Re: [Ifeffit] Fw: Re: Fit XANES spectra using Athena
Hi Jenny, 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 don't think the two methods are normally used together but rather are used to get completely different kinds of information. As Bruce mentioned, there is no relationship between the results of one in relation to the other. 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? I am not sure what you mean by 'more accurate'. I suppose it depends on how you define accuracy. I hope this this doesn't sound banal but the basic principle of both peak fitting and linear combination fitting is the same. You are trying to use some basis set of functions to model a spectrum. A point that I think Bruce was making is that the important part is in how you interpret the functions. Obviously, a collection of mathematical functions has no physical meaning in terms of species. On the hand, if you just randomly combine some spectra from a standard list that give you a nice fit it does not have any more physical meaning that the Gaussian functions. 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 I hesitant to mention but I suppose you could take a brute-force approach and fit many combinations of your standards. The result though is that you will likely find multiple combinations that all add up to fit your spectrum with equal statistical goodness of fit. You then have to decide which (if any) might be the right one. You need chemical information to either know what is in your sample or at least what is most likely. You could then perhaps narrow down the search space to find something that is consistent with the data. For example if you happen to have a species with a particularly unique signature. However, there are a large number of organic sulphur species so this seems unlikely. Rather than trying to fit specific species you might try to see if you can classify groups of related sulphur compounds. Can you match peaks in your spectra with major features of a class of sulphur species? In other words, using vibrational spectroscopy terms, look for 'functional groups' first. Once you have separated groups of candidates then use chemical or other information to narrow the list. You might not be able to identify exact species but that may not be necessary. I have no idea what you what to know but do you need to know the exact composition? Or only the types of products? Or how reduced/oxidized the sample is? Inorganic/organic sulphur? You may be able to answer these sorts of questions without knowing the exact composition. I hope this helps. Cheers, Adam ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fit XANES spectra using Athena
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fit XANES spectra using Athena
PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Sun Oct 26 13:05:32 2008 Subject: Re: [Ifeffit] Fit XANES spectra using Athena 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Fit XANES spectra using Athena
I haven't been following this discussion closely, but actually it is possible to use PCA to help with a single spectrum of a single sample. The trick is to use linear combinations of the spectra of the standards to create spectra which look like mixtures with various amounts of different phases in them. Try to include all the phases that you think might be in the sample, except one. Then run the sample and the mixtures of standards together through PCA. Finally try a target transform to the missing phase. If it's in the sample, it should work pretty well. As a control, you have to also try PCA with the mixtures of standards but with the sample left out, and try the same target transform--it should work poorly. I've used similar tricks before to confirm the presence of certain substances in a sample...it can be a very useful technique when you can't pin down one of the substances in the sample, but suspect what some of the other contributors are. --Scott Calvin Sarah Lawrence College On Oct 26, 2008, at 1:16 PM, Frenkel, Anatoly wrote: PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Sun Oct 26 13:05:32 2008 Subject: Re: [Ifeffit] Fit XANES spectra using Athena 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] EXAFS simulations
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: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Fri 10/24/2008 09:57 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 21 Send Ifeffit mailing list submissions to ifeffit@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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Subject: [Ifeffit] EXAFS simulations To: ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] 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
