March 2018 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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Artemis Error
by Lê Ngọc Chính 19 Apr '18

19 Apr '18

Dear Demeter developer I have some trouble when using artemis. I have used artemis normally on windows 10, but recently I can't use it anymore. The error message appears after I click "FIT" button. I also have tried re-install the software, but nothing happened. Please provide me the way to fix it. Thank you so much -- Chính

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Problem building latest demeter on Debian 32bit Stretch
by Al Kwiatkowski 30 Mar '18

30 Mar '18

Hello - We're trying to install demeter on a 32-bit system running Debian 9.2 Stretch. The 'perl Build.PL' and 'Build' run into no issues, but when we try running 'Build test' we get the following error messages: t/001_base.t ............ String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. Compilation failed in require at t/001_base.t line 22. BEGIN failed--compilation aborted at t/001_base.t line 22. # Looks like your test exited with 255 before it could output anything. t/001_base.t ............ Failed 24/24 subtests t/002_types.t ........... String found where operator expected at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" (Do you need to predeclare croak?) syntax error at /home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line 273, near "croak "Couldn't unlink $self->{__error_log}: $!"" Compilation failed in require at /home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244. The "croak" command not getting found appears to come from the "Carp" perl module - we have version 6.06-1 of the 'libcarp-clan-perl' package installed. Any suggestions as to what's causing this error? Again, the 'perl Build.PL' command shows no issues with the installed modules, but since most of them were installed from the Debian repository, maybe there's a discrepancy with the modules installed when we run './Build installdeps'? Thanks for any assistance - Al Kwiatkowski kwiatal(a)phys.iit.edu

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Athena crashes on windows10
by Lisa Bovenkamp-Langlois 28 Mar '18

28 Mar '18

Hello. Me and other people running windows 10 have problems with Athena (demeter version 0.9.26). when switching to the LCF window the program crashes. I tested that indeed sometimes this happens when the list of data sets is long. However, it recently happened with only 3 data sets in the list. In one case Athena crashes at this same spot repeatedly. In other cases if works after restarting Athena or the PC. Is there a fix in sight or do I have to go back to windows7? Thanks, Lisa Lisa Bovenkamp-Langlois, PhD CAMD/LSU 6980 Jefferson Hwy Baton Rouge, LA 70806 Email: lbovenkamp(a)lsu.edu website: http://www.camd.lsu.edu/

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Athena (Demeter 0.9.26) does not import all datapoints from ascci file
by Kathy Dardenne 28 Mar '18

28 Mar '18

Hello, I got a new trouble by importing datafile in Athena (Demeter 0.9.26). Athena from Demeter version 0.9.26 does not import all points from the datafile but some of them yielding a very poor resolution especially for the edge region. The given file has 275 points and only 143points are imported (see derivative after import with Athena(26) and with pymca were all points are imported). Importing data using Athena from an older version of Demeter and saving the file solved my import problem temporary. But there I notice that a priori only 202 instead 275 were imported but it was not obvious from the plot appearance that some points are missing . I joined some screenshots as well as Athena log file after importing the data (error message about a file not found but the name in stash is not the one Athena is looking for..?). I joined both Athena file (Demeter v26 and Demeter v19 after import of the same asci file) as well as the asci file. I got the problem of "partial import" with all my datafiles. Did somebody experienced this trouble too? Thanks a lot Kathy Dardenne Operating system : Windows 7 entreprise - Service pack 1 Programme : Demeter 0.9.26 last release Karlsruhe Institute of Technology (KIT) Institute for nuclear waste disposal (INE) Dr. Kathy DARDENNE Hermann-von-Helmholtz-Platz 1, Building 712 76344 Eggenstein-Leopoldshafen, Germany Tel. : +49 721 608-26669 Fax : +49 721 608-23927 E-mail : <mailto:kathy.dardenne@kit.edu> dardenne(a)kit.edu Internet : <http://www.kit.edu/> www.ine.kit.edu KIT - The Research University in the Helmholtz Association.

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Larch 0.9.37 now available
by Matt Newville 27 Mar '18

27 Mar '18

Hi Folks, I'm happy to announce the release of Larch 0.9.37. It's been a while since I announced updates to Larch, and there has been steady progress on a number of areas over the past year. While much of the effort has been centered on X-ray fluorescence imaging and diffraction mapping work done at X-ray microprobes especially at GSECARS, there has also been been some work on XAFS and XANES. Larch now includes both Feff6l and Feff8l (that is, Feff85 for EXAFS-only calculations), with routines for running these from within Larch scripts or from Python. I want to draw your attention in particular to the program with the rather boring name "XAS Viewer" (formerly XYFit) that is included with Larch and may be of interest to several Ifeffit users. XAS Viewer is currently focussed on doing pre-edge peak fitting, but we do intend to add more XANES and EXAFS visualization and analysis tools. Feedback and suggestions of any kind would be helpful and greatly appreciated. Currently, XAS Viewer can read data from plain ASCII files or from recent "new-style" Athena Project files. Like Athena, it can merge groups and plot one or more XAFS spectra in various stages of the XAFS normalization process. XAS Viewer can also save data to Athena Project file, or save multiple data sets to CSV files. While XAS Viewer does basic XANES processing (normalization, etc) and visualization similar to Athena, its main emphasis is on fitting of pre-edge peaks. A dedicated panel helps the user first fit a baseline curve, then adds peaks (Gaussian, Lorentzian, Voigts, etc) and fits the entire model to the pre-edge region. Bounds and constraints can be placed on any of the parameters for the peaks, and full fit reports including uncertainties are generated. Fit models can be saved to a file and re-loaded. These saved models can be used from Python code. We will soon be generating fitting scripts for batch processing, but this is still work in progress. Some screenshots, and a bit more information are at https://xraypy.github.io/xraylarch/guis/xas_viewer.html Again, feedback or suggestions on this or any other aspects of Larch are most welcome. Larch can be installed with installers for Windows, Mac OSX, Linux. At the moment, these installers all assume 64-bit operating systems. If anyone needs to use Larch with 32-bit Windows please let me know, and I will try to build an installer for that platform. Larch can also be installed as a "conda package" for Anaconda Python, as with conda install -c GSECARS xraylarch Currently both Python 2.7 or 3.6 are supported. Finally, Larch can also be used as the "backend" for Athena/Artemis, and I strongly encourage all Athena/Artemis users to install Larch so that it can be used in place of the old and unsupported ifeffit library. --Matt Newville

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synthesis of EXAFS via larch
by Katy Smith 20 Mar '18

20 Mar '18

Dear Colleagues, I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I wonder if that would be the right way. I can synthesise the paths in Demeter/Artemis but I have no idea how to sum them in order to obtain a single EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am looking for. Best regards, Kate

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Error in Atoms output
by Kaustubh Priolkar 20 Mar '18

20 Mar '18

Hello! We are trying to fit low temperature V K edge EXAFS data in V2O3. As per the cif files available (attached herewith – V2O3_10K data.cif) the structure is described by I2/a space group. When this file is read by ATOMS it gives an erroneous output ( attached herewith - feff.inp). In particular the values of V-O and V-V bond distances are not correct and do not match with bond distances reported in literature (Phys. Rev. B 2 (1970) 3771). Could anyone tell me where am I making a mistake. I am aware that I2/a is a non standard space group but I am not sure if I need to take any precaution while reading the cif file in ATOMS. Thanks and regards, Kaustubh Sent from Mail for Windows 10

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Report a bug
by Zhengrui Xu 19 Mar '18

19 Mar '18

To whom it may concern, I found a bug when I am dealing with my data. I am using Windows system, and the software version is 0.9.26. I can plot my data in E, however, not in k, R and q. This problem happen to all of my data. My other three group members also have this problem. My raw data is attached for your review. We really appreciate your help. Best, Zhengrui Xu First-year PhD student Department of Chemistry Virginia Tech

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2018 APS/IIT XAFS Summer School - schedule set
by Carlo Segre 19 Mar '18

19 Mar '18

Hello All: The APS/IIT XAFS Summer School will be held form July 8-12 on the Illinois Tech campus in Chicago. Please see attached flyer for details. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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