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

Sulfur EXAFS k oscillations
by Miller, Elizabeth Christine 11 Apr '18

11 Apr '18

Hi all, I am analyzing some sulfur K-edge EXAFS data taken at 4-3 at SSRL. When I use a k-weight of k^3 to plot, my oscillations at high k reach over 100, which doesn't make sense to me. I have looked over the data with Riti, and it seems that while the XANES are rather self-absorbed due to high concentrations of sulfur-containing salt, the data can be normalized, and the EXAFS should contain some information. I've included screenshots in the attachment of plots of all of the k-weights as well as my parameters. The mixtures are solutions of organics (acetonitrile, 1,1,2,2-Tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether) with bis(trifluoromethane)sulfonimide lithium salt. I am also not hitting any other edges, as sulfur is the highest Z element in the solution. Any thoughts would be greatly appreciated! Thank you, Beth Elizabeth C. Miller, Ph.D. Postdoctoral Scholar Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory E-mail: ecmiller(a)slac.stanford.edu<mailto:ecmiller@slac.stanford.edu>

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Re: [Ifeffit] [Ifeffit} Sulfur EXAFS k oscillations
by fred.mosselmans＠diamond.ac.uk 10 Apr '18

10 Apr '18

Dear Beth, Apart from the fact it looks like there is a trace Cl impurity in one of the samples (sharp line at ca. 9.5 k), it is hard to tell how a spline is going wrong without seeing the spline, thus posting the Athena file might get a better response. It may well be there is not much data beyond 10 k for soft scatterers at the S K-edge. Best wishes Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 -- 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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Mac install issues
by Webb, Samuel M. 04 Apr '18

04 Apr '18

Hi all - I've run into a lot of problems with Mac installs in general with my compiled XAS programs as well, particularly with the latest High Sierra update. It's been pointed out to me by a few users that another potential work around is to use Wine 3.0 https://www.winehq.org as an emulator of sorts (and its free) to run a windows program within the MacOS environment. It's smaller and more compact than say Parallels or VMware as it doesn't do the whole operating system, hence the free part. Its seems easy to install, and also makes for one less OS to maintain a distribution for. It may not be the most elegant solution, but it could work for some... I may end up using this for myself rather than maintaining a native Mac distribution in the future. Sam

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install for mac error
by Christopher Patridge 04 Apr '18

04 Apr '18

Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, Chris -- Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Chemistry SASE 315 D'Youville College 320 Porter Ave., Buffalo, NY 14201 716-829-8096

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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 26 Mar '18

26 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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