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

artemis doesn't read user's epsilon(k)
by Victor Streltsov 18 Sep '16

18 Sep '16

Hi Bruce, Epsilon(k) input "A user specified values for measurement uncertainty" in Artemis does not change the default value determined by Ifeffit. It assumes that input is a value of 0. I've tried the latest Artemis versions for Windows and Linus and they both behave the same. Best regards, Victor Streltsov

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Larch user base?
by Sean Fackler 01 Sep '16

01 Sep '16

Hello all! Do you have an idea of Larch user base or Larch package download stats? Thanks for any information. Regards, Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

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Phase correction not working in Athena
by Sebastian George 31 Aug '16

31 Aug '16

Dear all, I hope that I am writing this in the correct place, and if I am not, I apologize. The problem I'm having is pretty much summed up in the Subject line. I'm analyzing some experimental EXAFS data in Athena, and it seems that ticking the "phase correction" box has no effect on my Forward Fourier transform. Has anybody run into this problem, and if so, were you able to fix it? The material I'm studying is amorphous SmCo. Could it be that having multiple backscattering species or a lack of crystalline structure causing problems for the phase correction? More generally, I'm wondering how exactly this phase correction is determined anyway. If used, is it the sort of thing that can put the first peak in my FT fairly close to the true nearest neighbor distance? Perhaps a better phrased question is: when can the phase transformation be expected to give a quantitatively accurate radial distribution (in terms of peak positions), and when is it more likely to only be qualitatively useful? Also, I would have assumed that a backscattering species would need to be given in order to calculate the phase shift, but I haven't found anywhere to do that. Have I missed something? Thank you for any help in advance! Regards, Sebastian

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pgplot and ifeffit installation on current linux systems
by Loges, Anselm G 26 Aug '16

26 Aug '16

Dear all, I hope this is the right platform for my question. If not, sorry to bother anyone. The question: Has anyone successfully installed pgplot and ifeffit on a recent Arch Linux system and could provide a quick how-to guide (also for the Demeter website maybe)? Although I have not yet tested it, my problem may also be relevant for current Debian/Ubuntu systems. Here's the situation: I am trying to install ifeffit on a current Arch Linux machine and therefore need to install pgplot first. The PGPLOT_install script on the respective GitHub page (as linked by a tutorial on the Demeter page, see links below) does not work because it relies on several outdated paths to dependencies. The one culprit I was able to isolate and fix was the path to the X11 libraries, which the script looks for here: /usr/X11 or /usr/X11R6 but in current Arch Linux (at least in mine, which is Manjaro to be precise, link below) is here: /usr/share/X11 This alone does not fix all problems, there are several dependencies missing in the X11 directory and I could not find out what the actual relevant package names are in Arch (Debian/Ubuntu names cannot be found). Also the config files of pgplot seem to have a bunch of similar problems that (at least partially) seem to stem from use of an old fortran-to-c translator (f2c) instead of the gcc fortran frontend and missing dependencies for that. If I am not mistaken, the latest Ubuntu LTS (16.04.) also has the /usr/share/X11 path, so the script should not work there either. I'd be happy to provide an updated installation script if I ever get it running but I thought I'd ask if someone has done that already or has solved the related problems so as not to invent the wheel anew. Links: <https://bruceravel.github.io/demeter/documents/SinglePage/installation.html>https://bruceravel.github.io/demeter/documents/SinglePage/installation.html https://github.com/newville/ifeffit <https://manjaro.github.io/>https://manjaro.github.io/ Best regards, Anselm

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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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