Re: [Ifeffit] Ke
Dear Pushkar/Ke, I normally use different e0 values in Athena based on what I want to do: 1. e0 for energy scale calibration A generally accepted method is to use derivatives to match the energy scales, as described in the previous threads. I apply this to a known standard and shift the energy scale of the other spectrum that I want to calibrate by the same extent. 2. e0 in EXAFS modelling After I know that the energy scale I have is correct, then in EXAFS modelling, e0 is now the point where your EXAFS backscattering starts. That's why we are trying to avoid white lines here. It took me some time to figure out that e0 could mean several different things. There is a rich history in IFEFFIT discussion on e0, examples: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-June/011841.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-June/011836.html http://cars9.uchicago.edu/pipermail/ifeffit/2004-June/005614.html Best wishes, Sin Yuen -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Carlo Segre Sent: 15 October 2014 22:56 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ke Either way is fine but I would suggest taht you not use the calibrate function, just read off the zero crossing and put it into the E0 location. Calibrate actually shifts the data and that is not necessarily what you want to do, particularly if you are comparing spectra.. Carlo On Thu, 16 Oct 2014, Pushkar wrote: Dear Ke Is there a reason you use first derivative?? I thought if you take second derivative on Athena and then click find zero and then calibrate that value is the correct way. I am learning XAFS myself for the first time and I am novice too. So may be I make no sense but just want to confirm if I am not doing anything wrong. What's your stake in this?? Pushkar Pushkar Shejwalkar Post-doctoral researcher, JSPS fellow, Catalysis Research Center Hokkaido University, Sapporo Japan-0010020 On १६ ऑक्टो, २०१४, at १२:२७ म.पू., Ke Yuan key...@umich.edu wrote: Hello Sin Yuen, Thanks for forwarding me that study materials on E0. I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen. Tks! Ke ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498Fax: 312.567.3494 se...@iit.edu http://phys.iit.edu/~segre se...@debian.org ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS xQuartz
On 10/15/2014 11:00 AM, Gaspard Jean-Pierre wrote: Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : X11 is not installed. I am missing something but I do not know what. I would guess that you are not getting an answer to your question because you are asking about an unsupported, 8-year-old version of the software. If you have some compelling reason to use that particular version, you could search through the archives of this mailing list for some hints on how to address your problem. Not being a Mac owner myself, I surely don't know how to solve it. Another option is to use a recent, supported version of the software: http://bruceravel.github.io/demeter/#mac B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] (no subject)
Hello Pushkar, I think the peak value of the first derivative and the zero value of the second derivative does the same thing. My sec deriv is very noisy so it's easy for my to pick the peak value of the 1st deriv instead. I would suggest you to watch the video from Bruce which explained HOW TO PICK Rbkg at: http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html Click the Athena: Data processing II Actually all the other video lectures are very helpful, too! Best, Ke ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] XAFS Analysis using Ifeffit
Hello Drew, Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic? For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials? Best, Ke ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] XAFS Analysis using Ifeffit
Hi Ke, Unfortunately, it looks like your data is showing the classic symptoms of self-absorption . The white line for UO2 is fairly pronounced, and should look like the attached picture. Not sure on the setup at 12-BM-B, but next time ask if you could collect both fluorescence and transmission data at the same time. It can really save your behind. You can dilute in whatever low Z compound you’d like, I think things like SiO2 and boron nitride are common because of their low Z. Graphite might work also. Powder smears on tape are pretty common because you can fold/unfold to vary the amount of material in the beam. (though one can’t manipulate those at the beamline with a dispersible rad powder like UO2.) Best, Drew From: Ke Yuan [mailto:key...@umich.edu] Sent: Thursday, October 16, 2014 8:39 AM To: ifeffit@millenia.cars.aps.anl.gov; Latta, Drew E Subject: Re: XAFS Analysis using Ifeffit Sorry here is the picture! On Thu, Oct 16, 2014 at 9:37 AM, Ke Yuan key...@umich.edumailto:key...@umich.edu wrote: Hello Drew, Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic? For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials? Best, Ke -- Ke Yuan PhD Candidate Department of Earth and Environmental Sciences 1100 North University Ave 3021 C.C Little University of Michigan, Ann Arbor MI 48109-1005 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] XAFS Analysis using Ifeffit
Thank you! Best, Ke On Thu, Oct 16, 2014 at 11:01 AM, Latta, Drew E drew-la...@uiowa.edu wrote: Hi Ke, Unfortunately, it looks like your data is showing the classic symptoms of self-absorption . The white line for UO2 is fairly pronounced, and should look like the attached picture. Not sure on the setup at 12-BM-B, but next time ask if you could collect both fluorescence and transmission data at the same time. It can really save your behind. You can dilute in whatever low Z compound you’d like, I think things like SiO2 and boron nitride are common because of their low Z. Graphite might work also. Powder smears on tape are pretty common because you can fold/unfold to vary the amount of material in the beam. (though one can’t manipulate those at the beamline with a dispersible rad powder like UO2.) Best, Drew *From:* Ke Yuan [mailto:key...@umich.edu] *Sent:* Thursday, October 16, 2014 8:39 AM *To:* ifeffit@millenia.cars.aps.anl.gov; Latta, Drew E *Subject:* Re: XAFS Analysis using Ifeffit Sorry here is the picture! On Thu, Oct 16, 2014 at 9:37 AM, Ke Yuan key...@umich.edu wrote: Hello Drew, Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic? For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials? Best, Ke -- Ke Yuan PhD Candidate Department of Earth and Environmental Sciences 1100 North University Ave 3021 C.C Little University of Michigan, Ann Arbor MI 48109-1005 -- Ke Yuan PhD Candidate Department of Earth and Environmental Sciences 1100 North University Ave 3021 C.C Little University of Michigan, Ann Arbor MI 48109-1005 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] PCA not enabled on Mac version of Demeter: Athena
Frank, I apologize for not responding sooner, other urgent issues suddenly came up! I followed Bruce's installation directions on the Demeter page ( http://bruceravel.github.io/demeter/) and the Xcode ( https://guide.macports.org/#installing.xcode) and Macports ( https://www.macports.org/install.php) installation instructions. I had issues the first time I tried to install Demeter (i.e. text in Terminal indicated things weren't proceeding successfully and it was taking a long time), but the second time, it appeared to work. I now am receiving the command not found response when trying to open the Athena program in Terminal. I don't know why that didn't happen earlier. Ellen On Wed, Oct 8, 2014 at 3:55 PM, Schima, Frank frank.sch...@nist.gov wrote: On Oct 7, 2014, at 5:08 PM, Ellen Daugherty daughert...@gmail.com wrote: Bruce and Frank, In response to Bruce's suggestion: A simple way to test from the command line whether the modules can be loaded is to do perl -e 'use PDL::Lite' My output is: Can't locate PDL/Lite.pm in @INC (@INC contains: /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at -e line 1. BEGIN failed--compilation aborted at -e line 1. In response to Frank's suggestions: $ port installed perl5 My output is: -bash: port: command not found And for, $ echo $PATH My output is: /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Does this mean that there is a problem with the Macports location? It means your path is not setup to find Macports. It says nothing about if Macports is installed or not. So when you run “perl” you are using the OS X perl and of course that won’t work. Now I’m really curious. Given this, how did you install the demeter-devel port and how are you actually running demeter programs? You would have encountered the same “command not found “ errors unless your path was correct like mine is. -Frank Thank you! Ellen On Tue, Oct 7, 2014 at 2:18 PM, Schima, Frank frank.sch...@nist.gov wrote: On Oct 7, 2014, at 1:29 PM, Bruce Ravel bra...@bnl.gov wrote: On 10/07/2014 02:43 PM, Schima, Frank wrote: I’m going to need specific steps to reproduce the issue. As I understood the issue from Ellen's first message, the problem is that Athena is not able to find the modules PDL::Lite (which should be installed when PDL is installed) and/or PDL::Stats::GLM. If I force Athena to fail to load one of them, then selecting Principle Components Analysis from the main menu will look like the first attachment. If Athena can find those two modules, the selecting Principle Components Analysis will look like the second attachment. The test in Athena is really simple. If those two modules can be loaded successfully, then the PCA tool will display properly. If not, that message is the graceful fall back. My guess is that one or both of those perl modules is not being found on Ellen's computer. A simple way to test from the command line whether the modules can be loaded is to do perl -e 'use PDL::Lite' or perl -e 'use PDL::Stats::GLM' If they cannot be found, then perl spits up an error message. If they can, then nothing happens. Nothing happens for me. So they are installed. At this point it looks like an issue with her Macports install. I would start by verifying that she is correctly using perl 5.16 in Macports. What is the output of the following? $ port installed perl5 Here is my output. The following ports are currently installed: perl5 @5.12.4_0+perl5_16 (active) Then the Macports perl needs to be in your path. What is the output of the following? $ echo $PATH My output is: /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin Cheers! Frank B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ pca_wrong.pngpca_right.png ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov
