Excellent writing and communication skills in English, Experience in XAFS analysis. The position begins at any time in this year but earlier is better. If you are interested in this position, please send your CV including list of publications to Dr. Kug-Seung Lee. (lks3006(a)postech.ac.kr) Additional documents can be required including references. Kind regards, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Scopus : https://www.scopus.com/authid/detail.uri?authorId=56953635300 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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