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

Los
by Eugenio Otal 03 Feb '09

03 Feb '09

Hi everybody, thanks for your time, knowledge and pacience. The first shell is can be fitted by 2 sub shells with this composition: n_first_1 = 2.4702860 r = 1.782161 n_first_2 = 9.2476950 r = 2.342539 This is really far from Zn in ZnO, is closer to Er(OH)3, with 8 between 2.40 and 2.43 and ErOOH presents 7 neighbors between 2.26 and 2.45, with something like 2 sub-shells. Er2O3 has two sites with octahedral simmetry, one is perfectly Oh and the other distorted with 2.21 to 2.36 for Er-O. I chequed the doping element incorporation and found that what I suppose to be 1% is in fact 0.6% (by ICP quantification) the incorporation is less I though. Maybe that is the reason to do not find call parameters change. What kind of difference could I find between nanoparticles and bulk for incorporation? Cheers, euG -- "I posti più caldi nell'inferno sono riservati a coloro che in tempo di grandi crisi morali mantengono la propria neutralità". Dante Alighieri (1265-1321) 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Lic. Eugenio H. Otal CINSO - CONICET - CITEFA San Juan Bautista de La Salle 4397. Villa Martelli (B1603 ALO) Buenos Aires TEL: 54 11 4709-8100 Int. 1212. FAX: 54 11 709-8241. E-mail: eotal(a)citefa.gov.ar eugenioh(a)gmail.com 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

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Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

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Re: [Ifeffit] Self absorption Correction
by Jens Kruse 03 Feb '09

03 Feb '09

Hi, Thanks Richard and Carlos for the the links. But is the "Fluo"-Algorithm for self absorption correction also valid if I have the concentrated sample (standard) applied as a fine powder to a carbon tape or is it only valid for much much thicker samples? thanks, Jens > ------------------------------ > > Message: 4 > Date: Mon, 2 Feb 2009 09:51:10 -0500 > From: Richard Mayes <rtmayes(a)gmail.com> > Subject: Re: [Ifeffit] Self absorption Correction > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <5a2a54820902020651nfaf1af7q4ec435fc207fc38a(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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 (this is a link from the > tutorials page of 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 > > 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 <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 >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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Lost second shell
by Eugenio Otal 02 Feb '09

02 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 01 Feb '09

01 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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"Hard tests failed in fovrg"
by tony vitova 30 Jan '09

30 Jan '09

Hi all, I am trying to fit Eu L3 edge EXAFS data of Eu complex whose structure is known (hopefully correct). The default feff6l in Artemis reports an error “Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small“. When I run feff8.2, this error exchanges with the following message “The phase shift correction is accurate to k=19”. I guess that this is not a problem, because my data is until k equal 12 A^-1. However, the fit of the first shell (9O/9N) gives Eo equal to 13, which is unrealistic. This fit with paths calculated with feff6l gives reasonable Eo value. But the phase shifts seem to be calculated incorrectly. I will be very thankful for any hint! Thanks in advance Tonya

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