November 2007 - 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

9 21

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

12 22

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 >

8 9

2007 APS XAFS School
by Julie Olmsted Cross 04 Apr '08

04 Apr '08

The on-line application for the 2007 APS XAFS School is now available at xafs.org http://www.xafs.org/Workshops/APS2007 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Julie O. Cross Advanced Photon Source Argonne National Lab 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 327 7825 fax: 630 252 0580 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

5 9

negative amplitude
by Wojciech Starosta 30 Nov '07

30 Nov '07

Sorry if it is FAQ. But I spent some time on fitting without success and have not found answer to this. Does anybody could explain me if negative value of amplitude has any sense. I can get beautiful plot after fit, but unfortunately the message appear concerning negative value of amplitude (amplitudes). How to avoid it. Any written material will be very helpful. I know that I can define amplitude as squared value of new variable. But sometimes it does not work. Ifeffit stops with message that value of this variable cannot be determined With the best regards Wojtek Starosta Institute of Nuclear Chemistry and Technology 03-195 Warsaw, Dorodna 16 Institute of Nuclear Chemistry and Technology --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0649-1, 2006-11-18 Tested on: 2007-11-30 13:45:41 avast! - copyright (c) 1988-2007 ALWIL Software. http://www.avast.com

2 1

(no subject)
by Bindu R. 27 Nov '07

27 Nov '07

could you tell me how does one tune the bond angles from the multiple scattreing paths? Bindu Dr.Bindu R. Visiting Scientist DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- Chat on a cool, new interface. No download required. Click here.

4 4

Exafs distance resolution
by Eric Breynaert 27 Nov '07

27 Nov '07

Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to the fourier transform traditionally used for exafs analysis. If exafs fitting is done in k-space, on the raw exafs data without applying fourier or any other filtering transformation is there a physical limitation determining exafs bond distance resolution? This question comes down to the following practical problem. If one has a theoretical model developed using computational chemistry that predicts two different bond lengths within one shell, e.g. an octahedral metal center surrounded by 6 oxygen atoms and this shell is predicted to be split in three subshells for wich the bond length differs only 0.05 angstroms; and this model can be fit very well in k-space with the splitted shell, off course keeping the number of fit parameters below the nyquist criterion. Is there in such a case any physical reason not to fit the experimental data with the splitted shell , but with an averaged 6-atom shell with a larger Debye Waller factor? Best regards, Eric Breynaert

4 3

Re: [Ifeffit] Exafs distance resolution
by Frenkel, Anatoly 27 Nov '07

27 Nov '07

Yes and a very important one - see Ed Stern's talk at the 2001 EXAFS workshop "advanced methods and tricks etc. " His talk is online. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Nov 27 04:44:48 2007 Subject: [Ifeffit] Exafs distance resolution Dear all, Is there a physical limitation determining exafs bond distance resolution? Very often the equation r = pi / 2 deltak is quoted as a measure for bond distance resolution. But as i understand this equation is related to the fourier transform traditionally used for exafs analysis. If exafs fitting is done in k-space, on the raw exafs data without applying fourier or any other filtering transformation is there a physical limitation determining exafs bond distance resolution? This question comes down to the following practical problem. If one has a theoretical model developed using computational chemistry that predicts two different bond lengths within one shell, e.g. an octahedral metal center surrounded by 6 oxygen atoms and this shell is predicted to be split in three subshells for wich the bond length differs only 0.05 angstroms; and this model can be fit very well in k-space with the splitted shell, off course keeping the number of fit parameters below the nyquist criterion. Is there in such a case any physical reason not to fit the experimental data with the splitted shell , but with an averaged 6-atom shell with a larger Debye Waller factor? Best regards, Eric Breynaert _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

(no subject)
by Bindu R. 27 Nov '07

27 Nov '07

Could you tell me how does one gets the information about bond angles? or How does one tune the bond angles in the artemis software? Bindu Dr.Bindu R. Visiting Scientist DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- Now you can chat without downloading messenger. Click here to know how.

1 0

GaN atoms imput page
by codruta.zoican＠yale.edu 26 Nov '07

26 Nov '07

Dear All, Does anyone have an atoms imput page for GaN. I was trying to construct one myself to run a fitting in Artemis but I'm having some difficulties. Thank you, Codruta.

3 2

Reply:Ifeffit Digest, Vol 57, Issue 20
by 于志国 24 Nov '07

24 Nov '07

Dear prof: I have received your answer,thank you very much! I'll try it ,if i still can not use it ,i will post it to you! Yours sincerely! yuzhiguo

1 0

excuse me!
by 于志国 23 Nov '07

23 Nov '07

Dear prof: I am a postgraduated student in envirnmental science,so i have litte knowlege of this field ,now,i want to use athena to process date of XANES from Bsrf. but which format can be used in athena? my data format is xxxx.dat ,how can i to convert it to fit athena! Thank you very much! yuzhiguo

2 1

Ifeffit development tools?
by Mauro Rovezzi 21 Nov '07

21 Nov '07

Hello all, As a daily-user of Ifeffit&friends I found many times the necessity to implement new functionalities for XAFS analysis that surround Athena and Artemis. At the moment the Fortran/C/Perl/Python/Tcl interfaces to Ifeffit are great and Bruce's Demeter OO-project is fantastic but still broken in some important functions (I know that developing an open source project is a lot of voluntary work). For these reasons I would like to know your point of view on the idea to find a standard in the creation of Ifeffit applications in order to permit the interested community to contribute/share in the programming effort. Practically speaking, if someone would like to implement a new functionality based on the Ifeffit library which directives should follow to integrate the existing applications? Cheers, M. -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

4 8

Re: [Ifeffit] Farrel-Lytle database query
by Frenkel, Anatoly 13 Nov '07

13 Nov '07

It makes sense. An easy check would be to compare EXAFS of samples 13 and 14. If 13 was taken at lower temperature than 14 it will be shown by higher EXAFS oscillation intensity Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: Andy Higginbotham <andrew.higginbotham(a)physics.ox.ac.uk> CC: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Nov 13 09:11:53 2007 Subject: Re: [Ifeffit] Farrel-Lytle database query Hi Andy: I peeked into the database and there are 2 files here fb.013.Z FE83 B17 HT=400C, AT NT fb.014.Z FE83, B17 AS CAST It looks to me as if the HT that is referred to by the first file is the annealing temperature of the sample. The "AT NT" leads me to believe that the data is taken at "NT" which might be Nitrogen Temperature. This is just speculation but I wouldn't bet on the data having been taken at the high temperature. Carlo On Wed, 7 Nov 2007, Andy Higginbotham wrote: > Dear All, > > I am comparing some simulated EXAFS signals to the file fb.013 from the > Farrel-Lytle database. I would be hugely grateful if someone with more > knowledge of this data could comfirm the meaning of the line - > > # FE83 B17 HT=400C, AT NT > > In particular I need to know the sample temp but to my untrained eye the line > is ambiguous (I am hoping it is 673K...) > > The whole header is below for reference but it's only temp I need. > > Many thanks in advance, > > Andy > > # CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. > # DELTA: 2000. 15. 90. 150. 210. > # DELEND: 217740. 214450. 200860. 187700. 174080. > # SEC: 1. 1. 1. 1. 1. > # FE83 B17 HT=400C, AT NT > > -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

3 2

Farrel-Lytle database query
by Andy Higginbotham 13 Nov '07

13 Nov '07

Dear All, I am comparing some simulated EXAFS signals to the file fb.013 from the Farrel-Lytle database. I would be hugely grateful if someone with more knowledge of this data could comfirm the meaning of the line - # FE83 B17 HT=400C, AT NT In particular I need to know the sample temp but to my untrained eye the line is ambiguous (I am hoping it is 673K...) The whole header is below for reference but it's only temp I need. Many thanks in advance, Andy # CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. # DELTA: 2000. 15. 90. 150. 210. # DELEND: 217740. 214450. 200860. 187700. 174080. # SEC: 1. 1. 1. 1. 1. # FE83 B17 HT=400C, AT NT

2 1

Build intrinsic defect vacancy structure with doping atom.
by 沛昌蔡 13 Nov '07

13 Nov '07

Dear Prof. ; Thanks for your great informations about build doping atoms, and now we consider the real intrinsic defect structure for LiNbO3 single crystal, as people know about Nb vacancy (means there is a hole on Nb atom site) can be exist in this crystal, and our question is; The input file is correct or not? ps: because we had not see the relation example, maybe you can remark the mistake on it and e-mail back. Thanks for your time and help! Pei-chang Tsai ___________________________________________________________________ 體驗全新Yahoo!奇摩電子信箱2.0 - 馬上體驗！

2 1

Re: [Ifeffit] query regarding ARTEMIS
by Ravel, Bruce 12 Nov '07

12 Nov '07

> Currently I am learning the EXAFS fitting program ARTEMIS posted at > your website. I have some doubt regarding the tuning of the path > parameters for fitting. For example, If I am using feff0001.dat and > feff0002.dat as two different paths in the fit and I want to tune > the parameters corresponding to the above paths, then what syntax I > have to use for the path parameters (e0, delR,sigma^2,N) in the > section "GUESS,DEF,SET" so that it distinguishes different > paths. Please explain to me with an example. Bindu Bindu, This is a good sort of question to ask on the Ifeffit mailing list. http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit The advantage of using the mailing list is that you have access to lots of experts and lots of opinions. You'll find it to be a very useful resource. You question is answered in lots of different ways among things available on the web. If you have not yet looked over the tutorials at xafs.org (http://xafs.org/Tutorials) you should do so. You'll find lots of very helpful information. Shelly Kelly's analysis tutorial might be just what you are looking for. Scott Calvin's series of example explaining how to analyze ZnO using Artemis is quite useful. It is a tutorial in the form of Artemis projects. He uses the project journal space to explain what is going on at each stage of the analysis. http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib You may find this talk by me helpful: http://cars9.uchicago.edu/~ravel/talks/Welcome.html#methyltin If, after reviewing all the material that available, you have specific questions, please do not hesitate to ask on the mailing list. I and the others on the list will be happy to try to answer. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

conversion to Artemis k^0*chi(k) form
by Matthew 09 Nov '07

09 Nov '07

Re the recent discussion of importing data into Artemis: I've just posted to my beamline website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm a progran which takes a 2-column k vs. k^n*chi(k) file, divides by k^n and interpolates to a uniform grid to make it suitable for Artemis or Sixpack. This will work on earlier versions of Artemis which expect k to be tabulated starting at k=0 and going up in 0.05A^-1 steps. Look for the link to EXAFS to Artemis.zip, download that and also lvanlys.dll and the LabVIEW run-time engine, if you don't have these already. mam

2 1

Windows Vista
by snnn01ag＠uniba.it 09 Nov '07

09 Nov '07

Hi, I want only to inform Bruce and all the ifeffit´s users that I downloaded the ifeffit 1.2.10 version on my new computer that uses Window Vista software! After trying several times to load it from your site (and this is a problem of Vista!), now I have my athena, artemis and hephaestus. I must admit the program works a quite good. Ok, somethimes it crashes by itself, but you have only to close and reopen it (so, save all every 5 minutes). I hope no other problems emerge! Anna. ------------------------------------------------------- Questo messaggio e' protetto da un sistema di cifratura

6 17

Re: [Ifeffit] Self absorption questions
by s440697＠stud.uni-goettingen.de 08 Nov '07

08 Nov '07

Hi Bruce, i'm interested in the script at http://www.aps.anl.gov/xfd/people/haskel/FLUO/fluo.ps I tried to download/open it, but it didn't work. And for the folder http://www.aps.anl.gov/xfd/people/haskel/FLUO/ i need a login and password. Can you help me, to get this script? Thank you very much, Eckhard --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

2 1

Re-check for build lower doping concentration structure in TKAtoms program.
by 沛昌蔡 07 Nov '07

07 Nov '07

Dear Prof: Thanks for your link informations that about AgBr(1-x)Cl(x=0.1667), but in our Zn doped case the concentration x=0.06, following your ratio doping rule, the doped Zn atom can't replaced the second layer 7 Li atoms, it should stand far away from Nb core atom(~7th layer), and we make sure the doped effect can't be ignored, so it's a strict situation, and we also can't deny the possibility for Zn atom stand the second layer Li atoms, so can you tell us the great experiences that you deal with these problem. Thanks for helping! Pei-chang Tsai ___________________________________________________________________ 體驗全新Yahoo!奇摩電子信箱2.0 - 馬上體驗！

2 1

Linear combination fitting
by Jens Kruse 06 Nov '07

06 Nov '07

Hi, I have a general basic question about linear combination fitting (LCF) with Athena. I have XANES spectra from two different mixtures. Both were mixed from two reference compounds in a 1:3 ratio. In one mixture the ratio is based on the weight of both reference compounds and in the other the ratio is based on the concentration of the element of interest (the concentrations in the reference compounds are not equal). If I am doing LCF on these spectra, which spectra would yield to the expected weighting parameters 0.25 and 0.75? What actually represent a normalized spectrum? Is a normalized spectrum a spectrum what one atom of interest would produce ? thanks a lot, jens

2 1

How to generate the input information for Atom
by Fenglong Sun 06 Nov '07

06 Nov '07

Hi, Bruce, I am working on an experiment of arsenic adsorption on pyrite particles. I have the data of mu(E)~E. I use Anthena to do the Fourier transform. Now I want to know the cordination information of arsenic atom. How can I get the input file for Atom if I want to do the fitting job by using Iffefit package? Thanks!

2 1

Build lower doping concentration structure in TKAtoms program.
by 沛昌蔡 06 Nov '07

06 Nov '07

Dear Prof: We have some questions about build lower doping concentration structure in TKAtoms program, as following; Q1: The TKATOM program can build up doping structure for lower doping concentration (below 10%) or not? Q2: If it can work, how should we build up the doping site? Q3: For lower doping case, how do these doped atoms choose where to go in TKATOM program, is it have physical description? ps: The attach ppt. file show more detail about our questions. Thanks for helping! Pei-chang Tsai ____________________________________________________________________________________ 怎樣減少垃圾信？只要看到垃圾信，立即按下「這是垃圾信」按鈕，垃圾信剋星幫助你清除你信箱垃圾。

2 1

help: can I use ifeffit to predict chi?
by Tai-Yen Chen 02 Nov '07

02 Nov '07

hi, Can anyone tell me whether I can use ifeffit to do this job? I want to know the % change in chi when the molecule have 3% change in radius? All I have is just the crystal struture of gamma-Fe2O3, which means I can only get the Feff. How can I introduce 3% change in redius so that I can get the difference of chi? Can anyone help me? Tanks a lot. TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu

4 4