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

Re: [Ifeffit] Athena Question
by Bruce Ravel 27 Jul '16

27 Jul '16

On 07/27/2016 12:01 PM, Tyson, Trevor A. wrote: > Hi Bruce, > > I know that you are very busy building beaminles but I could not > resist adding more to your load. I have an Athena question. I have > aligned a large set of data to a reference. Now for each data set > Athena records the energy shift. Is it possible to export the list of > shifts? Thanks. > > Trevor > Hi Trevor, Hope you don't mind that I am CCing this to the Ifeffit mailing list. The question seems broadly interesting, so leaving an answer in a place that can be found by google seems like a good idea. There are a several ways of doing this: 1. Right click on the label that says "Energy shift". one of the options is "Show energy shifts of all groups". That will post a dialog like the one in the attached picture. Click the "Save" button to write the contents as a text file. 2. Click on the File menu, then on the Export submenu. Select "Excel report on marked groups". This will write an XLS file. You can open that up in Excel or any other spreadsheet program. Column E has the energy shifts. 3. For the sake of completeness, if you are a command line kinda guy, you can use the "dlsprj" program that gets installed when you install the rest of demeter: dlsprj myproject.prj --params=bkg_eshift,bkg_delta_eshift This will print the shifts and their uncertainties to the screen. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Problem with Artemis opening an Athena project
by Irina Pi 27 Jul '16

27 Jul '16

Dear all, I have a problem opening an Athena project with Artemis. When I have selected it, it appears this error: Use of uninitialized value in addition (+) at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Prj.pm line 132 And after selecting OK and import selected data, everything closes. This Prj.pm file is attached in the mail, if it is of any help. Thank you. Best regards, Irina Pi.

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about sigma square
by Bruce Ravel 26 Jul '16

26 Jul '16

Shaofeng Wang asked this question on the mailing list that some may not have seen because it got marked as spam somewhere along the line. Kinda weird. Not quite sure why that happened.... > I have a question about sigma square. Must this parameter be in the > range of 0.003-0.02? I obtained some of it in the range of > 0.0001-0.002. Is this reasonable? Could please provide some > reference? There are no hard rules for anything. That sigma^2 is 0.00something is a good guideline and often the case, but not an actual rule. The problem with a sigma^2 in the range of 0.0something is that it tends to attenuate the path so much that it doesn't really have an impact on the quality of the fit. In that case the uncertainty is often very large precisely because the path no longer contributes significant spectral weight to the fit. A sigma^2 in the range of 0.000something means that the bond is very stiff. In some situations, that would be correct. As an example, consider the sort of negative thermal expansion material that is a network of metal-ligand octahedra. The NTE effect happens in that case because, as the material heats, up the octahedra tilt within the network, pulling the network inwards. This happens because the metalligand (usually metal-oxygen) bond is very strong -- much stronger than the forces connecting the octahedra. In an EXAFS measurement of an NTE material, you will likely find a very small sigma^2 for the first shell. (And a very large one for the second shell.) Regardless of the size of sigma^2, the bottom line is that the value is defensible. This means that you can understand and explain why sigma^2 is the size that it is. It also means that the uncertainty is such that you can support your conclusion. While the red line might overplot the blue with sigma^2=0.0003+0.001, that may be a troubling result because sigma^2 is not positive definite! Executive summary: a reasonable value is a defensible value. If you are willing to explain a result to your thesis committee or let one of us review it in a manuscript, then the result is probably reasonable. HTH, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Help with Athena
by Irina Pi 26 Jul '16

26 Jul '16

Dear all, I am just getting started with XAFS projects and I am using Athena software for processing and analysing the data. I am learning how to use it, and I have a little problem. The thing is that when I plot the XANES data, the automatic created plot is not labeled and plus it doesn't have the option of selecting a point of the spectrum. I mean, when I want to choose E0 for example, I need to do it changing the number in the Athena screen, and I don't know exactly what I am choosing because it doesn't appear anything in the graph. Was I clear? Do you know any way which I could solve it? Thank you very much, Regards, Irina Pi.

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Re: [Ifeffit] Regarding time resolved XAS
by Chris Milne 26 Jul '16

26 Jul '16

Hi Mazhar, Usually time-resolved (pump-probe) XAS is measured in data set pairs at each X-ray energy: one with laser on, one with laser off. This means that you can always directly reference your laser-excited measurement to your laser un-excited measurement. To calibrate to an absolute scale you would then use a reference foil as normal and shift both data sets according to the reference values. If you had significant delays between your laser on/off measurements then drifts and other noise sources will affect your data, making it very difficult to determine a reliable difference signal. You could try to use a reference foil measurement to correct for these kinds of drifts but you need to be very careful with the corrections to ensure you aren’t just seeing an artifact. Ideally you would be measuring laser on/off differences on a millisecond to microsecond timescale between acquisitions, this gets rid of most of the possible noise sources. Best, Chris > On 30 May 2016, at 19:00 , 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. Regarding time resolved XAS (mazhar iqbal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 May 2016 06:20:36 +0000 (UTC) > From: mazhar iqbal <mazharphy_05(a)yahoo.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Regarding time resolved XAS > Message-ID: > <349705754.1395970.1464589236411.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > hello.. I am sorry if am not posting on right place. > I want to ask about the aligning the XAS spectra that is given in Athena. Can we do the alignment of time resolved spectra? As you know that the resolved spectra (IR pump X-ray probe) may have edge shift due to laser pumping. Do you think that the same method of the alignment can be applied here as well. An additional piece of information is that ?we have a reference fluorescence line always on the screen that well behind the K absorption edge. > Hoping to see your response.? > Best Regards >

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Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Ifeffit] Bug Report importing file.
by Samy Ould-Chikh 25 Jul '16

25 Jul '16

Just a quick idea on why I cannot import the .txt file attached with previous email. I realized that the files contain 11948 points ! (it's QEXAFS data). Athena might have an hard limit of 8200 points that may be imported in a single file. Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx -----Original Message----- From: Samy Ould-Chikh Sent: Sunday, July 24, 2016 10:56 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Bug Report importing file. Hello, I have some issue to import a file in Athena: just a simple x-y column (.txt attached with this email). Ti K-edge. Data range in the file : 4916.30 up to 5436.88 eV. Issue: only data up to 5260 eV are imported (see screenshot: bug-importation). Version: Demeter 0.9.24 System: Windows 7 Professional SP1 Well, I hope it's just not me not being able to find a proper way to import the file... Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa Website: http://kcc.kaust.edu.sa/Pages/Home.aspx ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Dear all, I recently upgraded my mac to OSX El Capitan, and tried to install demeter following the steps at http://bruceravel.github.io/demeter/ XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo port install xorg-server demeter”, it showed: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter ---> Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a long list) Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from various websites, it showed: Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0 Error: Failed to install libcxx Please see the log file for port libcxx for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log The log file is attached. What should I do to fix it? Any suggestion will be appreciated. Thanks. Yuan

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Re: [Ifeffit] demeter installation in OSX El Capitan
by Ping, Yuan 21 Jul '16

21 Jul '16

Hi Joe, Thanks for your reply. In my first email I forgot to mention that I did install MacPorts-2.3.4-10.11-ElCapitan. Yuan On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" <ifeffit-bounces(a)millenia.cars.aps.anl.gov<mailto:ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of joe.fowler(a)nist.gov<mailto:joe.fowler@nist.gov>> wrote: Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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demeter installation in OSX El Capitan
by Fowler, Joseph W. (Assoc) 21 Jul '16

21 Jul '16

Dear Yuan, Thanks for the log file, but I’m afraid I don’t know what your Mac Ports problem is. The log file indicates a failure to fetch the archive at all. After waiting a day, did the problem go away? My workplace has lots of rules about how and when to upgrade to El Cap. As a result, I have not done it myself yet. Have you visited the Mac Ports team’s page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems There are no specific problems mentioning libcxx, I notice. Did you remember to re-install Mac Ports itself? If not, then problems are inevitable. Also, are Xcode and its command-line tools both updated to match the OS? If you’ve followed all the upgrade instructions and cannot install libcxx, then I think you have a Mac Ports problem and should look to that project’s issue tracker (possibly filing an issue yourself). Best wishes, Joe Fowler NIST Boulder Labs

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