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

Larch 0.9.43
by Matt Newville 02 May '19

02 May '19

Hi Folks, Larch 0.9.43 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you already have installed Larch, you should be able to update to the latest version with ~> conda update -c gsecars xraylarch from a terminal on Linux or Mac OSX. On Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can simply remove the xraylarch installation folder and reinstall. If you would like to install Larch into a different Python environment, please read https://xraypy.github.io/xraylarch/installation.html Version 0.9.43 has several improvements to the XAS Viewer GUI application, including: - better handling of read/write cycles of multiple Athena project files. - better default normalization and better control over normalization, especially for XANES data. - improved PCA analysis (in part from the recent discussion here with Joselaine Cáceres Gonzalez), so that it now reports IND values to help determine the number of components and reports eigenvalues from simple matrix inversion (not SVD) so that they more closely match those in the XAFS literature. - addition of Partial Least Squares and LASSO regression analysis for selection and prediction of external quantities (valence, for example) based on training sets of XANES data with known values for these quantities. This machine-learning approach is based on work of M Dyar, et al in a series of papers over the past several years. I encourage and request anyone interested, and especially MacOS users, to try out the XAS Viewer app and let us know what needs improvement. For people interested in using Larch from Python, Version 0.9.43 includes a complete refactoring of the code to make Larch work better as a "normal" Python library. Specifically, the previous code organization with most of the real analysis code in "plugins" has been replaced with all code now placed within the main larch module, still organized by topic. This improves packaging -- `pip install xraylarch` can now work. This code reorganization also means that the python programmer can use more normal imports to get at the Larch library so that one can simply do >>> from larch.xafs import pre_edge, autobk, xftf We also fixed a serious and deep flaw that selected a matplotlib plotting library too early, making larch difficult to use with Jupyter, Spyder, or other Qt-based GUIs. This is now fixed, and import statements like the one above can be seamlessly used in Jupyter notebooks. I should note that the documentation and examples are definitely lagging behind the code especially regarding the most recent developments, but this will be worked on. If you having any questions, trouble, or suggestions on any part of Larch, please let us know. --Matt Newville

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Pseudo Voigt crash Athena
by Lawley Craig Richard (PSI) 02 May '19

02 May '19

Dear Mailing list, I have run into an issue with the peak fitting section included in Athena. If I include a peak that is a Pseudo-Voigt and then save the project file. Upon trying to reopen the same project file, Athena becomes non responsive with the error message "PV is not yet implemented". The log file for the crash is as follows: Started at 2019-05-01T17:37:06 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin DEMETER_BASE is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl IFEFFIT_DIR is: C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\share\ifeffit\ perl version: v5.24.0 backend: ifeffit @INC: C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/vendor/lib C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/lib . Demeter version 0.9.26 Can't call method "SetValue" on an undefined value at C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/PeakFit.pm line 916. -------- Where lines 910-920 in the PeakFit.pm file readout as: 910 if ($result == wxID_NO) { 911 $::app->{main}->status("Not deleting lineshape."); 912 return 0; 913 }; 914 ## demolish the LineShape object, if it exists 915 $this->{'lineshape'.$n}->DEMOLISH if exists $this->{'lineshape'.$n}; 916 ## dig through the hierarchy of the StaticBox and Remove/Destroy each element 917 foreach my $s ($this->{'func'.$n}->GetChildren) { 918 foreach my $w ($s->GetSizer->GetChildren) { 919 $w->GetWindow->Destroy if defined($w->GetWindow); I couldnt find any previous thread regarding this issue. If anyone knows a solution or could link me to a pre existing thread I would much appreciate it. Thanks in advance Craig _______ Paul Scherrer Institut Craig Lawley OFLB/U109 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 5054 E-Mail: craig.lawley(a)psi.ch<mailto:craig.lawley@psi.ch> www.psi.ch<http://www.psi.ch/>

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Demeter Mac issues
by Elizabeth Tomaszewski 29 Apr '19

29 Apr '19

Hello all, Is anyone currently using the Demeter package on a Mac? I have followed the instructions given and have the package installed. However, when I try to open Athena through the terminal window, it gets stuck on the opening Athena image and the question box asking "Athena found an autosave file would you like to import it?" I can open Artemis and Hephaestus, but get the error message as follows: 12:29:30: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563. This message is repeated five times. Only after opening and closing each software several times can I get them to run. Any suggestions as to: 1) how to make the Demeter package run more smoothly and 2) how to get Athena to open at all. Thank you for your assistance, Beth Tomaszewski -- Dr. E J Tomaszewski Postdoctoral Researcher Eberhard Karls Universitaet Tuebingen Center for Applied Geoscience (ZAG) Geomicrobiology Sigwartstrasse 10 72076 Tuebingen Germany

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Question about PCA
by Joselaine Cáceres gonzalez 25 Apr '19

25 Apr '19

Dear all, I performed PCA in a set of 11 XANES spectra and I was trying to use some of the functions and tests developed by Malinowski to extract the number of primary components. I found differences between eigenvalues calculated whit a matrix calculator and those calculated by ATHENA, but they are equivalent in some way since they explain the same amount of variance and when I calculate the IND function or Malinowski F-test I reach the same conclusions. To calculate the eigenvalues with the matrix calculator I first normalized my data matrix (step height normalization) with ATHENA, then I export the data to an Excel spreadsheet where I centered them: z=(value-mean)/standard_dev. Then I used SVD and Eigenvalue decomposition to find the eigenvalues and those obtained with SVD explain exactly the same amount of variance than those found with ATHENA but they are different. In all the calculation I did, I used the same amount of points 161, points in each spectrum in ATHENA and in the matrix calculator, exactly the same energy interval. I´d like to know if I am missing some step in the data pre-treatment that is prevented me to find the same eigenvalues obtained by ATHENA but also I´d like to know if I can straight forward use the values obtained with ATHENA to evaluate the functions proposed by Malinowski since these equations might be different depending if calculations are made using "covariance about the origin" or "correlation about the origin" and I am not sure what is the case. Thanks in advance! Best regards Joselaine

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can't open Athena 0.9.26!
by m.rezaie 23 Apr '19

23 Apr '19

Hi, I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my computer which is Win 7, 32 bit. How can I solve this problem? Best Regards Mahsa

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2019 APS/IIT Summer XAFS School
by Carlo Segre 18 Apr '19

18 Apr '19

Greetings: The 2019 APS/IIT Summer XAFS School will be held on the Illinois Tech Campus from July 7, 2019 to July 12, 2019. Please see the attached announcement for details and information on how to apply. 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 it helps to get the year right > On Apr 18, 2019, at 10:38 AM, grant bunker <bunker(a)agni.phys.iit.edu> wrote: > > Greetings, All - I would appreciate your help in the disseminating this announcement > > thanks - Grant > > <2019 XAFS summer school announcement.pdf>

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Regarding FEFF9
by Manju 18 Apr '19

18 Apr '19

Hi I am trying to see the effect of crystal defects on XANES. Is there any way that I could create charged vacancy in feff.inp file, before importing it into FEFF9? Regards Manju Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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LANL EXAFS Postdoc position
by Daniel Olive 17 Apr '19

17 Apr '19

Greetings all, Los Alamos National Laboratory has a postdoc position involving EXAFS for use in nuclear forensics/actinide research. The vacancy name is IRC72104, linked below, and contains additional information. https://lanl.jobs/jobs/?q=IRC72104 Please have a look and/or forward to those who may be interested. Best, Dan -- ------------ Daniel Olive Los Alamos National Laboratory MST-16: Nuclear Materials Science P.O. Box 1663 MS E574 Los Alamos, NM 87545 Chemical Sciences Division Lawrence Berkeley National Laboratory ------------

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Re: [Ifeffit] Demeter - Athena Warning, crashing
by Ravel, Bruce 16 Apr '19

16 Apr '19

Hi, The Demeter problem that presents itself with error messages like: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. is one that comes up pretty often here on the mailing list. It is also a problem that is already solved on github, but I haven't made a new release in quite some time. The solution to this particular problem is shown here: https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L994-L996 You could simply edit the copy of Demeter.pm on your computer to have the three lines highlighted at that link. Or you could click the "Raw" button at the top of that page, then save the raw file in place of Demeter.pm on your computer. A bit more effort would be to remove the version of Text::Template that is on your computer and install an older version of Text::Template on your computer. This one should work: https://metacpan.org/release/MJD/Text-Template-1.46 The bottom line is that Demeter uses a perl module for which the documentation of a feature and its implementation used to agree and, at some point, stopped agreeing. The fix that I link to above addresses that problem, but the specific combination of Demeter and Text::Template that makes it onto some people computers expose this problem. Any of the solutions explained above should address this in the short term. Eventually I will make a new release and this problem will go away. Until then, hopefully people will find this email. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Demeter - Athena Warning, crashing
by natalia martin 16 Apr '19

16 Apr '19

Hi, I have just installed Demeter on my Mac and get the following error when trying to Launch ATHENA: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I saw a previous post from Chris on the 2018-04-02 with a similar error ("Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236.) which was solved by replacing the /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With another template from p5.24. https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s… <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s…> This solution does unfortunately now work for my case. Does anyone have an idea of how this error can be fixed? Best, Natalia

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