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

Larch 0.9.51
by Matt Newville 27 Apr '21

27 Apr '21

Hi Folks, Larch 0.9.51 is now available for download and use. It's been several months since the last release, and there have been some important improvements to XAFS data processing and to the XAS Viewer application: - Parameters saved in an Athena Project File are now correctly saved and read into XAS Viewer (thanks Tyler Valentine!) - There is now a simple "Apply to all marked groups" feature for pre-edge peak fitting. That is, you can define a pre-edge peak model with one data set and then apply it to many others, either inspecting the individual fits or saving a CSV file with all the parameters and uncertainties for each fit to each data set. - XAS Viewer can now import multiple scans from a Spec file (thanks Mauro Rovezzi for help with this). It may seem that Specfiles are "legacy", but the reader should also be able to handle the ESRF Bliss HDF5 files (as read in with the silx package, from ESRF), which is their way of efficiently stacking multiple scans into a single binary file. While support for this here should be considered "beta" (or maybe "alpha"!), it is also reasonable to expect that this or a similar HDF5 format file will become a common way to collect and store XAFS data. - There are binary installers for Windows, MacOSX, and Linux. There are also now "GetLarch.sh" and "GetLarch.bat" scripts (that are very short) that can be run to do the download and install, essentially mimicking what the binary installer does. This may be useful for folks wanting to install Larch on multi-user servers or in existing (or "other") Python environments. This might also be useful for those who run into permissions issues, especially on MacOS, where installing a package from an untrusted source is often blocked by default. With the installer script, the unprivileged user is simply running a script that downloads a bunch of files and places them in the home folder. These scripts might also be useful for those who run into problems downloading very large files from millenia.cars.aps.anl.gov, as the installer scripts will use Anaconda and PyPI resources that are better distributed throughout the world. ... which brings me to a final note (I'll send out another message next week): The APS will have a planned power outage from April 30 to May 4 . This will take millenia.cars.aps.anl.gov off-line for those 5 +/- 1 days. That machine hosts the binary installers and also this mailing list. Mail sent to this list during that time will likely be lost (email routing servers can handle destination servers being down for a few hours, but not days). So, if you're planning on sending announcements here, either do it before April 29 or wait until May 5. If you have any questions, problems, or suggestions, please let me know. --Matt

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Fourier transform parameters not saved in Larch XAS Viewer
by Tyler Valentine 18 Apr '21

18 Apr '21

Hello, I am using Larch XAS Viewer. I noticed that when I save my work to an Athena project file (.prj) and reopen it later, the Fourier transform parameters are reset. It seems to be correctly saving other values that I set such as the pre-edge and normalization ranges, so I am unsure why it does not also save the transform parameters. Is it possible to have these values saved? Thank you, Tyler

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XAFS 2021 Virtual Conference deadlines
by Matt Newville 18 Apr '21

18 Apr '21

Hi Folks, I hope most of you have seen information about the 2021 Virtual XAFS Conference this summer: https://xafs2021.org/ There will be an in-person conference in the summer of 2022 in Sydney and a briefer, virtual conference this summer: 11-13 July 2021. I especially want to draw your attention to the Virtual Poster session for students and early-career scientists. The abstract deadline is 1 May, a little less than two weeks from now: see https://xafs2021.org/call-for-abstracts.php for details. Please consider submitting a poster or encouraging your colleagues to do so. There will also be a Virtual Workshop on Data Analysis with Larch: I'll be pre-recording lectures, and then going over some of the finer details of using XAS Viewer and doing simple XAFS analysis during the workshop. Hope to see you there, --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Looking for the XAS of Zn3P2
by Madeleine Han 16 Apr '21

16 Apr '21

Dear Ifeffit community, I am looking for the X-ray absorption spectrum of Zn3P2 to use as a reference to determine the composition of an unknown compound. Does anyone know if it has already been recorded? If so, where can I find it? Thank you in advance for your help, Yours sincerely Madeleine Han

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Re: [Ifeffit] Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 27 Mar '21

27 Mar '21

HI, I hope I am replying to the thread correctly. Thank you for your insights, I have spent a lot of time tinkering with installation and I have a partial solution. To first answer your questions: - yes, the fit ran ok and comparing it to the same fit using ifeffit (done by a a machine using ifeffit that works correctly), the calculated parameters are almost the same, with slight differences of 10-5 order of magnitude. The plot after the fit also looks fine. -the log I attached was from the example Cu data set, but the issue happens on every fit I try to run. -I'm not sure about the feff.dat file used, I haven't been able to locate it in my installation. - Feff6 (or Feff6l if I set it in preferences) are able to run as far as I can tell -I have run the example larch scripts to which you pointed me, and most of them were able to run ok, with no obvious issues (the parameters looked ok and reduced chi-square and R vales were reported). There was an error in running a few of the tests something to do with PlotDisplay, but I'm pretty sure these aren't related issues. To me, all of this points to some trouble Artemis has communicating with larch. I have tried downgrading the installation from 0.9.50 (that installs with pip) to 0.9.49 (that the website says is the current) and an even older ones but no luck. The solution war disappointingly trivial: If I completely removed larch and demeter suite along with everything else I installed in the last few days, from my computer and tried to compile it again, this time with ifeffit, I finally managed to get the reduced-chi square and R values. I have no idea why it didn't work when I tried it a few times before before but now I am able to get the fit and all required parameters. It still doesn't work with larch, but for now, at least I'm able to get the results. I'll re-install Larch and tinker with it a bit more to try to figure out where the error was coming from and report back if I find anything that might help someone else facing the same issue. Thanks again for the help Best, Ava

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Unable to load Demeter modules with Perl
by Tyler Valentine 27 Mar '21

27 Mar '21

Hello, I am learning how to use a perl script to structure a fit with Demeter. However, when I input the 'use Demeter;' command into my script, I receive the following error: Can't load 'C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:The specified module could not be found at C:/Users/Tyler/AppData/Roaming/DemeterPerl/perl/lib/DynaLoader.pm line 193. I have changed the @INC to include all the directories where Demeter modules should be located, so I am not sure why I am receiving this error. I would appreciate hearing back from you about ways I could resolve this. Thank you for your time, Tyler

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Artemis fit error - chi-square and R-factors are always equal to 0
by Ava Rajh 26 Mar '21

26 Mar '21

Hello, I have recently installed Demeter suite on my LinuxMint 20 machine with all required dependencies met. Athena works well and Demeter passed all tests during installation. When running Artemis however, there is an issue with fits that persists with provided examples any any other projects I open (including the ones done by colleagues and just re-run on my machine). After the fit (which completes fine and returns expected fit that looks ok when comparing it to experiment), when inspecting the log file, chi-square, reduced chi-square and R values are equal to 0 (example log file attached bellow). No errors accompany the fit. I am using Larch installed with anaconda, and Artemis uses Feff6 executable. I have re-installed Demeter and tried to get it to work with Ifeffit but the error persists. I have found an existing git hub thread dealing with similar issue (https://github.com/bruceravel/demeter/issues/62) but no solution that I could discern. Could it be an issue with my perl version (5.30.0)? If someone has any ideas what the issue could be and how to fix it, I would appreciate the help. Please let me know if I can provide any additional information, and I apologize if there is something obvious I may have missed. Sincerely, Ava -- Ava Rajh

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FW: Postdoc position at BNL for studying molten salts using synchrotron methods
by Gill, Simerjeet 24 Mar '21

24 Mar '21

Hello XAFS Community, On behalf of Energy Frontier Research Center on Molten Salts in Extreme Environments (MSEE) at Brookhaven National Laboratory (BNL), I would like to bring your attention to postdoctoral Research Associate position within the Energy Frontier Research Center (EFRC) on Molten Salts in Extreme Environments. The position requires a Ph.D. degree in chemistry, physics, materials science or a related field. The interdisciplinary research will focus on structural and spectroscopic investigation of molten salts, solutes in them, and liquid-solid interfaces. You can find the detailed description of the position requirements and apply online, go to https://jobs.bnl.gov<https://jobs.bnl.gov/> under Job ID 2335 (https://jobs.bnl.gov/job/upton/post-doc-synchrotron-studies-of-molten-salts…) The postdoc will investigate molten salt systems using NSLS-II beamline facilities at Brookhaven National Laboratory, with X-ray absorption fine structure along with x-ray scattering techniques. This position will be in Nuclear Science and Technology Department at Brookhaven National Lab, Under supervision of Dr. Simerjeet Gill. Responsibilities will include performing synchrotron experiments on molten salt systems with and without actinides and collaborating with other participants of MSEE-EFRC. For inquiries, please email me at gills(a)bnl.gov<mailto:gills@bnl.gov>. Thank you, Simerjeet K Gill, Group leader, Nuclear Science and Technology Department, Brookhaven National Lab, Upton, NY 11973

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Cobalt carbide EXAFS spectrum
by Antonio Aguilar 18 Mar '21

18 Mar '21

Dear community, I'm struggling with the data analysis of some Co samples, i think it might be some cobalt carbide. I was wondering if someone would be willing to share the spectrum of the Co2C reference please? That would be very helpful. Thank you in advance! Cheers, Antonio Aguilar -- Postdoctoral fellow Beamlines CRG FAME (BM30B) & FAME-UHD (BM16) | ESRF ESRF - The European Synchrotron 71 Avenue des Martyrs, 38043 Grenoble, France Tel: +33 (0)4 76 88 25 46 - Bureau : LOB 2-50

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Not possible to install Larch MacOS X 10.12.6 via anaconda (see report)
by Mangold, Stefan (IPS) 16 Mar '21

16 Mar '21

Dear all, I tried to reinstall; before I updated and couldn’t open larch anymore conda install -yc GSECARS xraylarch Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with each other:

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