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

Fit in R or k
by LIMA DA SILVA, WILL (PGR) 12 Oct '21

12 Oct '21

Dear IFEFFIT members, I have been fitting some EXAFS data, and my supervisor and I are having doubts if it's better to fit in k or R space. What are the main differences between the two approaches? I have learnt that R space is the right approach, but I am not sure how to explain it. Much appreciated, Will Silva

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Bug report: Athena, multiple data export
by Soyoung Kim 10 Oct '21

10 Oct '21

Dear Bruce and IFEFFIT community, Hope all is well. I found a bug with Athena's file export function. I had two normalized mu(E) data with very similar spectra but different x-axis values (collected with different energy step settings). [image: image.png] When I batch exported them to a .dat file using the purple E button while "Save next plot to a file" was turned on, the resulting data only had a single x-axis column, which was taken from the first data. Hence, when I plot the two spectra from this .dat file, they now look different: [image: image.png] If I export each data individually to .dat files, then they are correct. [image: image.png] I'm attaching the Athena project file containing the two data and the .dat files I exported, both together and individually. Please let me know if anything is unclear. Thank you in advance for your help. Best, Soyoung Kim

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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 12 Sep '21

12 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 07 Sep '21

07 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 07 Sep '21

07 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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