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

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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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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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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"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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Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Yordy Licea Fonseca 29 Jan '09

29 Jan '09

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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Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O
by Yordy Licea Fonseca 29 Jan '09

29 Jan '09

Hi Carlo and Ma 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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Re: [Ifeffit] Ifeffit Digest, Vol 71, Issue 32
by Juraci A. Sampaio 29 Jan '09

29 Jan '09

Hi Rich,I found out what was wrong. The extend path parameters in the paths tab was on. When I set it as off the fitting worked just fine.Thanks a lot for your help.Juraci> From: ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 71, Issue 32> To: ifeffit(a)millenia.cars.aps.anl.gov> Date: Thu, 29 Jan 2009 07:00:40 -0600> > 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> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/eb8… > > ------------------------------> > Message: 2> Date: Wed, 28 Jan 2009 14:29:58 -0500> From: Richard Mayes <rtmayes(a)gmail.com>> Subject: Re: [Ifeffit] Trouble with fitting with Artemis> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID:> <5a2a54820901281129n2b0d8fc4ib02a2ed2faeca8c5(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Juraci,> > Can you please attach a project file so we can look at it and try to find> the problem. My first guess would be the parameters are not defined in the> "guess,def,set" page like they are in the path list but without seeing the> project file, it's hard to be specific.> > -Rich> > On Wed, Jan 28, 2009 at 1:34 PM, Juraci A. Sampaio <jasampaio(a)hotmail.com>wrote:> >> 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>>>>>> ------------------------------>> Not?cias direto do New York Times, gols do Lance, videocassetadas e muitos>> outros v?deos no MSN Videos! Confira j?! <http://video.msn.com/?mkt=pt-br>>>>> _______________________________________________>> Ifeffit mailing list>> Ifeffit(a)millenia.cars.aps.anl.gov>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>>>> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/7f5… > > ------------------------------> > Message: 3> Date: Wed, 28 Jan 2009 18:18:00 -0200> From: Yordy Licea Fonseca <yliceafonseca(a)gmail.com>> Subject: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <6bc7d27d0901281218t6eac4721o1922c155b95a1087(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi,> > Sorry, I could not find enough information.> Would any of you tell me, please, how is the EXAFS data tabulated in Farrel> Lytle data base?> The first column is the energy, what about others?> I would like to obtain the absorption coefficient vs energy from this> file:> > http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095> > Best wishes,> > -- > Yordy E. Licea Fonseca> Departamento de F?sico-Qu?mica> Instituto de Qu?mica-IQ/UFRJ> Laborat?rio de Cat?lise Heterog?nea> Rio de Janeiro, RJ, CEP 21.949-909> Brasil> Email: yliceafonseca(a)gmail.com> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090128/cea… > > ------------------------------> > Message: 4> Date: Wed, 28 Jan 2009 14:24:22 -0600> From: Matt Newville <newville(a)cars.uchicago.edu>> Subject: Re: [Ifeffit] about Farrel Lytle data of Na2WO4.2H2O> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID:> <b8522e3d0901281224v42f22a8cs6489a5792c4588f0(a)mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1> > Hi Yordy,> > The first column for that file is not energy, it is angular steps. See> http://cars9.uchicago.edu/ifeffit/FAQ/Data_Handling#head-e7e2389af58d378379…> > and the other posts from earlier today for how to convert this data into mu(E).> > --Matt> > On Wed, Jan 28, 2009 at 2:18 PM, Yordy Licea Fonseca> <yliceafonseca(a)gmail.com> wrote:>> Hi,>>>> Sorry, I could not find enough information.>> Would any of you tell me, please, how is the EXAFS data tabulated in Farrel>> Lytle data base?>> The first column is the energy, what about others?>> I would like to obtain the absorption coefficient vs energy from this>> file:>>>> http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/W/wna.095>>>> Best wishes,>>>> -->> Yordy E. Licea Fonseca>> Departamento de F?sico-Qu?mica>> Instituto de Qu?mica-IQ/UFRJ>> Laborat?rio de Cat?lise Heterog?nea>> Rio de Janeiro, RJ, CEP 21.949-909>> Brasil>> Email: yliceafonseca(a)gmail.com>>>> _______________________________________________>> Ifeffit mailing list>> Ifeffit(a)millenia.cars.aps.anl.gov>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>>>> > > > ------------------------------> > Message: 5> Date: Thu, 29 Jan 2009 13:33:08 +1100> From: "Pushan Shah" <pshah(a)gse.mq.edu.au>> Subject: [Ifeffit] uncertainty in linear combination analysis> To: <ifeffit(a)millenia.cars.aps.anl.gov>> Message-ID: <4981B014.0BBD.0060.0(a)gse.mq.edu.au>> Content-Type: text/plain; charset=US-ASCII> > Hello Everyone!> > How can I estimate an uncertainty in linear combination analysis and calculate them in percentage error?> > Many thanks,> Pushan> > > > > > > ------------------------------> > Message: 6> Date: Thu, 29 Jan 2009 15:41:55 +0530> From: abhijeet gaur <abhijeetgaur9(a)gmail.com>> Subject: [Ifeffit] Artemis parameters> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <862a39070901290211s6a928d40yc902a09ff532f2a9(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi> I am fitting a copper foil whose data is taken at room temperature. So> do I need to change the guess value of parameters enot, ss,amp, delr to some> other value or I should take them as the default guess value. Also what> should be the ideal fitting range in R for the copper foil.> > > With thanks> > Abhijeet> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/bd2… > > ------------------------------> > Message: 7> Date: Thu, 29 Jan 2009 11:00:32 -0200> From: Eugenio Otal <eugenioh(a)gmail.com>> Subject: [Ifeffit] Energy shift> To: ifeffit(a)millenia.cars.aps.anl.gov> Message-ID:> <da22ad30901290500s14de8d2dy4cbaf8ec693e6796(a)mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Hi Matt,> Thanks for your time, the shift is between calculated and experiment. I> attach two figures with and without correction, it matchs really good if I> change 5.5eV the energy.> Thanks, euG> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > -------------- next part --------------> A non-text attachment was scrubbed...> Name: without energy shift.jpg> Type: image/jpeg> Size: 58982 bytes> Desc: not available> Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > -------------- next part --------------> A non-text attachment was scrubbed...> Name: energy shift.jpg> Type: image/jpeg> Size: 69194 bytes> Desc: not available> Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090129/a2f… > > ------------------------------> > _______________________________________________> Ifeffit mailing list> Ifeffit(a)millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > End of Ifeffit Digest, Vol 71, Issue 32> *************************************** _________________________________________________________________ Cansado de espaço para só 50 fotos? 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Energy shift
by Eugenio Otal 29 Jan '09

29 Jan '09

Hi Matt, Thanks for your time, the shift is between calculated and experiment. I attach two figures with and without correction, it matchs really good if I change 5.5eV the energy. Thanks, euG

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