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

Academic Career Opportunity in X-ray Spectroscopy at the University of Leeds
by Sven L. M. Schroeder 23 Aug '15

23 Aug '15

Dear colleagues I would like to advertise an exciting career opportunity for an X-ray spectroscopist at the University of Leeds. Leeds is one of the top 10 research-intensive Universities in the UK. Through our international academic recruitment programme ( http://250greatminds.leeds.ac.uk ) we wish to consolidate our strategic relationship with Diamond Light Source by appointing a University Academic Fellow in Structure-Function Determination in Complex Soft Matter Systems Chemical product and process engineering can now take advantage of structure analysis with a broad range of X-ray techniques that have become available at the UKs synchrotron radiation source, DIAMOND. The focus of the research is to determine structure information across length scales, ideally in situ under process conditions, and from molecular to macroscopic dimensions, and to combine such information with multi-scale models to generate a seamless understanding of the relationships between microstructure, processing conditions and product performance. The Fellowship is an exciting opportunity for an engineer or physical scientist with an interest in determining structural/performance relationships in complex products, particularly soft matter systems, with synchrotron radiation techniques. Salary: £38,511 to £45,954 Closing Date: Wednesday 30 September 2015 Reference: ENGPE1026 Career Pathway: Successful completion of a 5 year probationary period leading to appointment to Grade 9, Associate Professor. More particulars are available at: https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026 - UAF in Structure-Function Determination in Complex Soft Matter1.pdf <https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026%20-%20UAF%20 in%20Structure-Function%20Determination%20in%20Complex%20Soft%20Matter1.pdf> For informal enquiries about the role please feel free to contact me as per details below. -- Sven L. M. Schroeder Royal Academy of Engineering Bragg Centenary Chair School of Chemical and Process Engineering | Institute for Particle Science and Engineering (IPSE) | University of Leeds | Leeds LS2 9JT | UK Room 2.22 | Engineering Building T +44 (0)113 343 2401 | PA/secretary (Kirn Jutlla) +44 (0)113 343 2404 | F +44 (0)113 343 2384 E <mailto:s.l.m.schroeder@leeds.ac.uk> s.l.m.schroeder(a)leeds.ac.uk | W <https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder> https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder

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Re: [Ifeffit] XANES simulation K-edges
by Joshua Kas 19 Aug '15

19 Aug '15

Hi Debora, The edge energies are very difficult to calculate, and FEFF only calculates them to roughly 5% accuracy. In this case the accuracy is actually much better. However, relative edge energies between different systems may be more reliable. Most comparisons between theoretical and experimental XANES allow for a shift of the edge to align the spectra. If the comparison is of several systems, a single shift should be used for all of them. Cheers, Josh Kas On Wed, Aug 19, 2015 at 10:00 AM, <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. XANES simulation K-edges (Debora Meira) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Aug 2015 08:50:47 +0000 > From: Debora Meira <debsmeira(a)hotmail.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES simulation K-edges > Message-ID: <BLU181-W70FD27721CD14A2C97998CAD670(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > I'd like to know which kind of concern I should have for feff to simulate > the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge > and I have around 30 eV energy shift for the edge position. Can it be > related with a wrong parameter for one of the cards? > Thank you, Debora Meira >

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XANES simulation K-edges
by Debora Meira 19 Aug '15

19 Aug '15

Dear all, I'd like to know which kind of concern I should have for feff to simulate the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge and I have around 30 eV energy shift for the edge position. Can it be related with a wrong parameter for one of the cards? Thank you, Debora Meira

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MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)
by Fowler, Joseph W. 14 Aug '15

14 Aug '15

Dear Bruce: Wait a minute! In fact, I updated the Mac Ports package demeter within the last two weeks to use Demeter version 0.9.22. Mac users might want to use the latest version and should consider doing a "port self update && port upgrade demeter". Users who installed the development version port called demeter-devel will also land on 0.9.22 if they upgrade to the latest. Note that the latest Mac Ports version is known as 0.9.22_1, where the revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which the MacPorts team is pushing on). For many users, there will be numerous dependency upgrades when you upgrade to 0.9.22_1, but I found they took only a few minutes in my particular case. This change in Perl versions could conceivably cause problems, but I haven't heard of any. Best wishes, Joe Fowler (MacPorts maintainer for demeter) ________________________________ From: Bruce Ravel <bravel(a)bnl.gov> Sent: Tuesday, August 11, 2015 6:55 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Energy shift after deglitch I don't see the behavior you describe when I follow your recipe. Perhaps it got fixed when I fixed this fellow's issue...? http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html Of course, the Mac package is a fair bit behind at this point. B On 08/06/2015 06:10 PM, George Sterbinsky wrote: > Hello, > > I am writing to report a bug in Athena running on OSX 10.10.4. Here are > the steps to reproduce the problem. I'm not sure that all steps are > necessary. > > 1. Open Athena and import the attached project, which contains two > groups that are both marked. > 2. Change plot range to plot from -30 to 30 eV. > 3. Select the "deglitch and truncate" window. > 4. Select group "Ref data.merge". > 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to > -20. > 6. Click replot margins. > 7. Click remove points. > 8. Click return to main window. > 9. Click the derivative check box to plot marked groups as normalized > derivative. > 10. Click mu(E) button to plot marked groups as derivative of mu(E). > > When the last step is done the groups appear to shift with respect to > each other. One can switch between Normalized and mu(E) and see the > shift come and go. > > Thank you, > George > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- 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/

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La2Zr2O7 EXAFS fitting
by herve muguerra 14 Aug '15

14 Aug '15

Dear All, First of all, I am still very new in EXAFS analysis, so please excuse me for any misunderstandings. My sample is a crystalized La2Zr2O7 thin layer (thickness = 100 nm) on a NiW substrate and we have realized EXAFS measurements by grazing angle under primary vacuum at Lathanum L3 edge (ESRF, Grenoble, France). My objectives are to establish the local distortions due to the different constraints in the oxide thin layer. The La2zr2O7 crystalized in a pyrochlore structure (SG = Fd-3m ; a = 10.78A). First scattering path La-O2.1 2.3352A La-O1.1 2.6453A But I have a problem: I observe the first peaks at 1.28A and 1.80A on the EXAFS spectra as a function of R. How do you explain this feature? Can you point me in the right direction for these issues? I attached the project file La_80_LZO_1000.prj of my sample: LAHM045 to LAHM50 = 6 different scans La_80_LZO_1000 = Data merge Thanks Best regards Hervé Muguerra

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Demeter installation on Debian
by Isabelle Kieffer 14 Aug '15

14 Aug '15

Dear all, I am trying to install demeter on my debian 7 computer and I cannot reach the end of the compilation. I followed the instructions from the https://gist.github.com/3959252 page. First, the "perl ./Build.PL" still requires "PDL::stats" even after several "./Build installdeps". I have the following message: """""""""""""""""""""""""""""""""""""""""""""""""""" letard@pcikieffer:~/demeter$ perl ./Build.PL Checking prerequisites... requires: ! PDL::Stats is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version 'v0.9.21' If all dependencies are met, build and install Demeter by doing: ./Build ./Build test ./Build install # (or sudo ./Build install) If you are reinstalling Demeter after updating your operating system (or updating perl), you may find that none of the programs will run successfully. You may need to do: ./Build touch_wrapper ./Build test ./Build install # (or sudo ./Build install) """""""""""""""""""""""""""""""""""""""""""""""""""" Then, I decided to continue despite this missing prerequisite and the "./Build" ends with the folowing error: ##### Building Artemis User's Guide Building Athena User's Guide ! plugin error - Can't locate Clone.pm in @INC (@INC contains: /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. Compilation failed in require at /usr/local/share/perl/5.14.2/PPI.pm line 19. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm line 19. Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5. BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm line 5. Compilation failed in require at /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Template/Plugins.pm line 206. ##### So I don't know if something is missing on my computer or if one of you encountered similar problems. If one of you has some ideas to help me going further, I would really appreciate! Thanks a lot in advance. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

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Energy shift after deglitch
by George Sterbinsky 11 Aug '15

11 Aug '15

Hello, I am writing to report a bug in Athena running on OSX 10.10.4. Here are the steps to reproduce the problem. I'm not sure that all steps are necessary. 1. Open Athena and import the attached project, which contains two groups that are both marked. 2. Change plot range to plot from -30 to 30 eV. 3. Select the "deglitch and truncate" window. 4. Select group "Ref data.merge". 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to -20. 6. Click replot margins. 7. Click remove points. 8. Click return to main window. 9. Click the derivative check box to plot marked groups as normalized derivative. 10. Click mu(E) button to plot marked groups as derivative of mu(E). When the last step is done the groups appear to shift with respect to each other. One can switch between Normalized and mu(E) and see the shift come and go. Thank you, George

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Unable to install demeter
by pushkar shejwalkar 10 Aug '15

10 Aug '15

Dear Users and Bruce, I am trying to install demeter with 64bits for my windows 7 professional laptop {4 gb ram, ample amount of free memory} . I tried downloading using both available links 1( on the left side of the window with the button for 64 bits and then by cliking the link in the text too. For some reason it didnt downloaded the file. I tried using 32 bits just to check and it started downloading * i didnt finish that and canceled the download since I dont need that one. Following error message appeared in the window This XML file does not appear to have any style information associated with it. The document tree is shown below. Could anyone help me with this whats wrong? I am using demeter on my other laptop and its working perfectly. Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

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XAFS short course in BNL on Nov 5-7: Save the date
by Anatoly I Frenkel 07 Aug '15

07 Aug '15

Dear IFEFFIT subscribers: Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National Laboratory. As many of you may know, we vary our themes from year to year, and we also vary the target levels for participants from beginners to intermediate to advanced. This year the target level for participants is "advanced", as suggested by the course title "Advanced topics in XAFS data modeling". It is similar in scope to our other courses on this subject (the latest one was offered in Brookhaven in 2010) that are available online: http://www.yu.edu/scc/workshops-courses/ This time the course will be divided in two parts: non-linear analysis methods (FEFF theory-based) and linear methods (based on methods of multivariate analysis and linear algebra such as LCF, PCA and MCR-ALS). Nov. 5 (Thursday) and Nov. 6 (Friday) will be devoted to lectures and demonstrations of the software. Nov. 7 (Saturday) will be practical session, in which registered participants will practice problem solving methods discussed in the previous days. Confirmed instructors are: Alain Michalowicz, Stephen Wasserman, Faisal Alamgir, Scott Calvin and Anatoly Frenkel. A full list of instructors and additional information on the course will soon appear on BNL web site. Participation in the practical data analysis session will be limited to 30 registered attendees, although auditors are welcome to attend the lectures and demonstrations on Thursday and Friday. For any inquiries please use contact info on the course web that will soon come online. Best regards, Anatoly Frenkel Yeshiva University Anatoly Frenkel, Ph.D. Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

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Demeter installation on partition "d" on Windows 7 32 bit -- programs do not start
by Rene Genz 05 Aug '15

05 Aug '15

Dear sir or madam, I would like to file a bug report. I can reproduce the problem with the following versions of Demeter: Demeter_Installer_for_Windows_0.9.22_(32).exe Demeter_Installer_for_Windows_0.9.23_(32)_pre1.exe downloaded from: http://bruceravel.github.io/demeter/ I have not tested other versions. I am using Windows 7 32 bit. I could reproduce this problem on two different computers with Windows 7 32 bit. During installation you are asked to define the installation directory. The default value is: c:\strawberry If you specify: d:\strawberry and continue with installation there are no error messages. However, after installation Artemis will not start. The start picture is shown but vanishes after a second. No other output. I tried Hephaestus (if memory serves right) and it has the same problem. I did not try other programs from the Demeter package. The log file taken from "%appdata%\demeter\dartemis.log" produced by Demeter_Installer_for_Windows_0.9.23_(32)_pre1.exe is attached. The mentioned files in the log are present. I replaced / with \ in the terminal commands: > dir d:\strawberry\perl\site\lib\auto\Ifeffit Volume in drive D has no label. Volume Serial Number is 7CA2-C104 Directory of d:\strawberry\perl\site\lib\auto\Ifeffit 05.08.2015 17:03 <DIR> . 05.08.2015 17:03 <DIR> .. 25.06.2014 16:18 0 Ifeffit.bs 08.07.2014 14:19 795.136 Ifeffit.dll 2 File(s) 795.136 bytes 2 Dir(s) 11.455.164.416 bytes free > dir d:\strawberry\perl\lib\DynaLoader.pm Volume in drive D has no label. Volume Serial Number is 7CA2-C104 Directory of d:\strawberry\perl\lib 15.04.2014 18:12 25.696 DynaLoader.pm 1 File(s) 25.696 bytes 0 Dir(s) 11.455.164.416 bytes free A workaround is: - uninstall demeter - install demeter to default installation directory "c:\strawberry" Kind regards, René

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