August 2015 - Ifeffit - millenia.cars.aps.anl.gov

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 06 Aug '15

06 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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Possibly non-reproduceable fits
by Godfrey, Ian 05 Aug '15

05 Aug '15

Dear All, Please bear with me here - it's possible I've done something stupid without spotting it - but I was fitting some data in Artemis and have two fits, that I am convinced should be identical (same data, same k and r windows, same paths, same GDS etc. etc.), but are not. What I did was as follows (fit numbers refer to the Artemis history file in the attached project): I set up a fit to some data, simultaneously refining at Au and Ag edges to Au-Au/Au-Ag/Ag-Au/Au-Ag paths (fits 1 & 2), and then tried a different fit, this time with Ag-Cl paths as well (fits 3&4). I then fitted the original model again (fit 5 - this was slightly different to 1 & 2, but not enough for me to notice at the time). I then closed Artemis and finished for the day. Today I came back, reloaded the project file, saved it in a new location, and tried to pick up where I left off. I performed one fit where I'd set the values to def, rather than guess, by mistake (fit 6) and then corrected this when I realised what I'd done. However when I tried to re-run the model with Ag-Cl paths I was getting wildly different results to the first time (Fits 7&8). As far as I can tell these models should be identical to fits 3&4. Both datasets were chi(k) data imported directly into Artemis. OS: Win 8.1 Ent x64 Demeter: 0.9.22 pre something x64 I've attached the following: Artemis project (artemis.fpj) Logs from fits 3 and 7 for comparison (fit3.txt, fit7.txt) Artemis log file (dartemis.log). (Also possibly worth noting is that Artemis seems to have lost the file locations (in the log files and the data window), first for the Au edge data, and then for both datasets; however when I plot the data it all seems present and correct!) Any insight gratefully received! Thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Localisation issue with plots in Demeter 0.9.22
by Godfrey, Ian 04 Aug '15

04 Aug '15

Dear All, There seems to be an issue with the way plots are displayed on non-English computers: My office PC is Japanese (although set to English) and I'm seeing spurious katakana (Japanese) characters in the GNUPlot plots generated by Artemis (as well as an Angstrom that's missing its circle)! Screenshot attached. System: Demeter 0.9.22 x64, Win 8.1 Ent x64. Regards, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 3
by Abhijeet Gaur 04 Aug '15

04 Aug '15

Hi Max, Thanks for the explaning the probable reason of smaller particle sizes determined by EXAFS. I will also try to refine my fittings. Hi Anatoly, Can you please send me the link of that recent paper again as I am unable to find it in your earlier message. Abhijeet On Mon, Aug 3, 2015 at 6:04 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. Re: Ifeffit Digest, Vol 150, Issue 2 (Abhijeet Gaur) > 2. Re: Measuring particle size by coordination number (Maxim Boyanov) > 3. Re: Measuring particle size by coordination number > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Aug 2015 13:49:40 +0200 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2 > Message-ID: > < > CAEq27Q1Fde2qTQyrgaAMaTJ1wUpoXydxOcS0v73MPXdAKJs_zA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thanks for your quick reply. So, I have to add more paths to > the fitting and then try to determine the size of the particle. > > Also, I want to add some analysis details to confirm that I am > on the right path. > > The value of amp is obtained from fitting of metal foil, i.e., > 0.84 (0.03) and is kept fixed during the fitting of the sample. > > S02 is defined by the formula S02 = > amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). > > With thanks > > Abhijeet > > > > > > > > > > Message: 2 > > Date: Mon, 3 Aug 2015 07:11:53 -0400 > > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Measuring particle size by coordination number > > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Abhijeet, > > > > The formula looks poorly when it is only applied with one path. > > > > The strength of this approach, and of Anatoly Frenkel?s alternative > > strategy for finding particle sizes, is that it compares coordination > > numbers for different shells, helping to break the correlations between > N, > > S02, and sigma2. > > > > Even then, it tends to report sizes that are small compared to those > > provided by other techniques, but compares sizes between different > samples > > quite well. > > > > ?Scott Calvin > > Sarah Lawrence College > > > > > > > > > -- > *Dr. Abhijeet Gaur* > *Post doctoral fellow in the Institute for Chemical Technology and Polymer > Chemistry * > *Karlsruher Institut f?r Technologie (KIT), Karlsruhe Germany.* >

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Measuring particle size by coordination number
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi all, Sorry, I may be asking a question already asked in the mailing list, but I am unable to get it from the earlier discussions. I am reading one of the research article ´´ Determination of crystallite size in a magnetic nanocomposite using extended x-ray absorption fine structure´´ .J. Appl. Phys,. vol 94, page 778, 2003 In this paper there is a formula N_nano = [1-3/4(r/R)+1/16(r/R)^3]N_bulk, which you said can be used in the Artemis for extracting the particle size. I am trying to use this formula for determination of size of Ni particles in an Ni / Al2O3 catalyst. From TEM the size determined is around 4 nm. So, I am trying to fit the theoretical model of Ni metal to the sample data in the Artemis I defined a guessed parameter R and then put the whole formula for S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). The value of R I am getting is 0.81 (0.05) which is quite small. Is there something I am missing in the formula or I have to define the N seprately for sample cooridnation number. Currently, I am using only the first path in the fitting. With thanks Abhijeet Gaur -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi Scott, Thanks for your quick reply. So, I have to add more paths to the fitting and then try to determine the size of the particle. Also, I want to add some analysis details to confirm that I am on the right path. The value of amp is obtained from fitting of metal foil, i.e., 0.84 (0.03) and is kept fixed during the fitting of the sample. S02 is defined by the formula S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). With thanks Abhijeet > > > Message: 2 > Date: Mon, 3 Aug 2015 07:11:53 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Measuring particle size by coordination number > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Abhijeet, > > The formula looks poorly when it is only applied with one path. > > The strength of this approach, and of Anatoly Frenkel?s alternative > strategy for finding particle sizes, is that it compares coordination > numbers for different shells, helping to break the correlations between N, > S02, and sigma2. > > Even then, it tends to report sizes that are small compared to those > provided by other techniques, but compares sizes between different samples > quite well. > > ?Scott Calvin > Sarah Lawrence College > > > -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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