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

Demeter Installation issues
by Gaurab Rimal 23 Aug '16

23 Aug '16

Hello, I have been trying to install demeter in my archlinux machine but have issues in the build process. I had issues installing pgplot from ifeffit git source so I installed pgplot separately (as outlined in the original pgplot instructions). After installing ifeffit and after all dependencies were met, I ran ./Build and got an error about 'cpg/libgcc_path.sh'. Below is the full output from ./Build. I am unsure of this error because it seems to be related to ifeffit and pgplot and do not know how to resolve this. $ ./Build Ifeffit's installations directory is /usr/local/share/ifeffit (found by capturing `ifeffit -i`) Compilation flags (from /usr/local/share/ifeffit/config/Config.mak): -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath cc -I/usr/lib/perl5/core_perl/CORE -fPIC -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -o src/ifeffit_wrap.o src/ifeffit_wrap.c cc: error: `/cpg/libgcc_path.sh`: No such file or directory error building src/ifeffit_wrap.o from 'src/ifeffit_wrap.c' at /usr/share/perl5/core_perl/ExtUtils/CBuilder/Base.pm line 174, <C> line 11. Gaurab

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Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17
by Christopher Thomas Chantler 13 Aug '16

13 Aug '16

Topic 1: We have a routine /edit within ifeffit (our modified version) which propagates and fits uncertainty. Working on a couple of minor details before passing it on to Matt and Bruce for general use. Topic 3: Monochromator glitches should be eliminated in absorption spectra under normal circumstances if the dark current estimation is well defined. I recommend careful measurement and recording of this for all spectra. ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, 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 chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ 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: Friday, 12 August 2016 11:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 162, Issue 17 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. Statistical errors in linear combination fits (Joshua Kas) 2. Re: Statistical errors in linear combination fits (Bruce Ravel) 3. Athena interpolation when removing mono glitches (Michael Gaultois) 4. Re: Athena interpolation when removing mono glitches (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Aug 2016 13:31:45 -0700 From: Joshua Kas <joshua.j.kas(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Statistical errors in linear combination fits Message-ID: <CAHuhYRm_Dx5+_HAUuOZ0nCwzXwCrS-Subxb9dmBXDsQp8wmSRQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Athena interpolation when removing mono glitches
by Michael Gaultois 12 Aug '16

12 Aug '16

Dear members of the Ifeffit list, I recently collected some EXAFS data with some significant monochromator glitches that I am looking to remove. I have used a python script graciously written by the beamline scientist to remove the offending regions, but when I import the data into Athena, Athena does some funny business in an attempt to join together the regions outside of the data gap. (See the bending away in the dataset and/or attached image.) I have confirmed by plotting with other software that the strange step-like behaviour in the mu(E) is present only after importing into Athena (the raw data is fine). I have looked through the mailing list archives and also the user manual, but can't seem to find anything that explains it, or other people who have experienced this problem in the past. From what I can determine, Athena joins together the segments to obtain a linear interpolation in the norm(E)? This leads to a warping in the mu(E). ==How does Athena try to treat this data?== I was wondering if other people have had similar issues, and what steps can be taken to remedy the problem. For example, replacing removed data points with artificial points along a linear interpolation would be possible, but the act of adding artificial points that don't exist is concerning to me. ==What is the best way to treat data with mono glitches to reduce spurious features not intrinsic to the sample?== If you are interested, I have included links to .prj datasets and images to highlight these problems below. With thanks for your time, Michael ---------- .prj file with 4 ways of working up the same data: http://bit.ly/2bnfNZ5 1) raw data 2) mono glitches removed 3) rebinned data 4) rebinned and manually removed points (This leads to some strange-looking features in k-space, and this would be less than desireable on the many datasets we have collected) images to highlight these problems: a) mu(E) http://bit.ly/2aYaJIf b) norm(E) http://bit.ly/2aYaX27 c) k http://bit.ly/2baWh0h

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Statistical errors in linear combination fits
by Joshua Kas 11 Aug '16

11 Aug '16

Hi All, I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Thanks in advance for any help and sorry if this info is already available in the archives, Josh Kas

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 09 Aug '16

09 Aug '16

Hello All, I apologize in advance if this is not the correct method to reply to the thread. Thank you for your replies and suggestions. I will look further into determining the atomic structure of the Hf-Al intermetallics through their papers. Once I obtain this information, how do I go about creating the actual CIF file? Can I just open up any arbitrary CIF file and then change the parameters and name to match that of the Hf-Al systems? Lastly, going through some CIF files from crystallography.net, I notice that some of the 3D models from the CIF has a different stoichiometry from the designated crystal. For example, I have attached a CIF file of SiO2 that I have found; however, the 3D representation only has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity? Regards, Ed Han

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Ti data problem
by Siliang Chang 08 Aug '16

08 Aug '16

Dear all, I am new to XAFS data analysis. Im currently working on the XAFS data of atomic layer deposited mixed oxide thin film: SnTiOx. I have both Sn and Ti K edge data, and was able to fit Sn edge using a model of (Sn,Ti)O2 solid solution. However, Ti data really confuses me (please see attached file). With Rbkg set to 1, there is a doublet in 1-2 Å region in every data, this is something I have never seen in the literature. Im wondering if this is normal? Does this mean I should set a larger Rbkg value, say, around 1.5? Ive tried to fit the abovementioned Ti data using several models: anatase, rutile, (Sn,Ti)O2 solid solution, perovskite (N is fixed at 6 for all of those), so far no success. I would really appreciate if you can comment on my data processing, any suggestions are welcomed, as Im new to this, Im not sure if Im doing it the right way. Thank you very much. Best regards, Siliang Chang

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Converting PDF files to CIF files for usage in Artemis
by Ed Han 08 Aug '16

08 Aug '16

Dear All, In the upcoming fall, my research group plans on performing XAS studies observing the Hf L3-edge for various Hf-Al intermetallic samples. In preparation for the experiments, I am looking for CIF files of the various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc. Upon scavenging through a multitude of crystallographic databases, I was not able to find any CIF files of Hf-Al intermetallics. However, I have acquired powder diffraction files (PDF) for said intermetallics. Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to my knowledge), is there a way to convert PDFs into CIFs? I have attached one of the PDF files to demonstrate what information it contains. I would really appreciate your help! Regards, Edmund Han

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Amorphous
by Carlos Triana Estupinan 08 Aug '16

08 Aug '16

Dear Bruce I want to know if it is possible to obtain a 3D structure (.cif file) of an amorphous material from the EXAFS fitting carried out from artemis. I mean, there is a way to extract a .cif file with the structural data obtained from the refined spectra. Also, in amorphous materials there must be a distribution of interatomic bond distances and coordination, and so, how can I address such a structural distribitions. Regards.

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Multi-electron peak in Yb
by Matthew Marcus 05 Aug '16

05 Aug '16

Does anyone know of data on multi-electron peaks at the Yb L3 edge? One of the users here was just running Yb and finds on every spectrum a bump at the same energy. It's not a Bragg glitch from the sample or an I0 glitch or any other obvious artifact. It reminds me of the two little bumps at Ce. If someone has analyzed and parameterized this peak as a fraction of edge jump, then it would be possible to subtract it off. The attached papers show exmples for almost every lanthanide *execpt* Yb. For those doing Ce, I've written a program which does the correction, essentially as presented in the attached Gomilsek paper. Like Ce, Yb hs 2 valence states (other than 0), but the user is sure that his sample is all 3+. mam

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Re: [Ifeffit] Questions about fitting of EXAFS
by Scott Calvin 04 Aug '16

04 Aug '16

Just to clarify: the shape of the FT may certainly change when you change kmax. But if the data and the model change in the same way, then the fit is insensitive to the choice of kmax, in the sense that the fitted parameters remain stable to within their reported uncertainties. —Scott Calvin Sarah Lawrence College On Aug 4, 2016, at 2:50 PM, Fuxiang Zhang <zhangfx(a)umich.edu<mailto:zhangfx@umich.edu>> wrote: The Kmax effect on the shape of magnitude of FTs of one of my samples may come from the low signal/noise ratio.

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