July 2016 - Ifeffit - millenia.cars.aps.anl.gov

Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Just a quick idea on why I cannot import the .txt file attached with previous email. I realized that the files contain 11948 points ! (it's QEXAFS data). Athena might have an hard limit of 8200 points that may be imported in a single file. Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx -----Original Message----- From: Samy Ould-Chikh Sent: Sunday, July 24, 2016 10:56 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Bug Report importing file. Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at http://bruceravel.github.io/demeter/ XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo port install xorg-server demeter”, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

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Re: [Ifeffit] demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Hi Joe, Thanks for your reply. In my first email I forgot to mention that I did install MacPorts-2.3.4-10.11-ElCapitan. Yuan On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" <ifeffit-bounces(a)millenia.cars.aps.anl.gov<mailto:ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of joe.fowler(a)nist.gov<mailto:joe.fowler@nist.gov>> wrote: Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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demeter installation in OSX El Capitan
by Fowler, Joseph W. (Assoc) 21 Jul '16

21 Jul '16

Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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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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