October 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

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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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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 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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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

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Re: [Ifeffit] 1. Re xanes feff8 sulfur pyrite
by s440697＠stud.uni-goettingen.de 26 Oct '07

26 Oct '07

Hi Josh, i have made two calculations respectively pyrite. You can see the results in the postscript file. The first (A) plot is from your pyrite.dat, the second plot is based on your feff.inp but recalculated on my Computer. The last (C) plot is based on my own crystallographic data (spacegroup p 2_1 /a -3) and feff.inp (attached as eck-feff.inp) file, maybe the same crystallographic data you used? With my feff.inp i can approve all of your atom-positions with the exception of atom 11 in your list respectively atom Fe3 in my list. But the results in the diagramm are nearly the same. The third file (feff.inp) is again your feff.inp file you sent to me. >Hi Josh, > >thanks for your help and attached files. I will test your feff.inp files >and compare the results. > >cheers, >Eckhard > > Hi Eckhard, > Try the attatched feff.inp files (gypsum.inp and pyrite.inp). > I find that these produce different spectra with edges at > ~2468.5 - gypsum > ~2469.0 - pyrite > > If you use do not get the same results, then there is something wrong with the code and we will have some debugging to do. > > Also, if there are multiple sulfur sites in the material which have different local structure, you will > need to do a configurational average by running with each site as the absorbing atom and averaging the signals. > Cheers, > Josh > > P.S. > I am also sending the result (gypsum.dat and pyrite.dat) so that you can compare. > > > On Tue, 16 Oct 2007, 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. Re xanes feff8 sulfur (Kelly, Shelly D.) >> 2. Re: Re xanes feff8 sulfur (s440697(a)stud.uni-goettingen.de) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 15 Oct 2007 15:18:14 -0500 >> From: "Kelly, Shelly D." <SKelly(a)anl.gov> >> Subject: [Ifeffit] Re xanes feff8 sulfur >> To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "John J. Rehr" <jjr(a)leonardo.phys.washington.edu>, John Katsoudas >> <katsoudas(a)agni.phys.iit.edu> >> Message-ID: >> <0BC5625B1BD9494886EBA2F3CF10E957012C1C90(a)BIOPOST.bio.anl.gov> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi Eckard, >> >> >> >> I realize that you have posted a message every month for about 3 months in a row without any reply: Shame on us... I will try to answer some of your questions and maybe that will help to get some discussion going. The energy scale in feff8 is NOT defined as you would expect it to be for determining the absolute energy of an edge. The energy scale in FEFF8 is related to the difference between the energy level of the intersist (potential level inbetween the muffin tins that represent atoms) and the threshold energy level for the excitation of the electron. >> >> >> >> I realize that this doesn't solve your problem, but hopefully it will spark some discussion. >> >> >> >> Cheers, >> >> Shelly >> >> >> >> >> Mon Aug 13 06:00:19 CDT 2007 >> Does anybody know a person, who has experience respective the topics xanes+feff8 and sulfur K-Edges? >> I would be very thankful for an answer :-) >> >> sincerely yours, >> Eckhard Bosman >> >> >> >> >> Tue Jul 10 10:07:38 CDT 2007 >> >> Hello, >> >> i have problems with feff-xanes calculations related to pyrite. I try to get the k-edge of sulfur (as absorber) in FeS2. I get the edge at ~2472 eV >> and i think this is wrong because i get the same energy with gypsum and i >> think there should be an energyshift related to 2472 eV. My proceeding is >> as follows: >> >> calculate the atomic positions with the asymetric unit from the http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup Pa3) respectively >> http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif >> with "powdercell 2.4" >> >> feffrun with the feff.inp-file like in the attachment >> (thanks to Josh Kas for his feff-hints) >> >> I started the feff-run on the one hand with 12 atoms (unitcell) and on the >> other hand with 22 atoms (14x Fe and 8x S in the cube) >> >> After this i plotted from xmu.dat the absorbtion mu (column 4) as a function of the energy (column 1). The result is in the attachment too. >> >> I don't know why i get everytime the Sulfur-k-edge at the same position (for pyrite or gypsum) respectively without energyshift related to 2472 eV. >> >> many thanks for your help :-) >> Ciao, >> Eckhard >> >> >> >> Fri Jun 15 08:48:21 CDT 2007 >> >> Hallo @all, >> >> (first at all, sorry for my bad english) >> >> i'm a student working on my diploma thesis (nexafs/xanes) and my job is to >> simulate with FEFF 8.4 spectra, for example absorption as a function of energy (mu_(E)). I'm a newbie in this topic and i tried to get the k-edge >> of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm >> interested in the XANES-range of the spectra not the EXAFS. I get everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance i >> use (gypsum, pyrite,...). There are no differences with the peak position >> on the energy-scale or shifts. I'm really confused :-( I think, there should be differences in the spectra... I send you two feff.inp files from >> my feff-runs. My source is the mineralogy database >> (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the >> unitcell. Then i put the data in the XtalDraw program to get the positions >> of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell >> :-). Then i put the values of the positions into feff... >> I simulated pyrite with 12 atoms and gypsum with 48. >> I'm appreciative for every help :-) >> >> ciao, >> Eckhard >> >> >> >>

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scattering from H atoms
by Yael Politi 24 Oct '07

24 Oct '07

Hallo everyone, I have data of an hydrated mineral (a standard material, with known crystallographic structure), where the nearest neighbors are hydrogen atoms at about 0.8 angs from the absorber. my question, if anybody has had similar problem, is how do I differentiate between noise and contribution from H scattering in my exafs data. If I want to, I can get to a stage where I have almost no intensify in the FT data at r<1. but I don't know if this is a better interpretation. the feff input file suggest strong scattering from H atoms and I wouldn't want to just ignore these paths in the fit. Any suggestions would be most appreciated. Yael

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1. Re xanes feff8 sulfur
by joshua jason kas 21 Oct '07

21 Oct '07

Hi Eckhard, Try the attatched feff.inp files (gypsum.inp and pyrite.inp). I find that these produce different spectra with edges at ~2468.5 - gypsum ~2469.0 - pyrite If you use do not get the same results, then there is something wrong with the code and we will have some debugging to do. Also, if there are multiple sulfur sites in the material which have different local structure, you will need to do a configurational average by running with each site as the absorbing atom and averaging the signals. Cheers, Josh P.S. I am also sending the result (gypsum.dat and pyrite.dat) so that you can compare. On Tue, 16 Oct 2007, 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. Re xanes feff8 sulfur (Kelly, Shelly D.) > 2. Re: Re xanes feff8 sulfur (s440697(a)stud.uni-goettingen.de) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Oct 2007 15:18:14 -0500 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: [Ifeffit] Re xanes feff8 sulfur > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: "John J. Rehr" <jjr(a)leonardo.phys.washington.edu>, John Katsoudas > <katsoudas(a)agni.phys.iit.edu> > Message-ID: > <0BC5625B1BD9494886EBA2F3CF10E957012C1C90(a)BIOPOST.bio.anl.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi Eckard, > > > > I realize that you have posted a message every month for about 3 months > in a row without any reply: Shame on us... I will try to answer some of > your questions and maybe that will help to get some discussion going. > The energy scale in feff8 is NOT defined as you would expect it to be > for determining the absolute energy of an edge. The energy scale in > FEFF8 is related to the difference between the energy level of the > intersist (potential level inbetween the muffin tins that represent > atoms) and the threshold energy level for the excitation of the > electron. > > > > I realize that this doesn't solve your problem, but hopefully it will > spark some discussion. > > > > Cheers, > > Shelly > > > > > Mon Aug 13 06:00:19 CDT 2007 > Does anybody know a person, who has experience respective the topics > xanes+feff8 and sulfur K-Edges? > I would be very thankful for an answer :-) > > sincerely yours, > Eckhard Bosman > > > > > Tue Jul 10 10:07:38 CDT 2007 > > Hello, > > i have problems with feff-xanes calculations related to pyrite. I try to > get the k-edge of sulfur (as absorber) in FeS2. I get the edge at ~2472 > eV > and i think this is wrong because i get the same energy with gypsum and > i > think there should be an energyshift related to 2472 eV. My proceeding > is > as follows: > > calculate the atomic positions with the asymetric unit from the > http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup > Pa3) respectively > http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif > with "powdercell 2.4" > > feffrun with the feff.inp-file like in the attachment > (thanks to Josh Kas for his feff-hints) > > I started the feff-run on the one hand with 12 atoms (unitcell) and on > the > other hand with 22 atoms (14x Fe and 8x S in the cube) > > After this i plotted from xmu.dat the absorbtion mu (column 4) as a > function of the energy (column 1). The result is in the attachment too. > > I don't know why i get everytime the Sulfur-k-edge at the same position > (for pyrite or gypsum) respectively without energyshift related to 2472 > eV. > > many thanks for your help :-) > Ciao, > Eckhard > > > > Fri Jun 15 08:48:21 CDT 2007 > > Hallo @all, > > (first at all, sorry for my bad english) > > i'm a student working on my diploma thesis (nexafs/xanes) and my job is > to > simulate with FEFF 8.4 spectra, for example absorption as a function of > energy (mu_(E)). I'm a newbie in this topic and i tried to get the > k-edge > of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). > I'm > interested in the XANES-range of the spectra not the EXAFS. I get > everytime my peaks at ~2472 eV for Sulfur as absorber whatever substance > i > use (gypsum, pyrite,...). There are no differences with the peak > position > on the energy-scale or shifts. I'm really confused :-( I think, there > should be differences in the spectra... I send you two feff.inp files > from > my feff-runs. My source is the mineralogy database > (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for > the > unitcell. Then i put the data in the XtalDraw program to get the > positions > of the Atoms in Angstrom, by the way i get i nice 3D-View of the > unitcell > :-). Then i put the values of the positions into feff... > I simulated pyrite with 12 atoms and gypsum with 48. > I'm appreciative for every help :-) > > ciao, > Eckhard > > > >

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Fe-Co help
by Dominik Samuelis 21 Oct '07

21 Oct '07

Dear Chachi, first of all, you need to work on your crystallographic description of the system. I'm sure you are aware of the ordering transistion in Fe-Co at around 730 °C. Your description currently uses parts of the ordered phase, and other parts of the unordered. Above 730 °C, your description as a bcc structure is correct, however your atomic parameters and the neighbor shells are not. The system then has a bcc structure (Im-3m), with mixed Fe/Co occupancy on the single crystallographic position 2a. It should be modelled as such, with mixed occupancy on the neighboring sites. There's excellent tutorials how to deal with mixed sites. However, be aware that the scattering properties of iron and cobalt is very similar, you you won't really be able to fit your site occupancy. Below 730 °C, the system starts to order. The ordered phase is NOT bcc anymore, but consists of two intersecting primitive cubic lattices, shifted by (1/2 1/2 1/2). The structure prototype is often called B2, after its Strukturberichte symbol (http://cst- www.nrl.navy.mil/lattice/struk/index.html) Now, the rest of your crystallographic description matches. The neighbor shells will be N1=8Co and N2=6Fe. However, the symmetry is not bcc (Im-3m), but primitive (Pm-3m). Looking at your fit and feff calculation, it seems, that you have used the fully ordered phase for modelling your alloy. As you have pointed out yourself, it's not clear that the alloy really is fully ordered. Your alloy might be partially ordered, as also indicated by the Mossbauer data. In this case, you need to mix several feff calculations, with each cobalt and iron on the first and second neighbor position. You could start by assuming an ordering parameter 'op'. The first shell would then be N1=8(op Co+(1-op)Fe), the second is N2=6(op Fe+(1-op)Co). Cheers, dominik > Dear all > I?m trying to deal with exafs data of a Fe-Co alloy sample, using > Artemis. > The bcc structure is simple to modeling, Fe at 0,0,0 and Co at > 1/2,1/2,1/2 > (at Fe-edge, N1= 8Co, N2= 6Fe, theorically), > But in my fits N1=5.4 and N2=4.9, that is correct? > amp=0.811293 value I used from Iron calibration data, that is > correct too? > A possibility (I think), is that the sample is inhomogeneous, > because, by Mossbauer > spectroscopy, show two Fe magnetic sites, one attributed to ordered > phase, and the > other to disordered phase. -- Dipl.-Ing. Dominik Samuelis samuelis(a)pc.rwth-aachen.de Physikalische Chemie I RWTH Aachen University Phone: +49-241-80-94840 Fax: +49-241-80-92128 Landoltweg 2 52056 Aachen Germany

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negative e0 value
by mauricio.maps 20 Oct '07

20 Oct '07

Dear all, I´m trying to deal with exafs data of a Ni-phosphate compound, using Athena/Artemis. This is a simple structure (I think), with the hexacoordinated ion surrounded by water molecules on the first shell. The question I have concerns the negative value for e0 I´m having. Is this a bad thing? Maybe I´m doing something wrong? I´ve tried some issues, as those proposed on the Shelly Kelly´s tutorial, but without success. Can you help me, please? Attached are an example of the Athena and Artemis projects i´m using. Thanks a lot. Mauricio

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