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

Beg for Athena install package
by zangyp＠mail.ustc.edu.cn 16 Apr '18

16 Apr '18

Sir/Madam： I am sorry to disturbe you! Here, I am a PHD of USTC, China and I want use the Anthena tool to analysis EXFAS data, my compute is 32-bites versions, so I beg for a Ifeffit-1.2.10.exe. Could you provide it for me? Very thanks! Zang, Y. P. zangyp(a)mail.ustc.edu.cn

2 1

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>

4 4

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

1 0

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

2 1

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

5 8

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

3 5

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/

3 2

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.

3 6

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

1 0

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

4 8

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

3 3

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

3 4

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

1 0

Athena crushes
by Vasily Potapkin 16 Mar '18

16 Mar '18

Dear All, I am using latest version of Demeter package on Mac. I was working on unsaved project when Athena crushed for no apparent reason. Now when I restart Athena it suggest to me to recover project from autosave and couple of seconds later becomes unresponsive. Restarting the computer didn’t helped. Artemis works without issues. Does someone know the solution? warm wishes, Vasily

2 2

FeSe2 Se K-edge XANES request
by Robert Gordon 14 Mar '18

14 Mar '18

Hi Folks, Does anyone have a near-edge spectrum of FeSe2, Se K-edge, they could share? (Ideally with Se elemental reference measured simultaneous.) Thanks, -R.

3 3

Data Import Error
by Nathan Nakamura 12 Mar '18

12 Mar '18

Hello Everyone, I'm fairly new to XAS/Athena, and recently collected XAS data at the F3 beamline at CHESS. I have had trouble importing our data files into Athena for processing, and I did not see a plugin for this beamline. Has anyone experienced a similar problem and may be able to point me in the right direction? I've attached an example of one of our data files, as well as an image of the error I've been receiving. Thank you, -Nathan Nakamura

2 1

SSRL XAFS Summer School
by Ritimukta Sarangi 01 Mar '18

01 Mar '18

Hello, SSRL will host its annual summer school this year during the third week of August (13th-17th). The focus of the school will on EXAFS hands on data analysis. In addition, electronic structure determination from the XAS pre-edge analysis and advanced spectroscopies will be covered. Examples from a wide range of scientific applications will be covered, including metals in biology, chemical catalysis, heterogenous catalysis and materials. I will post more information here, as and when it becomes available (hopefully soon) and we hope that many of you can attend. Best Wishes, -Riti Sarangi

2 1

Error message "typo in Template.pm"
by Elizabeth Tomaszewski 26 Feb '18

26 Feb '18

Hello, I keep getting the error message ""Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.24/Text/Template.pm line 556, <DATA> line 236.” I located the Template.pm file but can not edit the template without changing permission in the terminal, which I don’t know how to do. Line 556 reads: local *SYM = *{"$ {dest}::$name”}; Line 236 reads: $cur_item .= '\\’; Athena will open when I type in the command window but I can only see the GUI for a second before the error message comes up and it has to shut down. Please help. Thanks, Elizabeth Tomaszewski

1 0

call for nominations for the IXAS Awards
by Matt Newville 16 Feb '18

16 Feb '18

Hi Folks, I realize that many of you will have received this from the IXAS mailing list, but I'd like to invite everyone here to consider nominations for the IXAS Awards too: The Awards Committee of the International X-ray Absorption Society (IXAS) seeks nomination for three awards. These awards will be presented at the XAFS17 Conference in Krakow, Poland. The three awards are: 1. The Edward Stern Outstanding Achievement Award: This is the highest award of the International X-ray Absorption Society. Nominations are invited across all disciplinary areas including both experimental andtheoretical studies of XAFS. Award: $1000 2. The Farrel Lytle Outstanding Young Scientist Award for Theory and Instrumentation: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 3. The Dale Sayers Outstanding Young Scientist Awards for Applications of XAFS: Nominee must have made remarkable contribution to the field of X-ray absorption spectroscopy. Nominee should be within 8 years of a Ph.D. (or equivalent) degree as of April 1, 2018. Award: $500 Nominations should include a CV with publications, a letter of recommendation and academic referees who can be contacted for further reference. The deadline for nomination is May 1, 2018. Please send nominations by email to IXAS vice chair Matthew Newville newville(a)cars.uchicago.edu Thanks, --Matt Newville

1 0

Job Posting
by Frejka, Jean M 16 Feb '18

16 Feb '18

Can you please post and/or upload the attached job posting? The position is for a Data Analysis Engineer at Brookhaven National Laboratory. I have attached a two pdf files: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

1 0

Artemis having trouble
by Sheraz Gul 09 Feb '18

09 Feb '18

Can anyone please explain why Artemis is failing to open the fpj file I have attached? It doesn't respond anymore and screen look like the screenshot attached. It has happened to me multiple times now; I'm using Demeter version 0.9.25 on windows 10. Best regards, -- Sheraz Gul

4 12

XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

4 7

larch warning that I don't understand
by Ravel, Bruce 08 Feb '18

08 Feb '18

Matt, When Larch starts, what is meant by warnings like this: No handlers could be found for logger "pyFAI.opencl.common" or No handlers could be found for logger "pyFAI.gui.matplotlib" The first one went away by installing python's opencl interface -- a rather sizable prerequisite! I haven't figured out how to make the second one happy. Thanks, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter

4 4

Demeter Mac install on High Sierra
by Alexandre Simionovici 05 Feb '18

05 Feb '18

Hi guyz, Trying to install Demeter on a Mac thru the Macports command: sudo port install xorg-server demeter neither demeter nor xorg-server is known ! Macs nowadays have XQuartz as X11 window manager so xorg is not needed but what about Zeus' wife ? Has someone managed to install it on High Sierra or even Sierra ? TIA, Alex -- _____________________________________________________________________ | Pr. Alexandre Simionovici | |Institut des Sciences de la Terre, UGA/CNRS tel. +33-(0)4.76.63.51.96 | |Observatoire des Sciences de l'Univers de Grenoble fax. +33-(0)4.76.51.40.58| |UMR 5275, Maison des Géosciences, alexandre.simionovici(a)univ-grenoble-alpes.fr| |CS 40700, 38058 Grenoble Cedex 9, FRANCE | |------------------------------------------------------------------------------------------------------------------|

1 0

Autosave; problem with Athena crashing on mac
by Astrid Avellan 16 Jan '18

16 Jan '18

All, I recently updated my mac OSX and had to change for iXAFS on my OSX 10.8 to the demeter servers on 10.12 It was runing fine, untill Athena crashed. When I was trying to restart it, it was frozen, asking me if I want to open the autosave file, but no being able to click anywhere. All the posts online says that you want to find the file athena.autosave in your Mac in the folder $home/.horae/stash The trick is that you CANNOT see these folders by default in your Mac. To show the hidden folders in your system, you have to type into your terminal $ defaults write com.apple.finder AppleShowAllFiles YES killall Finder Once you have done that, you can find the .horae folder ONLY manually in $home/.horae/stash. A search in your folder finder will NOT work. I deleted the Athena.autosave folder, AND open the Demeter.ini file (in $home/.horae/downloads) and chance “autosave=true” for “autosave=false”. Once you are done, you can hide the folders again by typing $ defaults write com.apple.finder AppleShowAllFiles NO killall Finder Now, everything is running smoothly. But I don’t have any autosave : I autosave myself regularly! Enjoy a long life with Athena! Best Astrid

1 0