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

determining reasonable fitting parameters
by Neil M Schweitzer 21 Jul '16

21 Jul '16

Being somewhere between a novice and an advanced user of XAS, I have two "philosophical" questions about EXAFS fitting (I hope this is the correct forum to ask them!). I also have a bug to report. I have included a project file of a CeO2 powder for those interested. 1) Generally, I have developed my own methodology for EXAFS fitting which I think generates ok fits, at least from the standpoint that the red line seems to follow the blue line pretty closely. My question relates to interpreting the statistics of the fit. Generally, I am studying catalyst (i.e. very small metal or oxide nanoclusters supported on a different oxide phase). Due to the size of the clusters of interest, I wouldn't expect them to resemble a bulk crystal, and therefore it is difficult for me to reduce the number of independent variables using know crystal structures. For example in this reference material, I am giving every single scattering path its own delR and ss, and using a single delE and SO2 for all the paths since they come from the same feff calculation. Once I am through with my own methodology, I can usually get a close fit even while making every variable a guess (refer to fit 17 in the project file). Admittedly, the reduced chi is rather large (5262) and the error of each of the DWF's is the same magnitude as the value itself, which is troubling. However, if I use the best fit values of fit 17 and set all of the values except for the 3 DWF's and generate a new fit, all of the statistics significantly improve even though the values of the DWF's did not change at all (Fit 19). That is, merely setting the other variables improved the fit (the reduced chi square is now 2951) and improved the error of the guess variables (the errors of the DWF's are cut close to half). Why is the fit better since none of the values actually changed, and why do the errors improve? How should I be reporting the statistics (i.e. the errors) in a publication? Should I report the fit 17 errors or the fit 19 errors for the DWF's? 2) In terms of the DWF's in general, what value is considered too high? I know the DWF's have a component that relates to temperature induced disorder in the scattering shell and a component that relates to physical disorder in the scattering shell, but what value would be considered too big for a sample measured at room temperature. I have seen values as high as 0.03 and 0.04 in presentations (sorry, no references) but these seems too large to me. At some point, if the sample is disordered enough, it seems like EXAFS is no longer an appropriate characterization tool to use. What value of DWF would that represent (for a sample measured at room temperature)? 3) I found a bug in the log files in the history window. I am running Demeter 0.9.21 on Windows 7. When I generate a new fit, if I change the k-range of the fit, the k-range of previous fits in the history window will also change to the current range (e.g. fit 19 was run from 2.1-9.3, as shown in the data window. Fits 14-16 were run in smaller ranges). What's even stranger, is if I go to a very old fit (i.e. fit 1 or 2 in the project file) and then go back to the new fit, the log file will report the k-range from the earlier fit, not the current fit. Obviously, this is making it very difficult to keep track of fits generated with different k-ranges. I have not tested to see if the R-range behaves similarly. Neil

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fitting of S XANES with arctans and gaussians
by Matthew Marcus 19 Jul '16

19 Jul '16

I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica Acta 99 (2012) 206–223. In this paper, they fit spectra to two arctangents and 6 gaussians, with widths of the arctans slaved together and widths of gaussians 1-3 and 4-6 slaved (or all 6 to one value). I'm looking for recommendations as to how to do the fit. They give prescriptions for how to set the initial estimates to give robust values. Manceau has told me that 'Athena works quite well', but I don't see any obvious way there to do the parameter constraints called for, or to keep peak heights from going negative. Athena also has a habit of assuming you want it to do the normalization for you; I've already done that and need no further 'help'. Any ideas? I've tried using Genplot, but that offers no way to restrain parametsrs to ranges to keep them from going nuts. PCA seems to want 6-8 components, so it's not all that helpful. These spectra were taken at various spots on a biological structure (abalone radula) so there's no sense of sequence which would enable the use of evolving factor analysis or something like that. LCF doesn't give satisfying fits with the references I have. I've attached a couple of the files, truncated to the range Manceau&Nagy fit to. The originas were taken over the range 2460-2550eV. mam

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Artemis - Atom/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

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Artemis - Atoms/Feff issues
by M.F.Bertuzzo 18 Jul '16

18 Jul '16

Dear all, Having a spot of trouble with Feff calculations at the moment, any help would be much appreciated. A little info before I describe the problem: I have performed Crystal14 calculations on a system to optimise its geometry. After completing this, I opened the output file in J-Ice so that I could then save the file in .pdb format, so I could then open it inside of Mercury (v3.8) which would then allow me to save the file as a .CIF, to be used for Feff a calculation in Artemis. All okay so far. But, when I open the CIF file inside of Artemis it thinks that some of the atoms sit only 0.02Angstroms apart from one another - obviously wrong. Yet when the file is viewed in Mercury (or whatever graphical interface you wish to use) it correctly displays the atoms, as opposed to Artemis which is somehow populating 500+ atoms within a small distance of just 5 Angstroms. Is this something to do with the Cluster size? I have tried to arbitrarily increase it to a higher number to prevent it from finding atoms just 0.02Angstroms apart, but even then it locates atoms 0.14Angstroms apart which is still wrong. I have attached the structure (in .XYZ format) I am trying to work on so you can view it as well as its CIF format that I have been trying to open up inside of Artemis to run Feff. Thanks for any assistance! Marcus Postgraduate Researcher in Chemistry University of Kent

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Artemis Antisite Simulation
by #GUPTA DISHA# 15 Jul '16

15 Jul '16

Dear All I am trying to simulate data for antisite disorder for LFP data. I import the CIF file and make sum of all the paths and save the file as an artemis file. I do this for different ratios of Li/Fe sites. However, I want to compare all these data in Origin. How do I open these artemis files in Origin to see how my data varies with different Li/Fe antisites? Thank you and Kind Regards Ms. Disha Gupta PhD Student School of Materials Science & Engineering (MSE) Nanyang Technological University 50 Nanyang Avenue, Singapore 639798 Tel: (65) 84087404 | Email: disha001(a)e.ntu.edu.sg ________________________________ 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: Wednesday, July 13, 2016 1:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, 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 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. Artemis (FEFF) question (Louis Forto) 2. Re: Artemis (FEFF) question (Matt Newville) 3. Re: Artemis (FEFF) question (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Jul 2016 10:13:17 +0100 From: Louis Forto <cforto10(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Artemis (FEFF) question Message-ID: <CAOfHeiQnRSZX98TrKvDasc2t1WB1gq1xBmboA_T3k3RwkBNbhQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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No Reference Foil... Continued
by Neil M Schweitzer 14 Jul '16

14 Jul '16

Thanks for the responses. When I had originally tried fitting the CeO2 data, the fit was awful, but I think it was because the Eo was really far off. I set it close to where it should be and was able to find a common feature in Io to calibrate the rest of the samples to. That being said, fitting CeO2 is still quite difficult. I found a reference online (EXAFS analysis of the L3 edge of Ce in CeO2: effects of multielectron excitations and final-state mixed valence: J. Synchrotron Rad. (1999). 6, 34-42) that, from my understanding, essentially suggests duplicating all the paths and using a second delta_Eo value for the duplicated paths while also weighing the SO2 of each set of paths based on the degeneracy of the excitations. This does tend to make the fit better (as one would expect from doubling the number of paths!), but does anyone know if this is a generally accepted correction for fitting ceria materials? Does anyone have a different reference that might help me? Thanks for all the help! Neil

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No Reference Foil
by fred.mosselmans＠diamond.ac.uk 13 Jul '16

13 Jul '16

Dear Neil, Sorry this may be too exact an interpretation of your English, but if you are looking at the exafs then calibration is normally pretty irrelevant as long as it is not wildly out, as you refine E0 anyway in the fitting. The bond distances will be very little altered by this. If you are looking at XANES and it is 3/4 then CeL3 as I am sure you know has two "white lines" for four and one for three and the ratio of the two peaks can be used to Look at oxidation state mixtures, I think you should be able to align the peaks and fit the area e.g. Burnham AD, Berry AJ, 2014, The effect of oxygen fugacity, melt composition, temperature and pressure on the oxidation state of cerium in silicate melts, Chemical Geology, Vol:366, ISSN:0009-2541, Pages:52-60 Best wishes Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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No Reference Foil
by Neil M Schweitzer 12 Jul '16

12 Jul '16

Hello, Long time follower/user and first time subscriber! I work at Northwestern University, and one of the services I provide is analyzing XAS data for users who collect data at APS. Generally, I am not at APS to help them collect spectra, I help analyze the data afterwards. A user came to me recently with some Ce L3 data that does not have reference foil data. If I am trying to compare the EXAFS of several different samples (all which should be similar oxidation state, and of which I have other references of similar oxidation state). Does anyone have a suggestion how to work up the data if I can't calibrate it? ------ Neil M. Schweitzer, Ph.D Operations Director, CleanCat Core Facility Research Assistant Professor Chemical and Biological Engineering Northwestern University 2137 Sheridan Road Evanston, IL 60208-3000 Office: 847-491-2955 http://cleancat.northwestern.edu

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Artemis (FEFF) question
by Louis Forto 12 Jul '16

12 Jul '16

Dear All, I am trying to run a FEFF calculations on a quaternary glass , when I import crystalline data obtained from ICSD website and try to run FEFF to calculate the scattering paths of nearest neighbour atoms relative to absorbing atom, I get an error message that says " generate one or more common positions and their occupancies sum to more than 1". I don't know how to go about this, any help , I will appreciate. Thanks.

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Athena crash on mac on import
by George Sterbinsky 08 Jul '16

08 Jul '16

Hello, Athena crashes upon import of the attached project file. I am using the latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open the file on windows. The message that is printed to the terminal when Athena crashes is pasted below. Please let me know if any further information would be helpful. Thank you, George [!!!] bkg_funnorm is not an attribute to set for Demeter::Data=HASH(0x7fe2e57967c8) at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm line 9. MooseX::SetGet::set(Demeter::Data=HASH(0x7fe2e57967c8), "bkg_spl2e", 110.195726042215, "y_offset", 0, "bft_rwindow", "hanning", "fft_kwindow", "hanning", ...) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 411 Demeter::Data::Prj::_record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 5, "psmtj") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm line 197 Demeter::Data::Prj::record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 1) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 802 Demeter::UI::Athena::IO::_prj(Demeter::UI::Athena=HASH(0x7fe2dc0226a8), "/Users...sta"..., "/Users...sta"..., 1, "") called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm line 164 Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 859 Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840), Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 782 Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x7fe2e28ff570), Wx::CommandEvent=SCALAR(0x7fe2e5781840)) called at /opt/local/bin/athena line 44 eval {...} called at /opt/local/bin/athena line 44

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