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

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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