Re: [Ifeffit] Fw: Re: Fit XANES spectra using Athena

Jenny, Here are some links to the work of A. Vairavamurthy who did extensive research on sulfur speciation, that may help: HYPERLINK "http://www.irnase.csic.es/users/delrio/repository/2002-OLIVELLA-JAAP-63-59. pdf"http://www.irnase.csic.es/users/delrio/repository/2002-OLIVELLA-JAAP-63- 59.pdf HYPERLINK "http://www.irnase.csic.es/users/delrio/repository/2002-OLIVELLA-FUEL.pdf"ht tp://www.irnase.csic.es/users/delrio/repository/2002-OLIVELLA-FUEL.pdf HYPERLINK "https://dspace.ucalgary.ca/bitstream/1880/44981/1/Jalilehvand_2005_J0007.pd f"https://dspace.ucalgary.ca/bitstream/1880/44981/1/Jalilehvand_2005_J0007.p df The good resource for many issues on sulfur speciation are original articles by Pickering (1998) and Vairavamurthy (1998). I think, putting it conservatively, you can use peak fitting to find the mixing fractions of each charge state of S, and you can use LCF to get a better idea of what functional groups each is in, which is obviously not the same (several functional groups may have S in the same state). Anatoly From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Jenny Cai Sent: Sunday, October 26, 2008 2:12 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Fw: Re: Fit XANES spectra using Athena Sorry, Bruce. I have to send it again to the group. -Jenny --- On Sun, 10/26/08, Jenny Cai wrote: From: Jenny Cai Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "Bruce Ravel" 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 wrote: From: Bruce Ravel Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: "XAFS Analysis using Ifeffit" 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@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _____ Now with a new friend-happy design! Try the new HYPERLINK "http://ca.beta.messenger.yahoo.com/" \nYahoo! Canada Messenger _____ Image removed by sender.HYPERLINK "http://ca.toolbar.yahoo.com/"Yahoo! Canada Toolbar : Search from anywhere on the web and bookmark your favourite sites. Download it now! No virus found in this incoming message. Checked by AVG. Version: 7.5.549 / Virus Database: 270.8.3/1747 - Release Date: 10/26/2008 9:27 AM No virus found in this outgoing message. Checked by AVG. Version: 7.5.549 / Virus Database: 270.8.3/1747 - Release Date: 10/26/2008 9:27 AM