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

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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Possibly non-reproduceable fits
by Godfrey, Ian 04 Aug '15

04 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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Vanadium-Chromium Prussian Blue Analog XANES fitting
by Adora Graham 31 Jul '15

31 Jul '15

Hello, First of all, I am still very new to XAS analysis, so please excuse any misunderstandings I may have. I have a series of compounds nominally consisting of KxVx[Cr(CN)6] Prussian blue analogs (where x is ~1) with Cr(III) and presumably V(II) present in the system. From other evidence, the V(II) may be oxidizing to V(III). I have XAS data collected at the V and Cr K-edges from APS and have been struggling through trying to analyze my data using Athena. I am trying to get two things out of this data: First, I would like to get the oxidation state of the Vanadium sites. If they are not V(II), to get the ratio of V(II) to V(III) present, if possible. I have been trying to follow a similar analysis to Wong (Phys. Rev. B, 1984, 30, 10, 5596-5610). However, I seem to be running into the issue of finding standards with a similar ligand set to my sample. I have XAS data for the following standards: VO, V2O3, V2O4, V2O5, V(acac)3, VO(acac), VOSO4, and VSO4. I start with VSO4 as my initial vanadium source, so that could be useful for a comparison. Our initial idea was to use the vanadium oxides to give a standard curve to then extrapolate the oxidation state of my compound, but using this gives me an oxidation state of ~4.2 which seems unreasonable for my system. I am kind of lost otherwise as to what else I could do with this. Second, I would like to get the ratio of V to Cr. I was told I could compare the un-normalized K-edge heights of the vanadium to that of the chromium to get this ratio. This doesn't seem right, as I would think that there should be some relative intensity factor involved. Also, this gives me a fairly unreasonable value of 4:1, since XPS measurements give me values of around 1:1. Can you point me in the right direction for these issues? I've also attached the project files for one of my samples. Thanks, Adora

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Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
by Fowler, Joseph W. 30 Jul '15

30 Jul '15

Dear Ie-Rang, I’m the demeter maintainer on MacPorts, but I admit I am anything but a MacPorts guru. I notice that the error you showed is a failure to install gcc49. I don’t know if that new GCC is compatible with your old version of OS X, but that’s an issue that’s beyond my expertise. You might edit your variants file (it’s /opt/local/etc/macports/variants.conf on my installation) to insist on an earlier version by adding a line containing, e.g., “+gcc47” or whatever is your installed and preferred version of GCC. In fact, the port demeter does not depend (directly) on gcc, which you can see by issuing the command > port echo depof:demeter > port echo depof:demeter-devel So it looks to me like you have several steps to get ready for installing demeter. I admit that I recently discovered—but have not fixed—a flaw in the demeter port description file. The code depends on ports p5.16-file-which and p5.16-math-round, but these are not made explicit. I need to figure out how to add these to the explicit dependency list. I’m just back from vacation and a conference, so I have no excuses now. If you get far enough that you can install *but not run* demeter’s executables, then a workaround for this is > sudo port install p5.16-file-which p5.16-math-round And for MacPorts users in general: I understand that the project as a whole is in the process of trying to move to Perl 5.22 instead of 5.16. I’ll be updating the port file to reflect that change, too. Joe Fowler NIST Boulder Laboratories On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@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. HELP: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster (Ganesh Subramanian) From: Ie-Rang Jeon <jeon(a)northwestern.edu> Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:11:08 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:21:06 PM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang Perhaps there's anything useful in that log file? B ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed _______________________________________________ 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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Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 30 Jul '15

30 Jul '15

Dear all, I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems. 1. *Using the FOLP card*: The actual cluster size is about 180 atoms extending upto 18 A in radial distance from the central cobalt atom. But there are quite a few instances of Hydrogen atoms that are too close. I tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a syntax type error, that i cant figure out. I checked the crystal structure and the smallest hydrogen bond distance is 0.89 A. (I have attached the corresponding input and log file with suffix 'full cluster') 2. *SCF for small cluster*: Since the problem with the hydrogen distances persisted, I decided to run the calculation for a smaller cluster (about 50 atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this smaller cluster, there were about 3 of them, and none in the first or second shell of co-ordination) were removed manually. Now, I did not have the error on distances, did not require the FOLP card to be manually altered, but the log1 file seems to suggest that the SCF is not calculated. I cant figure why that is the case. (I have attached the corresponding input and log file with suffix 'small cluster') Sorry for the long email, and thank you for any suggestions. Ganesh

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HELP: failed to install gcc49 on mac (v10.6.8)
by Ie-Rang Jeon 29 Jul '15

29 Jul '15

Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed

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Setting ranges in peak fitting
by Kenneth Latham 28 Jul '15

28 Jul '15

Hi Bruce, To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their literature values with what I know about the material/where obvious peaks are in the NEXAFS. The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In other words, it would move peaks away from where I would expect them to be based on the literature. This can be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every peak multiple times. What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit quickly based on those. Cheers, Ken Latham ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Saturday, 25 July 2015 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 149, Issue 23 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. Setting ranges in peak fitting Athena (Kenneth Latham) 2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce) 3. Re: Setting ranges in peak fitting Athena (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jul 2015 00:14:18 +0000 From: Kenneth Latham <Kenneth.Latham(a)uon.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <CY1PR02MB1416E3DBC230406B078F9A07AA810(a)CY1PR02MB1416.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken ------------------------------ Message: 2 Date: Fri, 24 Jul 2015 13:14:03 +0000 From: "Ravel, Bruce" <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <xp7hq5h11j0ygmcc2btiht0f.1437743641853(a)email.android.com> Content-Type: text/plain; charset="us-ascii" Hi Ken, I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me. Are you asking whether you can put gaps in the fit range? B On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham(a)uon.edu.au> wrote: Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Two postdoctoral positions
by Anatoly I Frenkel 27 Jul '15

27 Jul '15

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunities. Physics Department of Yeshiva University in New York City has two openings for postdoctoral research associate positions, beginning in September 2015. The first position is for the project: "Collaborative research: Toolkit to characterize and design bi-functional nanoparticle catalysts." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for X-ray absorption spectroscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods, including analysis and modeling of nanoparticles, and experience with in situ characterization methods by XAS and other techniques. The second position is for the project "Multidisciplinary research for the advancement of filtration materials: Uptake, decomposition, and catalysis for Agent-POM/MOF Chemistry". The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for high energy XRD-PDF characterization of novel POM/MOF materials in reaction conditions. Required qualifications: Ph.D. in chemistry, chemical engineering or materials science, expert knowledge of XRD-PDF technique and data analysis, experience with analysis of MOFs, experience with in situ and/or operando methods of synchrotron characterization. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Setting ranges in peak fitting Athena
by Kenneth Latham 24 Jul '15

24 Jul '15

Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken

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Plotting chi(k) linear combination fit in energy
by Ellen Daugherty 21 Jul '15

21 Jul '15

Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab <http://borch.agsci.colostate.edu/> Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/

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Artemis Crashing on Opening Project Files (Windows 7)
by alexander.thoma＠diamond.ac.uk 20 Jul '15

20 Jul '15

Hi all, I couldn't seem to find anything like this on the mailing list, I'm having issues reopening saved Artemis (0.9.21) projects on Windows 7, the program opens and runs through the 'importing' text in the bottom left of the control window before shutting down immediately with no error message or warning before any other windows appear. The problem seems to occur sporadically with projects with fits from crystal structures and all the time with those done with quick first shell fits, and doesn't occur with project files where no fits have been made. Attached is the log file for one of the non-opening projects, any suggestions? Many thanks, Alex -- 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

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Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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phase problem copper
by Neeb, Matthias 15 Jul '15

15 Jul '15

Dear all, I have a standard exafs spectrum of copper K-shell and everything looks as expected (Chi(E), Chi(k), Chi(R), Chi(q) …) when using Demeter 0.9.21 . However the phase spectrum of (Chi(q)) appears quite different to literature (e.g. B.K. Teo, Inorganic Chemistry Concepts 9; Martens et al, PRB 17, p1481 (1979), i.e. positive slope, a factor of ~10 larger values on y-axis. Any reason why? Thanks for your answer in advance. Regards, Matthias ________________________________________________________________________ Matthias Neeb Helmholtz-Zentrum-Berlin fuer Materialien und Energie - senior scientist - ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 12 Jul '15

12 Jul '15

Dear Matt, Thanks for that suggestion. I just got time to work on it again. In the meantime, I noticed your email response to another question of similar nature. It works fine now ! Of course, I have not yet performed any calculations/analysis to see if there are any additional problems (if any). But so far so good. Thanks for your help, Ganesh On Wed, Jul 8, 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. Re: Demeter Crashes on opening in Windows Bootcamp > (Ganesh Subramanian) > 2. Re: Demeter Crashes on opening in Windows Bootcamp (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jul 2015 01:07:56 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: > <CAAb9e-d2Kvx=VZRmNPOVBcgpCvqD3x= > t4VLLRdDRFtDJMBUURQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > > > > Dear Bruce and Matt, > > > > > > > > My first guess is that the culprit is anti-virus software running on > > Ganesh's computer. I have seen other examples of parts of Demeter being > > falsely identified as problematic and being removed, rendering the > > Demeter programs unusable. > > > > That said, on Ganesh's computer, the gnuplot executable should be in > > > > C:\strawberry\c\bin\gnuplot\bin > > > > Yes - I can locate it exactly at this path and the executable file does > open from there. > > > > > > > There are some other conceivable ways to see this problem, but I am > > placing my first bet on over-aggressive anti-virus software. > > > > I did have McAfee. I uninstalled the program and restarted my computer > and > the problem still persists. It seems very much the same, im posting the > most recent log-file. > > > > > *************************************** > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 149, Issue 8
by Ganesh Subramanian 12 Jul '15

12 Jul '15

Dear Matt, Thanks for that suggestion. I just got time to work on it again. In the meantime, I noticed your email response to another question of similar nature. And it works fine now ! Of course, I have not yet performed any calculations/analysis to see if there are any additional problems (if any). But so far so good. Thanks for your help, Ganesh On Wed, Jul 8, 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. Re: Demeter Crashes on opening in Windows Bootcamp > (Ganesh Subramanian) > 2. Re: Demeter Crashes on opening in Windows Bootcamp (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jul 2015 01:07:56 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: > <CAAb9e-d2Kvx=VZRmNPOVBcgpCvqD3x= > t4VLLRdDRFtDJMBUURQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > > > > Dear Bruce and Matt, > > > > > > > > My first guess is that the culprit is anti-virus software running on > > Ganesh's computer. I have seen other examples of parts of Demeter being > > falsely identified as problematic and being removed, rendering the > > Demeter programs unusable. > > > > That said, on Ganesh's computer, the gnuplot executable should be in > > > > C:\strawberry\c\bin\gnuplot\bin > > > > Yes - I can locate it exactly at this path and the executable file does > open from there. > > > > > > > There are some other conceivable ways to see this problem, but I am > > placing my first bet on over-aggressive anti-virus software. > > > > I did have McAfee. I uninstalled the program and restarted my computer > and > the problem still persists. It seems very much the same, im posting the > most recent log-file. > > > > > *************************************** > > >

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Demeter won't start in Windows 7
by willn 12 Jul '15

12 Jul '15

Hi everyone, My copy of Demeter on my Windows 7 machine stopped working at some point in the recent past, so I have re-installed it, but I still have the same problem - a command window and splash screen open briefly, before disappearing. In my Path variable I have bumped the perl addresses up above the MinGW one, as suggested in one of the common fixes, but this did not solve the problem. I had a good look through the mailing-list archive for similar problems to mine, but each seem to be different (the log file errors were different). I have commented out the appropriate lines in the batch files, but, predictably I guess, this only had the effect of removing the splash screen when the program attempts to start-up. I have also played around a little installing newer versions of Strawberry, but similarly to no avail. If time permits, would anyone mind helping me interpret my log file (attached)? I'm not really computer literate enough to understand what is written there! Grateful thanks in advance, William -- William Nash PhD Student, Experimental Petrology Earth Sciences Department Oxford University

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