February 2009 - Ifeffit - millenia.cars.aps.anl.gov

Lost second shell
by Eugenio Otal 03 Feb '09

03 Feb '09

Anatoly, Here I attach some pictures. I also have luminescence measurements an found a great disorder but I could not find changes in the cell parameters by XRD refinements. I perfored XANES simulations for ZnO sustituted by Er and the spectra is really different. I cannot believe that the Er is in Zn site, but maybe the structure changes and the simulation is not so "real". euG

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Re: [Ifeffit] Self absorption Correction
by Carlos Prieto 02 Feb '09

02 Feb '09

Jens, Let me give you an old reference (but still usefull) for the self absorption treatment: R. Castañer and C. Prieto, "Fluorescence detection of EXAFS in thin film samples", J. de Phys. III (France), 7, 337-349 (1997). Best regards Carlos Prieto At 15:51 02/02/2009, you wrote: >Jens, > >Since no one has answered yet, I'll chime >in. First let me direct you to a discussion of >self-absorption and other sample-related >distortions: ><http://www.xafs.org/Experiment/OverAbsorption>http://www.xafs.org/Experiment/OverAbsorption >(this is a link from the tutorials page of <http://www.xafs.org>www.xafs.org) > >As for your questions: > >I think that you should use the non-normalized >XANES data to perform the SA correction. > >for the angle-in and angle-out meanings, see >Grant Bunker's paper on self-absorption >here: ><http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf>http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf > >Now, how do you determine if you have >self-absorption effects? I have to defer here >to those with more experience. What you suggest >sounds appropriate, but I'm not sure how you >could determine this without studying multiple >concentrations of your absorber and watch the >signals, i.e. does a 10% increase in absorber >concentration translate to a 10% increase in >fluorescence yield (similar to what Matthew >Marcus and Alain Manceau describe in their >paper, from the over-absorption link above). > >HTH, >-Rich > >On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse ><<mailto:jens.kruse@uni-rostock.de>jens.kruse(a)uni-rostock.de> wrote: >Hi there, > >I have measured a pure reference compound with high absorber >concentration in fluorescence mode (P K-edge XANES). I tried to use the >Self absorption correction included in Athena but I don't really >understand the results. >Fist: Do I have to use the edge step normalized spectrum or the spectrum >without normalization ? I tried both and the results of course a quite >different. I would rather use the not normalized spectrum. >Second: the value "Angel in" is this the angle between the incident >beam and the sample surface" and "Angle out" the angle between the >sample surface and the detector position? >Third: More general- How can I identify a spectrum suffering self >absorption? Just comparing the relative peak intensities of total >electron yield signal with the fluorescence yield signal ? > >thanks a lot for your comments, >cheers, > Jens > >-- >Jens Kruse >Institute for Land Use >Faculty for Agricultural and Environmental Sciences >Rostock University >Justus-von-Liebig-Weg 6 >18059 Rostock GERMANY >Phone: +49(0)381-498 3190 > >_______________________________________________ >Ifeffit mailing list ><mailto:Ifeffit@millenia.cars.aps.anl.gov>Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ================================ Carlos Prieto Instituto de Ciencia de Materiales de Madrid CSIC Cantoblanco, 28049 - MADRID (Spain) Tel.: 91 3349017 e-mail: cprieto(a)icmm.csic.es =================================

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Self absorption Correction
by Jens Kruse 02 Feb '09

02 Feb '09

Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value "Angel in" is this the angle between the incident beam and the sample surface" and "Angle out" the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190

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Guessed parameter and Einstien temperature
by abhijeet gaur 02 Feb '09

02 Feb '09

Hi Thanks a lot Scott , I got that how to change ss for difeerent path by using the function debye(temp, thetad).But I am not getting the same result in case of delr . I took the different parameter as follow : guess amp 1 def delr alpha*reff guess enot 0 def ss debye(temp,thetad) set alpha .0002 set thetad 343 set temp 298 But I am not getting a very good fit. The value of debye temperature is 343 for Cu( Kittel book) but I got to know that some persons even guessed the value of thetad as 285+-16 . I am not getting that how we can guess the value of alpha and thetad . Also I am not getting the value of Ei, 3rd and 4th cumulant in the fit results . So How can I get the value of these parameters in the fit results . With thanks Abhijeet Gaur

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Lost second shell
by Eugenio Otal 02 Feb '09

02 Feb '09

Hi all, I am working with Er doped ZnO and the EXAFS measurements (Er L3) shows that I have not a second shell when I perform the FT. I checked that the phase is not destroying the signal, and that is not the guilty guy. I have two possibilities, that the erbium is segregated on the surface of the particles with a strong disordered phase that destroy second shell information (XANES simulation are different from oxide and hydroxides) or that the atoms are isolated in the surface of the particles. Should I use the card for molecules for isolated atoms? And for the disordered phase, what can I do? Is there another possibility to lose the second shell? Thanks in advance, euG

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Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Carlo Segre 01 Feb '09

01 Feb '09

Hi Yordy: I'm sorry. The xdp module is one that was written here by my group to provide I/O for data files produced at our beamline. I have packaged it for Debian but it is not out there for the general public yet. In the program I sent you the xdp module is only used to write out the converted data is a file format that we call SFF (Simple File Format). The xdp module is not necessary if you simply write out the converted data with a more normal set of commands. Your email got me thinking though that I should finish the progrram and make it useful to others. What I did, therefore, is to rewrite the program without the use of xdp and making it a bit more user-friendly. It now also handles both of the filetypes that Matt mentioned on a previous post, and which are documented at http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379… The program now runs fine under Python 2.5 (I don't know about 2.6 but let me know if it has problems!). It is used as a standard *nix filter, that is, rename it to "lytle_convert" (or make a link to it) and make sure it is executable and in the executing PATH so the system can find it. The program is invoked from the command line as $lytle_convert file0 [file1 file2 file3 ... fileN] It does take wildcards so you can process a bunch of files at once. Since all the Lytle database files are of the form "name.ext", the output file name is made to be "name_ext.sff". The program does its best to guess the steps per degree for the olert file type which does not include that information in the header. The d-spacing is assumed to be 1.92017. This may not work for all files (I have not checked and I didn't have time to put in more intelligence right now) so you might need to go in to modify the program to change these defaults. I am thinking that I will add options to let the d-spacing and steps per degree be set on the command line but that will have to wait for later. Enjoy! Carlo On Sat, 31 Jan 2009, Yordy Licea Fonseca wrote: > Hi Carlo, > > I´ve installed Python 2.6 for Windows XP to run your code. Latter I've > installed a numpy 1.2.1 compiled for 2.6. I did neither find the > *Numeric *module > nor the *xdp* module you initialized first in the code. So I've intalled Py > 2.4 version and again numpy, but didn not work. > In 2.6 there is a *math* module that works similar to *Numeric*. As I did > not find what *Numeric.zeros* does in line 32 I could not implement (if it > were possible) with *math.* > Could I use *xdrlib* module instead of *xdp?* > ** > Would you send me or tell me please where to find those modules and which > Python you recommend me to install? > > Best wishes, Yordy > > > > > 2009/1/29 Carlo Segre <segre(a)iit.edu> > >> Ah, just premature sending... >> >> Carlo >> >> On Thu, 29 Jan 2009, Yordy Licea Fonseca wrote: >> >> Hi Carlo and Matt, >>> >>> Thank you very much for your help. >>> >>> Best wishes, >>> >>> Yordy >>> >>> >>> On 29/01/2009, ifeffit-request(a)millenia.cars.aps.anl.gov < >>> 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. Trouble with fitting with Artemis (Juraci A. Sampaio) >>>> 2. Re: Trouble with fitting with Artemis (Richard Mayes) >>>> 3. about Farrel Lytle data of Na2WO4.2H2O (Yordy Licea Fonseca) >>>> 4. Re: about Farrel Lytle data of Na2WO4.2H2O (Matt Newville) >>>> 5. uncertainty in linear combination analysis (Pushan Shah) >>>> 6. Artemis parameters (abhijeet gaur) >>>> 7. Energy shift (Eugenio Otal) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Wed, 28 Jan 2009 15:34:55 -0300 >>>> From: "Juraci A. Sampaio" <jasampaio(a)hotmail.com> >>>> Subject: [Ifeffit] Trouble with fitting with Artemis >>>> To: <ifeffit(a)millenia.cars.aps.anl.gov> >>>> Message-ID: <COL107-W60310E438349CE1C72988AACC80(a)phx.gbl> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> >>>> Hi there!I'm getting the following message when I try to fit my >>>> data:WARNING. The following variables had no effect on the fit: !! >> >>>> amp !! >> >>>> enot !! >> >>>> delr !! >> ss The >>>> data >>>> that I am trying to fit is the Cu metal example that come with the >>>> iffefit >>>> package. I am running Artemis on a Mac, OSX 10.4.11.I could run the >>>> fitting >>>> on a mac OSX 10.5 and it worked fine. I reinstall the IXAFS package but >>>> it >>>> didn't work.I am wondering what could be wrong with my >>>> machine/software?Thanks a lot.Juraci Sampaio >>>> _________________________________________________________________ >>>> Confira v?deos com not?cias do NY Times, gols direto do Lance, >>>> videocassetadas e muito mais no MSN Video! >>>> http://video.msn.com/?mkt=pt-br >>>>

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