Re: [Ifeffit] Ifeffit Digest, Vol 108, Issue 17
Dear Bruce Thanks a lot for your suggestion. Yes, I did according your suggestion. I did the self-absorption correction and got the perfect spectrum as shown below. However, for the pure standards without dilution by BN, How to do the self-absorption correction? For example, I try one, but cannot get the credible spectra. ForDibenzyl Disulfide, the formula should be (C14H14S2)0.5435(BN)0, no dilution. I put (C14H14S2)0.5435(BN)0 in, but the spectrum I got is So can you tell me how to do the pure standards self-absorption correction using Athena? Much appreciated. Warm regards Juan Chen At 2012-02-15 02:00:01,ifeffit-request@millenia.cars.aps.anl.gov wrote:
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Today's Topics:
1. Re: fitting sulphur using standards by Athena (Bruce Ravel) 2. Re: fitting sulphur using standards by Athena (Matthew Marcus)
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Message: 1 Date: Tue, 14 Feb 2012 09:07:45 -0500 From: Bruce Ravel
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] fitting sulphur using standards by Athena Message-ID: <201202140907.45529.bravel@bnl.gov> Content-Type: Text/Plain; charset="utf-8" On Tuesday, February 14, 2012 07:55:54 am ?? wrote:
As I known, the spectra for standard diluted with BN and non-diluted are different. The peak of the non-diluted is low due to self-absorption, as shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur to about 3%. For dilution, the position of the peak is also changed. Therefore the non-diluted s1 spectra isnot the real spectra of dibenzothiophene. The question is what percentage should I dilute the standard to get the credible spectra for the standards?and how to explain the peak position change?
Although this sort of thing can be approximated from tables of absorption coefficients, the advice I usually give to my users is to prepare a series of samples of diminishing concetrations and measure then.
Having a good intuition for sample preparation and the effects of poor sample preparation is always important and even more so for low energy edges. The best way to develop that intuition is by doing the experiment yourself.
Can I use Athena to counteract the self-absorption and get the credible spectra for sdandards?
Yes it can -- in principle. Doing a good job of self absorption correction requires a lot of knowledge about your sample and its matrix -- often more than one has.
The use of the self absorption tool is explained in the Athena document. I have also written a lecture on this topic. Go to
https://github.com/bruceravel/XAS-Education/downloads
and download the "selfabs.pdf" file.
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/ifeffit/Demeter
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Message: 2 Date: Tue, 14 Feb 2012 07:33:38 -0800 From: "Matthew Marcus"
To: "XAFS Analysis using Ifeffit" Subject: Re: [Ifeffit] fitting sulphur using standards by Athena Message-ID: <03B21711433A40B4AA45C3DE3410452A@als.lbl.gov> Content-Type: text/plain; format=flowed; charset="utf-8"; reply-type=original To reiterate a point which is often not understood - dilution won't fix overabsorption if the particles of the concentrated material which are mixed in with the diluent are too big. For concentrated S compounds, "too big" is in the low microns. When I run a S standard, I do it in total electron yield to avoid this problem. When I fit a S spectrum, I use a crude oveabsorption model with a single parameter which is treated as an unknown fitting parameter, with the assumption that the reference spectra were collected in a way which avoids overabsorption. mam ----- Original Message ----- From: "Bruce Ravel"
To: "XAFS Analysis using Ifeffit" Sent: Tuesday, February 14, 2012 6:07 AM Subject: Re: [Ifeffit] fitting sulphur using standards by Athena On Tuesday, February 14, 2012 07:55:54 am ?? wrote:
As I known, the spectra for standard diluted with BN and non-diluted are different. The peak of the non-diluted is low due to self-absorption, as shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur to about 3%. For dilution, the position of the peak is also changed. Therefore the non-diluted s1 spectra isnot the real spectra of dibenzothiophene. The question is what percentage should I dilute the standard to get the credible spectra for the standards?and how to explain the peak position change?
Although this sort of thing can be approximated from tables of absorption coefficients, the advice I usually give to my users is to prepare a series of samples of diminishing concetrations and measure then.
Having a good intuition for sample preparation and the effects of poor sample preparation is always important and even more so for low energy edges. The best way to develop that intuition is by doing the experiment yourself.
Can I use Athena to counteract the self-absorption and get the credible spectra for sdandards?
Yes it can -- in principle. Doing a good job of self absorption correction requires a lot of knowledge about your sample and its matrix -- often more than one has.
The use of the self absorption tool is explained in the Athena document. I have also written a lecture on this topic. Go to
https://github.com/bruceravel/XAS-Education/downloads
and download the "selfabs.pdf" file.
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/ifeffit/Demeter
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End of Ifeffit Digest, Vol 108, Issue 17 ****************************************
On Wednesday, February 15, 2012 01:52:50 am 陈娟 wrote:
However, for the pure standards without dilution by BN, How to do the self-absorption correction? For example, I try one, but cannot get the credible spectra. ForDibenzyl Disulfide, the formula should be (C14H14S2)0.5435(BN)0, no dilution. I put (C14H14S2)0.5435(BN)0 in, but the spectrum I got is
So can you tell me how to do the pure standards self-absorption correction using Athena?
The self-absorption corrections are not particularly robust algorithms. For pure materials, they tend to be quite sensitive to errors in tabulated values, small errors in stoichiometry, and so on. I don't really know what dibenzyl disulphide is or how you prepare the sample for measurements. I would guess that, when specifying the stoichiometry, you will need to do something to account for the sample holder. For example, if you have a thin piece of polyimide tape between the beam and the sample, that will have the effect of "diluting" the sample, at least as far as the correction algorithm is concerned. This (along with Matthew's point about particle size and many other issues) is one of the reasons why self-absorption correction is such a tricky business. You could try making the coefficient for the (BN) something non-zero to approximate the effect of the tape (or of any water that might have been absorbed, or whatever). I suspect that if you do so, you will find that the correction will be numerically stable. Will it be right? Who knows! 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/ifeffit/Demeter
participants (2)
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Bruce Ravel
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陈娟