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

Re: [Ifeffit] EXAFS simulations
by Frommer Jakob 26 Oct '08

26 Oct '08

Ciao Sebastiano, did you use the mu-column of the xmu.dat? If so, the main difference between the chi.dat and the xmu.dat is that the mue_0 (as calculated by FEFF) is already subtracted in the former while it needs to be subtracted by Athena in the latter. Some of the difficulties you mentioned are thus due to problems of Athena to do a decent background (i.e. mue_0 and normalization) processing if there is no pre-edge region. Thus the effect of changing the absorption energy in Cu Bulk 4 from 8988.430eV to 8988.431eV is not caused by a *wrong* Enot but by a change in the edge-jump of almost 50% (due to a different *pre-edge*). Thus using the chi.dat seems to be the better (i.e. more reproducible) choice in this case (a precautionary note though: the mue_0 as calculated by FEFF will most likely differ between the central and the peripheral atoms; this may be part of the cluster-effect or an artifact (I assume that this is only a problem in the XANES region but I don't know, so you should check this by plotting the single mue_0). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Fri 10/24/2008 09:57 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 21 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: Fit XANES spectra using Athena (Adam Webb) 2. EXAFS simulations (Cammelli Sebastiano) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Oct 2008 07:39:55 +0200 From: Adam Webb <adam.webb(a)desy.de> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <49015FAB.5060802(a)desy.de> Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I don't know what exactly you are trying to do so I can't say which method is better but I can make a comment. It all comes down to the number of independent variables. The Gaussian and step functions are independent of each other. The heights, widths and positions can all be adjusted. In the linear combination you change everything together so for example, the ratio of the peak height and the step height doesn't change. The result is that you need more spectra to get the same number of degrees of freedom as in the least-squares peak fit. Cheers, Adam Jenny Cai wrote: > Hello everyone, > > Sorry for bothering you again. > > I am using least-squares peak fit and linear combination fit to analyze > my samples. I have spent tons of time on it, and it really makes me > crazy. Why can't I get consistent results from these two methods? > > Please see the attached file. Both of these methods work well > individually, but linear combination fit always need more peaks than > peak fit to get an 'ok' fitting. Should I stick on one method for all my > samples, no matter what results the other one gives? It is confusing me > so much. Could anyone help me out? > > Thank you in advance for your help! > > > Jenny > > ------------------------------ Message: 2 Date: Fri, 24 Oct 2008 09:57:35 +0200 From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> Subject: [Ifeffit] EXAFS simulations To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <AD99CE4B84C4D3468F69B0E4FB345D5804A5E78C(a)MAILBOX0A.psi.ch> Content-Type: text/plain; charset="us-ascii" Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli

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Re: [Ifeffit] Fit XANES spectra using Athena
by Andrew Campos 26 Oct '08

26 Oct '08

Jenny, I'm relatively new to the community XAFS, and have not done any sulfur work thus far... but have you considered doing a principal component analysis on the XANES of your samples? This method should help you identify how many phases are present (assuming that all of your samples aren't exactly identical; however the maximum number of independent phases it will return is the number of samples you tested), and with your standards you might be able to eliminate some of the phases (from the standards) as well as identify some of the phases that are in your sample. (There is software that will do this in the IFFEFIT package under Sixpack --> 'pc analysis') Andrew Campos

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Fw: Re: Fit XANES spectra using Athena
by Jenny Cai 26 Oct '08

26 Oct '08

Sorry, Bruce. I have to send it again to the group. -Jenny --- On Sun, 10/26/08, Jenny Cai <jennyh_cai(a)yahoo.ca> wrote: From: Jenny Cai <jennyh_cai(a)yahoo.ca> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "Bruce Ravel" <bravel(a)bnl.gov> Received: Sunday, October 26, 2008, 2:08 AM Hi everyone, Thank you for your reply. I understand the difference between peak fitting and linear combination fitting. It is like, If I don't know anything about my sample, peak fitting should be used. If I know the components of my sample, I can use linear combination. That is why I use peak fitting first, because I know very little about my sample. However, what I am thinking is that from the results of peak fitting, I know there may be some types of sulphur in my sample, and based on the peak positions, I can chose the standards for linear combination fitting. I can't use linear combination fitting in the first place, because I don't exactly know what sulphur forms in my sample, and I may miss an important species if I chose the wrong standards. However, I still want to try linear combination after peak fitting, because I think the linear combination fitting may be more accurate than peak fitting. It uses the whole spectrum of the standard, while the peak fitting neglectes the effect of small features on the fitting. Does it make sense? My samples are fluid coke and their activation products. They have reduced and oxidized sulphur species, more likely in organic forms. I have 26 standards covering the sulphur oxidation states from elemental sulphur to sulphate. Most of them are organic sulphur. Any more suggestions? Thank you! Best regards, Jenny --- On Fri, 10/24/08, Bruce Ravel <bravel(a)bnl.gov> wrote: From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Received: Friday, October 24, 2008, 9:06 AM On Friday 24 October 2008 00:59:21 Jenny Cai wrote: > Hello everyone, > > Sorry for bothering you again. > > I am using least-squares peak fit and linear combination fit to analyze my > samples. I have spent tons of time on it, and it really makes me crazy. Why > can't I get consistent results from these two methods? > > Please see the attached file. Both of these methods work well individually, > but linear combination fit always need more peaks than peak fit to get an > 'ok' fitting. Should I stick on one method for all my samples, no matter > what results the other one gives? It is confusing me so much. Could anyone > help me out? Jenny, I think you are comparing apples and oranges. I certainly think you are looking for some correspondance between peak fitting and linear combination fitting that probably does not exist. When doing linear combination fitting, you are making the implicit assumption that your data can be described in that way. Suppose that you go to the chemical cabinet and grab jars of 5 stable, non-reactive chemicals. Scoop out a spatula-full of each and mix them together very well in ajar. Then scoop out a bit of the mixture, spread it on a piece of tape, and measure some XAS. In that case, we certainly expect LCF to work well. The measured spectrum should be a linear combination of the spectra from each of the 5 original materials in proportion that has something to do with how many absorber atoms were in each scoop. Now suppose that you take a scoop of soil from a swamp. You might expect that your metal atom is distributed among oxide and sulfide species. You measure some xas on the swamp soil and on a library of standards. You may find that you can do LCF using some mixture of oxides and sulfide, or you might not. That may mean that you neglected to consider an important standard, a carbide, for example. *Or* it might mean that the oxides and sulfides in the real sample include some kind of exotic organic species that isn't quite like the standards you have available. In the latter case, your LCF fit results will be approximate in the best scenario. So, you don't say anything about what sulfur species you are using as standards, nor do you say anything about what the sample is. Should you expect a perfect fit from some number of standards? Do you know for a fact that your standard is simply a linear combination of standards. That is, should you expect the LCF to tell you what the components *are* or should you expect the LCF to tell what the sample resembles? As for the peak fitting, what do each of the line shapes mean physically? Chemically? No XAS data is described by a single Gaussian. Neither is any XAS data described by a single arc-tangent. So why should the number of lineshapes required to generate a mathematical function that resembles your data be related to the number of species you require in a linear combination fit? You seem to making yourself crazy based on the assumption that there is some magical relationship between the six lineshapes you used in the peak fitting and the number of standards you use in the linear combination fitting. It seems to me that you would make yourself a lot less crazy if you didn't cling to this unsubstantiated assumption. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Now with a new friend-happy design! Try the new Yahoo! Canada Messenger __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.

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feff8
by Guvenc Akgul (gakgul) 24 Oct '08

24 Oct '08

Hi all, I want to calculate L2and L3 absorption edges for Fe as theoretical. Where can I find feff8 software programme?? thanks guven

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Reference spectra for KCl
by shiryaev＠crys.ras.ru 24 Oct '08

24 Oct '08

Hi everybody, I would greatly appreciate if someone could provide me with K K-edge spectra for KCl and K2CO3. Cl K-edge in KCl would be useful too. Thanks in advance, Andrei Shiryaev Institute of crystallography, Moscow, Russia

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EXAFS simulations
by Cammelli Sebastiano 24 Oct '08

24 Oct '08

Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli

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Re: [Ifeffit] Crytallites AND polycrystalline - Artemis handling?
by Scott Calvin 20 Oct '08

20 Oct '08

Sure, Joseph. These were nanoparticles made with a reverse micellar method. Past experience has shown that this synthesis produces a passivating oxide layer on an iron core; the passivating layer is usually amorphous, which is a good thing; hematite has a lattice mismatch and thus doesn't passivate. Linear combination analysis suggested this samples was 75% metal and 25 +/- 5% oxide. A typical amp entry is: S02_Fe*Frac_bcc*(1-3/4*reff/R_Fe+1/16*(reff/R_Fe)^3) S02_Fe is just the usual S02 factor, and "should" be from 0.70 to 1.0. It's lower than that in the fit I've sent you; that's one of the indications the fit may not yet be done. (I've actually gone much further with this fit, but that would have made for a more confusing file.) Frac_bcc is the fraction of iron atoms in an ordinary bcc metal environment. In the fit I sent you, it optimizes to 34 +/ 9%. Notice that's consistent with the linear combination analysis. That makes me happy. R_Fe is the radius of the core, modeled as a sphere. The formula in which it appears accounts for the reduction in average coordination number due to surface termination, and is discussed in several of my papers, including my articles: S. Calvin et al., Appl. Phys. Lett. 87, 233102 (2005) and S Calvin et al, Phys. Scr. T115 744-748 (2005). The oxide amp entry is much simpler: S02_Fe*Frac_Ox*2 Frac_Ox is 1-Frac_Bcc; i.e. what's not metal is oxide. The factor of 2 is just because I was working with a path from hematite that had coordination number of 3 (there's some splitting in hematite); I multipled by 2 to get an assumed coordination number of 6. Much of my subsequent fitting has been using bond valence theory to try to distinguish between coordination of 4 or 6 for the amorphous oxide. --Scott Calvin Sarah Lawrence College On Oct 20, 2008, at 8:46 AM, Joseph Washington wrote: > Scott, > Thank you very much. I am looking at this file and I understand > everything as far as the isotropic expansion terms in the delr and > the debye term. Can you clarify the amp math expression? Also, just > so we're on the same page, tell me a little about this system? > > Thank you again for your help! > > Joseph > > Scott Calvin wrote: >> Hi Joe, >> Here's an in-progress Artemis file for a system with some broad >> similarities to the one your describe. Perhaps it will help. >> Disclaimer: This is /not/ a final fit! >> --Scott >> ------------------------------------------------------------------------ >> On Oct 17, 2008, at 2:15 PM, Joseph Washington wrote: >>> Hello all, >>> I am working on analyzing Ge edge EXAFS data of an annealed sample >>> which >>> is likely to be Ge-Te crystallites with some amorphous material at >>> the >>> grain boundary (or perhaps, just Ge-N crystal material at the >>> interface). I do not have any information about the grain size, only >>> possible constituents for the grain and the boundary. Can anyone >>> give me >>> some examples of how Artemis might handle this? >>>

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question
by Guvenc Akgul (gakgul) 17 Oct '08

17 Oct '08

Hi, This question very important for me.I have 5% Ti doped ZnO data.It includes not only Zn-K-edge but also Ti-K -edge data.I would like to figure out in following distances and Coordination numbers of them 1)Zn-O 2)Zn-Ti 3)Zn-Zn 4)O-O 5)Ti-Ti 6)Ti-O How can I do them?If you can help to me I will be very glad.Thanks for your help best regards guvenc

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Ifeffit 1.2.11b terminal output
by Gareth Jones 14 Oct '08

14 Oct '08

Hi all, The newest Ifeffit release dumps a whole lot of text to stdout. I've attached an example (hope that's okay), showing how it prevents the proper configuration of the Perl wrapper for Horae (see my previous post about the missing Ifeffit.pm file). Similar output is produced when using the Horae programs with the out-of-date wrapper, and even when running "ifeffit --help". This is in Ubuntu 8.04.1 (two machines), with gcc/gfortran 4.2.3-2ubuntu7 and pgplot 5.2.2-11ubuntu1, and Ifeffit 1.2.10a works fine. Is this normal, or did I manage to break Ifeffit somehow? Thanks, Gareth

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Horae 067 missing Ifeffit.pm (with solution)
by Gareth Jones 14 Oct '08

14 Oct '08

Hi everyone, This is a follow-up for a problem I encountered at the XAS08 PSI workshop, solved by Bruce, but it should probably be archived here in case anyone else discovers it. The Problem: Installation of Ifeffit and Horae following the build-from-source instructions [http://cars9.uchicago.edu/~ravel/software/downloads.html] appears to work, but Horae programs fail to start due to a missing "Ifeffit.pm" in "$prefix/lib/perl/...". You may at this point have copied Ifeffit.pm from the Ifeffit build tree, which at first seems to fix the problem. However, certain operations that require data to be copied between Perl/Horae and Ifeffit fail - in my case copying a group in Athena yields an apparently empty (or corrupt) group. This is reproducible for affected groups, but not all groups are affected. De-glitching is another test. The Solution: The Ifeffit Perl wrapper is apparently out-of-date. Bruce's Subversion repository contains an updated wrapper (libperlxray/Ifeffit) that fixes the problem, but hasn't been released as a source tarball yet - there are Subversion installation instructions at http://cars9.uchicago.edu/iffwiki/BruceRavel/EvolvingSoftware. Installation of the libperlxray/Ifeffit wrapper should be enough - you can use the release versions of the rest of Horae, but you may need Ifeffit 1.2.10a rather than 1.2.11b (more on this in another post). Anyway thanks to Bruce for figuring it out (and I hope my description isn't too inaccurate!) Gareth

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