Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3
Hi Bruce,
Thanks for your help, it's really appreciated.
I was trying to keep it simple but it seems I'm just messing around.
What I am trying to do is to perform a new developed self-absorption
correction using collected fluorescence absorption coefficient data on a
CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as
absorber, having different values of molarity and penetration depth.
The correction expression requires these measured quantity:
μX(E) : the absorption coefficient due to a given core excitation of the
absorbing atom
- I used the background function for this ( bkg(E))
μo = μ(E) : photoelectric total linear absorption coefficient of the sample
at incident energy E
- I used the xmu(E) for this
μh = μ(E) :photoelectric total linear absorption coefficient of the sample
at fluorescence emission Ef
- I used the xmu(Ef) with Ef the K absorption edge of Cu
( 8.9789 eV)
χ: and here I used the chi(E) values of the exported ascii .xmu file
Hope it's clear now.
Matteo
2016-04-02 19:00 GMT+02:00
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Today's Topics:
1. Re: Ifeffit Digest, Vol 158, Issue 1 (Matt Newville)
----------------------------------------------------------------------
Message: 1 Date: Fri, 1 Apr 2016 15:56:29 -0500 From: Matt Newville
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1 Message-ID: Content-Type: text/plain; charset="utf-8" Matteo,
On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi
wrote: Hi Bruce, Now this is clear. In my case the correction I have to perform requires these measured/evaluated parameters: chi, mu (not sure if it's better to work with normmu here) and the background function. Is it physically meaningless to have the mu(k) and bkg(k) data? If that is not the case I would like to have these two columns exported in the ascii chi(k) file. So then I can perform the correction and re-import the new corrected chi(k) and make comparison with the uncorrected.
Kind regards, Matteo
It would certainly help (and by that I mean "help you get the answers you're looking for") if you gave us more details about what you're trying to do rather than ask for how to what you think you want to do.
Just to be clear: Converting from E to k does not involve a Fourier transform, just k = sqrt((2m*e/hbar**2)*(E-E0))
for k in Ang^-1 and E in eV, that's k ~= sqrt(0.262468*(E-E0))
I'm not sure what you're trying, but I would image you want to use normalized mu(E) or at least pre-edge subtracted mu(E). That is, what we call mu(E) is typically really -ln(I/I0) where I and I0 are not the actual intensities before and after the sample, but counts or counts per time in some detector that samples the flux. These values include more or less arbitrary scale factors (amplifier gains, etc) included. That means that (unless you very careful) mu(E) does not have meaningful units, certainly not cm^-1 or cm^2/gram.
Normalized mu(E) doesn't have such units either, but it's an easier place to start.
--Matt
On Sun, Apr 3, 2016 at 6:56 PM, Matteo Busi
Hi Bruce, Thanks for your help, it's really appreciated. I was trying to keep it simple but it seems I'm just messing around.
What I am trying to do is to perform a new developed self-absorption correction using collected fluorescence absorption coefficient data on a CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as absorber, having different values of molarity and penetration depth. The correction expression requires these measured quantity: μX(E) : the absorption coefficient due to a given core excitation of the absorbing atom - I used the background function for this ( bkg(E))
Wouldn't using bkg(E) suppress the fine-structure you are trying to recover? Anyway what are the units, are you normalizing bkg(E) to something meaningful? I would suggest using data from Chantler or Cromer-Liberman here. Or perhaps match mu(E) or bkg(E) to these.
μo = μ(E) : photoelectric total linear absorption coefficient of the sample at incident energy E - I used the xmu(E) for this
Again, be mindful of what the units are.
μh = μ(E) :photoelectric total linear absorption coefficient of the sample at fluorescence emission Ef - I used the xmu(Ef) with Ef the K absorption edge of Cu ( 8.9789 eV)
I am pretty sure that this is not what you want. You probably want mu(E) at the Cu fluorescence energy (8.046 keV). This can make a significant difference. HTH, --Matt
<Rant> It shouldn't be called 'self-absorption'. That's a misnomer, which seems to have come from a 1992 paper (Troger, et. al."Full correction of the self-absorption in soft-fluorescence extended x-ray-absorption fine structure", PRB 46,3283 (1992). The effect was described and analyzed in a 1982 paper, which called it an "attenuation factor": Goulon, et. al. "On experimental attenuation factors of the amplitude of the EXAFS oscillations in absorption, reflectivity and luminescence measurements", J. Physique 43, 539 (1982). </Rant> mam On 4/3/2016 4:56 PM, Matteo Busi wrote:
Hi Bruce, Thanks for your help, it's really appreciated. I was trying to keep it simple but it seems I'm just messing around.
What I am trying to do is to perform a new developed self-absorption correction using collected fluorescence absorption coefficient data on a CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as absorber, having different values of molarity and penetration depth. The correction expression requires these measured quantity: μX(E) : the absorption coefficient due to a given core excitation of the absorbing atom - I used the background function for this ( bkg(E)) μo = μ(E) : photoelectric total linear absorption coefficient of the sample at incident energy E - I used the xmu(E) for this μh = μ(E) :photoelectric total linear absorption coefficient of the sample at fluorescence emission Ef - I used the xmu(Ef) with Ef the K absorption edge of Cu ( 8.9789 eV) χ: and here I used the chi(E) values of the exported ascii .xmu file
Hope it's clear now. Matteo
2016-04-02 19:00 GMT+02:00
mailto:ifeffit-request@millenia.cars.aps.anl.gov>: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov mailto: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 ifeffit-request@millenia.cars.aps.anl.gov mailto:ifeffit-request@millenia.cars.aps.anl.gov
You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov mailto:ifeffit-owner@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: Ifeffit Digest, Vol 158, Issue 1 (Matt Newville)
----------------------------------------------------------------------
Message: 1 Date: Fri, 1 Apr 2016 15:56:29 -0500 From: Matt Newville
mailto:newville@cars.uchicago.edu> To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1 Message-ID: mailto:fGzksbv1SezR3M5pRkXanNyDg@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Matteo,
On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi
mailto:basebush@gmail.com> wrote: > Hi Bruce, > Now this is clear. > In my case the correction I have to perform requires these > measured/evaluated parameters: chi, mu (not sure if it's better to work > with normmu here) and the background function. > Is it physically meaningless to have the mu(k) and bkg(k) data? If that is > not the case I would like to have these two columns exported in the ascii > chi(k) file. > So then I can perform the correction and re-import the new corrected > chi(k) and make comparison with the uncorrected. > > Kind regards, > Matteo > > It would certainly help (and by that I mean "help you get the answers you're looking for") if you gave us more details about what you're trying to do rather than ask for how to what you think you want to do.
Just to be clear: Converting from E to k does not involve a Fourier transform, just k = sqrt((2m*e/hbar**2)*(E-E0))
for k in Ang^-1 and E in eV, that's k ~= sqrt(0.262468 tel:%280.262468*(E-E0))
I'm not sure what you're trying, but I would image you want to use normalized mu(E) or at least pre-edge subtracted mu(E). That is, what we call mu(E) is typically really -ln(I/I0) where I and I0 are not the actual intensities before and after the sample, but counts or counts per time in some detector that samples the flux. These values include more or less arbitrary scale factors (amplifier gains, etc) included. That means that (unless you very careful) mu(E) does not have meaningful units, certainly not cm^-1 or cm^2/gram.
Normalized mu(E) doesn't have such units either, but it's an easier place to start.
--Matt
Hi Matthew,
On Sun, Apr 3, 2016 at 8:13 PM, Matthew Marcus
<Rant> It shouldn't be called 'self-absorption'. That's a misnomer, which seems to have come from a 1992 paper (Troger, et. al."Full correction of the self-absorption in soft-fluorescence extended x-ray-absorption fine structure", PRB 46,3283 (1992). The effect was described and analyzed in a 1982 paper, which called it an "attenuation factor": Goulon, et. al. "On experimental attenuation factors of the amplitude of the EXAFS oscillations in absorption, reflectivity and luminescence measurements", J. Physique 43, 539 (1982). </Rant> mam
Thanks!! I completely agree, though I wasn't aware of the historical precedence for the mistake. Using "over-absorption" is a far better term. In X-ray fluorescence, "self-absorption" actually means the attenuation of fluorescence generated within a sample as it travels out of the sample. For over-absorption in XAFS, the issue is measuring absorption in fluorescence mode when the concentration of the absorbing element is not infinitesimal or when the sample thickness is not infinitesimal. --Matt
Yup. In fact, self absorption, in the correct sense, can help reduce "self-absorption" in the misnomer sense! That's how the grazing-exit method works. I might also note that although many elaborate schemes have been proposed for correcting for the effect, they all require knowing things about the sample that you don't always know, e.g. the exact geometry of something that isn't planar, or the exact composition. I find that the simple parameterization which comes from a thick-planar-sample model works reasonably well as an empirical method with an unknown parameter. Still, I wouldn't necessarily trust Debye-Waller (ss2) values taken from EXAFS on strongly overabsorbed samples, even with a correction that gets the right coordination number. mam On 4/3/2016 7:04 PM, Matt Newville wrote:
Hi Matthew,
On Sun, Apr 3, 2016 at 8:13 PM, Matthew Marcus
mailto:mamarcus@lbl.gov> wrote: <Rant> It shouldn't be called 'self-absorption'. That's a misnomer, which seems to have come from a 1992 paper (Troger, et. al."Full correction of the self-absorption in soft-fluorescence extended x-ray-absorption fine structure", PRB 46,3283 (1992). The effect was described and analyzed in a 1982 paper, which called it an "attenuation factor": Goulon, et. al. "On experimental attenuation factors of the amplitude of the EXAFS oscillations in absorption, reflectivity and luminescence measurements", J. Physique 43, 539 (1982). </Rant> mam
Thanks!! I completely agree, though I wasn't aware of the historical precedence for the mistake. Using "over-absorption" is a far better term.
In X-ray fluorescence, "self-absorption" actually means the attenuation of fluorescence generated within a sample as it travels out of the sample. For over-absorption in XAFS, the issue is measuring absorption in fluorescence mode when the concentration of the absorbing element is not infinitesimal or when the sample thickness is not infinitesimal.
--Matt
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While I am agnostic on the issue of nomenclature of the effect in question, far be it from me to deny Matthew (or anyone else) his right to a quality rant. Well done! That said, this: On 04/03/2016 10:15 PM, Matthew Marcus wrote:
I might also note that although many elaborate schemes have been proposed for correcting for the effect, they all require knowing things about the sample that you don't always know, e.g. the exact geometry of something that isn't planar, or the exact composition.
is the most important comment in this thread. I would go a small step farther -- they all require knowing things about the sample that, except in certain contrived situations, you almost certainly don't know. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (4)
-
Bruce Ravel
-
Matt Newville
-
Matteo Busi
-
Matthew Marcus