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

Artemis fitting problem
by abhijeet gaur 07 Feb '09

07 Feb '09

Hi Scott, I know that alpha is not a temperature expansion coefficient .I guess it is a volume expansion coefficient( tell me if I am right). Actually I want to know that is it necessary to fit Ei, 3rd, 4th, cumulant in the fitting procedure .If yes then please tell me how to get them involve in the fit .when I give parameter like guess 3rd, guess 4th . Artemis dont take them . And about Ei I am completely blank.I dont know how to use it and from where i will get it. One more thing is that I am fitting Cu foil, CuO and Cu2O , so how many number of paths should I take . And Thanks a lot for your suggestions With regards Abhijeet

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Lost second shell
by Eugenio Otal 06 Feb '09

06 Feb '09

Hi Carlo, thanks for for help, really interesting your paper about ZnMnO. Cheers, euG

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Co2MnO4 atoms.inp files
by JeongEunSuk 06 Feb '09

06 Feb '09

Hello all I want to get Co2MnO4 atoms.inp. I know that Co2MnO4 is a spinel structure, however I dont know the position of each atom in unit cell. If anyone knows that, please answer me... _________________________________________________________________ 간편하고 정확한 나만의 맞춤 검색, Live Search! http://search.live.com

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An additional beta tester
by Scott Calvin 05 Feb '09

05 Feb '09

Hi Kathy, I just got a late volunteer for beta testing, whom I think will be a good addition: Ryan Hinrichs, professor of Chemistry at Drew University. Knows a little bit about XAFS, partially from collaboration with me, but has never used it himself. E-mail: Hinrich(a)drew.edu (Yes, his name ends in an "s" but his e-mail address does not.) --Scott

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Possible solution to trouble in artemis analysis
by Kleper Oliveira Rocha 05 Feb '09

05 Feb '09

Dear all, Recentilly I post a massage about trouble with analysis in artemis. Well, I think that find the solution. In Portuguese some words are write with symbols like: fam*í*lia (family), prepara*ÇÃ*o (preparation) that are not accept by IFFEFIT programs. In the basis of the instalation of Windows XP in my computer and some folders had this symbols and this caused the trouble in Athena and Artemis. Thanks for all for the help. -- Kleper de Oliveira Rocha Doutorando em Engenharia Química Departamento de Engenharia Química/UFSCar Tels. 55 016 3351-8694

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Lost second shell
by Eugenio Otal 05 Feb '09

05 Feb '09

Dear Carlo, with changes in function of time, you mean that repetitions of the spectra in the same sample are different from the firs to the last? What does this indicates? Thanks for you help, euG

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Artemis parameter
by abhijeet gaur 04 Feb '09

04 Feb '09

Hi Scott, I know that alpha is not a temperature expansion coefficient .I guess it is a volume expansion coefficient( tell me if I am right). Actually I want to know that is it necessary to fit Ei, 3rd, 4th, cumulant in the fitting procedure .If yes then please tell me how to get them involve in the fit .when I give parameter like guess 3rd, guess 4th . Artemis dont take them . And about Ei I am completely blank.I dont know how to use itand from where i will get it. One more thing is that I am fitting Cu foil, CuO and Cu2O , so how many number of paths should I take . And Thanks a lot for your suggestions With regards Abhijeet

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Los
by Eugenio Otal 04 Feb '09

04 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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