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

Multiple species with Artemis
by Mukundan, Vineetha 17 Jun '19

17 Jun '19

Hi All, A couple of questions. I was searching the previous threads to check if someone here had posted/explained an example with mixing parameters to find the % content of different constituents present in a sample with Artemis. This is for shell-by-shell fitting. Can Artemis fit multiple chemical species/phases to the experimental spectra simultaneously? OR fit the samples spectra measured at 2 different edges with one or two phase simultaneously? Don't know if I searched far enough. Apology if it has been discussed. In that case, could anyone please direct me to those threads. Thanks you, Vineetha

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Re: [Ifeffit] Ifeffit Digest, Vol 196, Issue 1
by Mahima Makkar 17 Jun '19

17 Jun '19

Dear Sir, This mail is regarding the quotation that you have sent. Please change the address to Prof. Ranjani Viswanatha ICMS JNCASR, Jakkur PO 560064 Bangalore, INDIA. Mail id: rv(a)jncasr.ac.in Please refer the mail id as mentioned above and resend the quotation. Thanks and regards, Mahima On Thu, Jun 13, 2019 at 10:30 PM <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. Problem with Demeter installation on mac OS Mojave (Ga?lle Creff) > 2. Re: Problem with Demeter installation on mac OS Mojave > (Ravel, Bruce) > 3. Re: Problem with Demeter installation on mac OS Mojave > (Ga?lle Creff) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Jun 2019 22:52:54 +0200 > From: Ga?lle Creff <gaelle.creff(a)unice.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Problem with Demeter installation on mac OS Mojave > Message-ID: <D0FD0963-0C63-4B93-9E99-E56654370D21(a)unice.fr> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > I have some troubles with the installation of Demeter on my mac (under OS > Mojave since this week end). > Athena crashed after the following message: > "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. > > 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at > /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> > line 236. ? > > Artemis does not work either. > > Can someone help me? > > Thanks a lot. > Ga?lle > >

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Problem with Demeter installation on mac OS Mojave
by Gaëlle Creff 13 Jun '19

13 Jun '19

Hi everyone, I have some troubles with the installation of Demeter on my mac (under OS Mojave since this week end). Athena crashed after the following message: "21:48:34: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. 21:48:34: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.28/Text/Template.pm line 572, <DATA> line 236. » Artemis does not work either. Can someone help me? Thanks a lot. Gaëlle

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Athena labels
by Stoll, Andreas (IAM) 24 May '19

24 May '19

Hi, Is it possible to change the x- and y-axes labels in the athena plots (energy against normalized xµE)? Greetings Andi

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Postdoctoral position at SSRL in XAS of catalysts
by Bare, Simon R 21 May '19

21 May '19

There is an opening for a postdoctoral research associate positon in the fall of 2019 at Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Lab. This postdoctoral position will involve using in-situ/in-operando synchrotron-based methods, primarily X-ray absorption spectroscopy (XAS), to study all aspects of catalysis. The focus of the project will be in developing advanced methods in data processing, data analysis and data modeling. The candidate will join a group at SSRL, under the guidance of Dr. Simon Bare, though the Consortium for Operando and Advanced Catalyst Characterization via Electronic Spectroscopy and Structure (Co-ACCESS); https://www-ssrl.slac.stanford.edu/content/science/chemistry-catalysis. Full details at: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Please send a letter with CV and list of publications, and names of two references, to the address below: Simon R Bare, email: simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu>

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Two postdoctoral openings at SBU and BNL
by Anatoly Frenkel 20 May '19

20 May '19

Dear mailing list subscribers, There are two openings for postdoctoral research associate positions, described briefly below (for more details please contact me). Position 1: A postdoc will investigate novel electromechanical materials using NSLS-II beamline facilities at Brookhaven National Laboratory, with primary technique being X-ray absorption fine structure. This position will be in Stony Brook University (located in close proximity to Brookhaven), under the supervision of Prof. Anatoly Frenkel. Responsibilities will include setting up new in situ operations for testing novel materials under applied electric field, developing and applying fast timing methods (such as modulation excitation spectroscopy), and collaborating with other participants of the NSF-BSF funded US-Israel collaboration. Annual trips to Israel for collaborative research will be required. Ph.D. in Physics, Chemistry or Materials Science, and expert knowledge of XAFS experiment, data analysis and modeling, documented in publications, are required. Position 2: Catalysis Center for Chemical Innovations (CCEI), an Energy Frontier Research Center (EFRC) at the University of Delaware, is hiring a postdoctoral research associate to work with multiple teams of catalysis researchers of CCEI on XAFS projects. The postdoc will lead collaborative efforts by helping develop synchrotron-based projects, plan experiments, lead the visiting researchers in data collection, and work with CCEI groups on subsequent publications. This position will be supervised jointly by Profs. Anatoly Frenkel (Stony Brook U.) and Jingguang Chen (Columbia U.). The postdoc will be stationed at Brookhaven National Laboratory and travel several times a year to U. Delaware for collaborative meetings. The background is recent Ph.D. in Chemistry or Materials Science. Strong background in catalysis and XAFS measurements, data analysis and modeling are expected. Three names of professional references are required with the applications that should include a cover letter describing prior experience and interest in the position, and a CV with a list of publications. These materials should be emailed to anatoly.frenkel(a)stonybrook.edu with a subject line: XAFS postdoc position. ------------------------------------------------------------------- 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 -------------------------------------------------------------------

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(no subject)
by Sameh Ibrahim Ahmed 20 May '19

20 May '19

Dear collegues I need the XAFS or XANES spectra for some material to use them in my analysis. Actually, I am not sure if there is a library for the XAFS spectra for different compounds available free online !. In fact, I need the spectra for the following elements and their oxides with different oxidation states as well 1- Ni 2- Fe 3- Mo 4- V 5- Co 6- Mn Thank you in advance for your help. Best regards -- سامح إبراهيم أحمد أستاذ مساعد الفيزياء جامعة عين شمس Sameh Ibrahim Ahmed Associate professor of Physics Ain-Shams University Abbassia-11588 Cairo-EGYPT email: sameh(a)sci.asu.edu.eg & sameh2977(a)gmail.com

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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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