Re: [Ifeffit] maximum number of paths in Artemis
Hmmm... that seems weird. I'll try to look into this tomorrow. B On Monday, November 22, 2010 08:15:07 pm Matt Newville wrote: > Yuan, All, > > I put several Windows dlls for Ifeffit at > http://cars9.uchicago.edu/~ifeffit/src/Win32_dlls/1.2.12/ > > There are versions there with 256, 512, 1024, and 2048 paths.I > have not tested these beyond loading them, and running a trivial > python script. Please let me know if there are problems. > > Unfortunately, as far as I can tell, Athena and Artemis uses a > built-in dll, and will not use this newer one. > > --Matt > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@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
Re: [Ifeffit] maximum number of paths in Artemis
Yuan, All, I put several Windows dlls for Ifeffit at http://cars9.uchicago.edu/~ifeffit/src/Win32_dlls/1.2.12/ There are versions there with 256, 512, 1024, and 2048 paths.I have not tested these beyond loading them, and running a trivial python script. Please let me know if there are problems. Unfortunately, as far as I can tell, Athena and Artemis uses a built-in dll, and will not use this newer one. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] maximum number of paths in Artemis
Thanks, Matt and Bruce. I need the windows version. Please make it at least 1024. Yuan On 11/22/10 3:19 PM, "Matt Newville" wrote: > Hi Yuan, Bruce, > > It looks like I need to make a dll with more than 512 paths. I'm > on this, but it might take me a day or so. > > --Matt > > On Mon, Nov 22, 2010 at 5:09 PM, Bruce Ravel wrote: >> >> Yuan, >> >> It seems unwise to post a new question at the end of a long and active >> thread. Presumably you are looking for an answer -- hiding your >> question at the end of another thread does not seem like a good way to >> get that answer. >> >> That said, the answer to the question of how to get more than 512 >> paths depends on your operating system. >> >> For Mac: See >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-October/009673.html >> >> For Windows: You will need the ifeffit dll compiled with more paths. >> Matt, does such a thing exist for the current version of the dll? >> >> >> If you are using linux, let us know. It is not hard to recompile >> everything to do what you need. I can write up a short howto. >> >> B >> >> >> >> -- >> >> Bruce Ravel bra...@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 >> >> > > ___ > 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] maximum number of paths in Artemis
Hi Yuan, Bruce, It looks like I need to make a dll with more than 512 paths. I'm on this, but it might take me a day or so. --Matt On Mon, Nov 22, 2010 at 5:09 PM, Bruce Ravel wrote: > > Yuan, > > It seems unwise to post a new question at the end of a long and active > thread. Presumably you are looking for an answer -- hiding your > question at the end of another thread does not seem like a good way to > get that answer. > > That said, the answer to the question of how to get more than 512 > paths depends on your operating system. > > For Mac: See > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-October/009673.html > > For Windows: You will need the ifeffit dll compiled with more paths. > Matt, does such a thing exist for the current version of the dll? > > > If you are using linux, let us know. It is not hard to recompile > everything to do what you need. I can write up a short howto. > > B > > > > -- > > Bruce Ravel bra...@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 > > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Distortion of transmission spectra due to particle size
On Mon, Nov 22, 2010 at 4:55 PM, Scott Calvin wrote: > Some follow-up. > This, for example, is from an excellent workshop presentation by Rob > Scarrow: > > Errors from large particles are independent of thickness Yes... one can have a sample that is uniform, or made of small particles, and still too thick. In that sense, having large particles or sample with widely varying thickness is a separate issue from having a sample that is too thick. > The relative (%) variation in thickness depends on the ratio (particle > diameter / avg. thickness), so it is tempting to increase the avg. thickness > (i.e. increase μx) as an alternative to reducing the particle diameter. > > However, simulations of MnO2 spectra for average Δμ0x = 1, 2 or 3 show that > the errors in derived pre-edge peak heights and EXAFS amplitude factors are > significant when diameter > 0.2 / Δμ0, but that they are not affected by the > average sample thickness. (Δμ0 refers to the edge jump) > > The equation at right is given by Heald (quoting earlier work by Stern and > Lu). D is particle diameter, μ1 is for just below the edge, and Δμ =μ(above > edge) - μ1. > > I've seen similar claims elsewhere, although Scarrow's is particularly clear > and unambiguous. OK. Are you saying there something wrong with this? Did he say that spheres were stacked directly on top of one another? I'm not seeing that assumption in what you quote. I read it as saying that you can't have spheres that are too thick. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] maximum number of paths in Artemis
Yuan, It seems unwise to post a new question at the end of a long and active thread. Presumably you are looking for an answer -- hiding your question at the end of another thread does not seem like a good way to get that answer. That said, the answer to the question of how to get more than 512 paths depends on your operating system. For Mac: See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-October/009673.html For Windows: You will need the ifeffit dll compiled with more paths. Matt, does such a thing exist for the current version of the dll? If you are using linux, let us know. It is not hard to recompile everything to do what you need. I can write up a short howto. B -- Bruce Ravel bra...@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
Re: [Ifeffit] Distortion of transmission spectra due to particle size
Some follow-up. This, for example, is from an excellent workshop presentation by Rob Scarrow: Errors from large particles are independent of thickness The relative (%) variation in thickness depends on the ratio (particle diameter / avg. thickness), so it is tempting to increase the avg. thickness (i.e. increase μx) as an alternative to reducing the particle diameter. However, simulations of MnO2 spectra for average Δμ0x = 1, 2 or 3 show that the errors in derived pre-edge peak heights and EXAFS amplitude factors are significant when diameter > 0.2 / Δμ0, but that they are not affected by the average sample thickness. (Δμ0 refers to the edge jump) The equation at right is given by Heald (quoting earlier work by Stern and Lu). D is particle diameter, μ1 is for just below the edge, and Δμ =μ(above edge) - μ1. I've seen similar claims elsewhere, although Scarrow's is particularly clear and unambiguous. The equation Scarrow gives is indeed the one from Lu and Stern, and the simulations are based on that equation. That Lu-Stern equation is derived for a monolayer of spheres, and then experimentally tested with multiple layers of tape. I'm still trying to work through the math to see how it works for multiple layers. I'm not convinced that the N divides out as is claimed in the article. As Matt says, it wasn't their main point. There is no question that if the particle size is large compared to an absorption length there will be nonuniformity and thus distortions. But compare a monolayer of particles with a diameter equal to 0.4 absorption lengths with four strips of tape of that kind stacked. Do we really think the distortion due to nonuniformity will be as bad in the latter case as in the first? In practice, I think many transmission samples fall in roughly that regime, so the question isn't just academic. I'll keep trying to work through the math and let you know what I find. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
Hi Edmund, Thanks for that post... I'd never seen the UV-vis literature on this and didn't know what a Ringbom plot was. A google search led to Ramirez-Munoz 1967 (doi:10.1016/0026-265X(67)90042-2) on Atomic-Absorption Photometry, which shows a very nice result that significant distortions don't really appear until outside 20 to 80% total absorption. The focus seems to be on total absorption, which makes sense as the most important term. But for XAFS, it's not that unusual to have fairly large total absorption due to window and sample cell materials (say, diamonds in a diamond anvil cell), but still have decent data that has an edge step between 0.2 and 1.5.Perhaps that means that counting statistics really never matter for transmission XAFS, and the reason to not go above an edge step of 3 or 4 is spatial inhomogeneity in the sample and beam, and harmonics. --Matt On Mon, Nov 22, 2010 at 7:13 AM, Welter, Edmund wrote: > Dear Jatin, > > the optimum mued of 2.x is not just derived by simple photon counting > statistics. As Matt pointed out, for transmission measurements at a > synchrotron beamline in conventional scanning mode this is seldom a matter. > Nevertheless, one should avoid to measure subtle changes of absorption at > the extreme ends, that is, transmission near 0 % or 100 %. In optical > photometry this is described by the more or less famous "Ringbom plots" > which describe the dependency of the accuracy of quantitative analysis by > absorption measurements (usually but not necessarily in the UV/Vis) from the > total absorption of the sample. > > This time the number is only near to 42, the optimum transmission is 36.8 % > (mue = 1). So, to achieve the highest accuracy in the determination of small > Delta c (c = concentration) you should try to measure samples with > transmissions near to this value (actually the minimum is broad and > transmissions between 0.2 and 0.7 are ok). In our case, we are not > interested in the concentration of the absorber, but we are also interested > in (very) small changes of the transmission resp. absorption in our samples. > Or, using Bouger, Lambert Beer's law, in our case mue (-ln(I1/I0) is a > function of the absorption coefficient (mue0). The concentration of the > absorber and the thickness (d) of the sample are constant. > > -ln(I1/I0) = mue0 * c * d > > But then: If the optimum is a mue between 0.35 and 1.6 why are we all > measuring successfully (ok, more or less ;-) using samples having a mue > between 2 and 3? ...and 0.35 seems desperately small to me! Maybe sample > homogeneity is an issue? > > Cheers, > Edmund Welter > > > > > > > ___ > 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] Distortion of transmission spectra due to particle size
Scott, I agree with Jeremy and Matthew. Layering very small (compared to an absorption length) spheres is exactly what "powder on tape" and mixing with a low-Z binder do, and that's why these are the preferred methods for turning a powder into a sample of uniform thickness. If the spheres are not small, then these techniques don't help. In fact, Lu and Stern show nicely that more layers of smaller particles is better than a few layers of thicker particles. I would say that is the main point of their work. Perhaps you read it differently. > "Finally, the attenuation in N layers is given by (I/I0)^N, where I is > the transmitted intensity through one layer. Xeff for N layers is then > the same as for a single layer since N will cancel in the final result." > > This is not the case, is it? It seems to me that their analysis assumes > that the spheres in subsequent layers line up with the spheres in > previous ones, so that thick spots are always over thick and thin spots > over thin. I don't think they are making that assumption. I interpret that to mean only that I/I_0 (the attenuation integrated over the layer) is multiplicative, and so that ratios of Xeff (what we would probably call mu) are not distorted by having multiple layers. I think they are assuming that the layers are close to consistent in the amount of total material they have, but not how that material is distributed within or between layers. > It's little wonder, then, that making the sample thicker does > not improve the uniformity according to that analysis. I don't think that is a conclusion that Lu and Stern make. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Distortion of transmission spectra due to particlesize
> I think you are correct in principle that more layers can reduce the > thickness effect problem. If harmonics were not an issue, eventually if > you pile up enough random layers, the thickness will be uniform. > Whether this is useful in practice is another matter, but suspect it may > not be when single particle absorption is large. I think I agree with this. Among my beamline's users, a very common problem is preping samples that, as Matthew suggested, have boulders either on tape or in BN. If the individual particles/agglomerates are 10's of absorption lengths (which *is* a common problem among my users) then ignoring harmonics and stackin' 'em up won't help. So stacking as a solution to pinholes only works if the particles are small enough to begin with -- in which case it won't be that hard to make a good sample in the first place! B -- Bruce Ravel --- bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage:http://cars9.uchicago.edu/~ravel 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
Re: [Ifeffit] Distortion of transmission spectra due to particle size
I think there is a confusion over what is being averaged. As an example, consider a layer of particles which are completely opaque, and let's say that the area fraction is 1/2. If the particles lined up, then the transmission would be 1/2 for any N, whereas if the layers were random, then you'd get a transmission of 1/2**N. The power law idea can be thought of in terms of probabilities. The transmission of a layer is the probability of a photon getting through. Now consider N layers which are unregistered. Then, for a photon to get through, it has to "roll the dice" N times, and the probability of transmission through each layer is independent, hence the (trans)**N law. That said, it is a common error for people to say things like "but I diluted the stuff 100x in BN; I should be immune to overabsorptiob and thickness effect because the edge jump in transmission is 0.01". Sorry, if the particles are mm-size, to give an extreme example, then you can dilute all you want and still not get the right answer. mam On 11/22/2010 11:45 AM, Scott Calvin wrote: Hi all, I'm tracking down a piece of EXAFS lore which I think is incorrect. I've seen it said that you cannot compensate for the distortion introduced by large particle sizes by making the sample thicker. Certainly thick samples have their own set of issues (e.g. "thickness effects" from harmonics), but I've seen the claim that the mathematics of the distortions introduced by nonuniformity means that there is a particle-size distortion that is independent of thickness. This claim is sometimes accompanied by an equation giving chi_eff/chi_real as a function of particle size diameter D and various absorption coefficients. I've eventually traced this equation back to a paper by Lu and Stern from 1983, have walked through the derivation, and believe there is a flaw in the logic that has led to the erroneous--and widely quoted--conclusion that thickness cannot compensate for particle size. The paper, for those who want to follow along, is K. Lu and E. A. Stern, "Size effect of powdered sample on EXAFS amplitude," Nucl. Instrm. and Meth. 212, 475-478 (1983). They calculate the intensity transmitted by a spherical particle, and from there calculate the attenuation in the normalized EXAFS signal for a beam passing through that particle. They then, however, extend this to multiple layers of particles by the following argument: "Finally, the attenuation in N layers is given by (I/I0)^N, where I is the transmitted intensity through one layer. Xeff for N layers is then the same as for a single layer since N will cancel in the final result." This is not the case, is it? It seems to me that their analysis assumes that the spheres in subsequent layers line up with the spheres in previous ones, so that thick spots are always over thick and thin spots over thin. It's little wonder, then, that making the sample thicker does not improve the uniformity according to that analysis. I've done a calculation for the effects of uniformity in a somewhat different way, and found that it is indeed true that multiple layers on particles show less distortion due to nonuniformity that a single layer of particles of the same size, just as one would intuitively imagine, and in contrast to Lu and Stern. Do you agree that the extrapolation to multiple layers in the original Lu and Stern paper is not correct, or have I misled myself somehow? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory P.S. None of this should be taken as an endorsement of overly thick samples! Harmonics and the like are a concern regardless of the uniformity issue. ___ 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] Distortion of transmission spectra due to particle size
Scott, I think you are correct in principle that more layers can reduce the thickness effect problem. If harmonics were not an issue, eventually if you pile up enough random layers, the thickness will be uniform. Whether this is useful in practice is another matter, but suspect it may not be when single particle absorption is large. Jeremy > -Original Message- > From: ifeffit-boun...@millenia.cars.aps.anl.gov > [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf > Of Scott Calvin > Sent: Monday, November 22, 2010 1:46 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Distortion of transmission spectra due to > particle size > > Hi all, > > I'm tracking down a piece of EXAFS lore which I think is incorrect. > > I've seen it said that you cannot compensate for the > distortion introduced by large particle sizes by making the > sample thicker. > Certainly thick samples have their own set of issues (e.g. > "thickness effects" from harmonics), but I've seen the claim > that the mathematics of the distortions introduced by > nonuniformity means that there is a particle-size distortion > that is independent of thickness. This claim is sometimes > accompanied by an equation giving chi_eff/chi_real as a > function of particle size diameter D and various absorption > coefficients. > > I've eventually traced this equation back to a paper by Lu > and Stern from 1983, have walked through the derivation, and > believe there is a flaw in the logic that has led to the > erroneous--and widely quoted-- conclusion that thickness > cannot compensate for particle size. > > The paper, for those who want to follow along, is K. Lu and E. A. > Stern, "Size effect of powdered sample on EXAFS amplitude," Nucl. > Instrm. and Meth. 212, 475-478 (1983). > > They calculate the intensity transmitted by a spherical > particle, and from there calculate the attenuation in the > normalized EXAFS signal for a beam passing through that particle. > > They then, however, extend this to multiple layers of > particles by the following argument: > > "Finally, the attenuation in N layers is given by (I/I0)^N, > where I is the transmitted intensity through one layer. Xeff > for N layers is then the same as for a single layer since N > will cancel in the final result." > > This is not the case, is it? It seems to me that their > analysis assumes that the spheres in subsequent layers line > up with the spheres in previous ones, so that thick spots are > always over thick and thin spots over thin. It's little > wonder, then, that making the sample thicker does not improve > the uniformity according to that analysis. > > I've done a calculation for the effects of uniformity in a > somewhat different way, and found that it is indeed true that > multiple layers on particles show less distortion due to > nonuniformity that a single layer of particles of the same > size, just as one would intuitively imagine, and in contrast > to Lu and Stern. > > Do you agree that the extrapolation to multiple layers in the > original Lu and Stern paper is not correct, or have I misled > myself somehow? > > --Scott Calvin > Faculty at Sarah Lawrence College > Currently on sabbatical at Stanford Synchrotron Radiation Laboratory > > P.S. None of this should be taken as an endorsement of overly > thick samples! Harmonics and the like are a concern > regardless of the uniformity issue. > > ___ > 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
[Ifeffit] Distortion of transmission spectra due to particle size
Hi all, I'm tracking down a piece of EXAFS lore which I think is incorrect. I've seen it said that you cannot compensate for the distortion introduced by large particle sizes by making the sample thicker. Certainly thick samples have their own set of issues (e.g. "thickness effects" from harmonics), but I've seen the claim that the mathematics of the distortions introduced by nonuniformity means that there is a particle-size distortion that is independent of thickness. This claim is sometimes accompanied by an equation giving chi_eff/chi_real as a function of particle size diameter D and various absorption coefficients. I've eventually traced this equation back to a paper by Lu and Stern from 1983, have walked through the derivation, and believe there is a flaw in the logic that has led to the erroneous--and widely quoted-- conclusion that thickness cannot compensate for particle size. The paper, for those who want to follow along, is K. Lu and E. A. Stern, "Size effect of powdered sample on EXAFS amplitude," Nucl. Instrm. and Meth. 212, 475-478 (1983). They calculate the intensity transmitted by a spherical particle, and from there calculate the attenuation in the normalized EXAFS signal for a beam passing through that particle. They then, however, extend this to multiple layers of particles by the following argument: "Finally, the attenuation in N layers is given by (I/I0)^N, where I is the transmitted intensity through one layer. Xeff for N layers is then the same as for a single layer since N will cancel in the final result." This is not the case, is it? It seems to me that their analysis assumes that the spheres in subsequent layers line up with the spheres in previous ones, so that thick spots are always over thick and thin spots over thin. It's little wonder, then, that making the sample thicker does not improve the uniformity according to that analysis. I've done a calculation for the effects of uniformity in a somewhat different way, and found that it is indeed true that multiple layers on particles show less distortion due to nonuniformity that a single layer of particles of the same size, just as one would intuitively imagine, and in contrast to Lu and Stern. Do you agree that the extrapolation to multiple layers in the original Lu and Stern paper is not correct, or have I misled myself somehow? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory P.S. None of this should be taken as an endorsement of overly thick samples! Harmonics and the like are a concern regardless of the uniformity issue. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] maximum number of paths in Artemis
Dear Ifeffit experts, Hopefully this is a short question: how can I increase the path number limit for fitting in Artemis? Currently it's 512, and I need to at least double the number. Thanks in advance. Yuan ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
On Nov 22, 2010, at 7:09 AM, Jatinkumar Rana wrote: Hi Scott, Sorry for mixing up the things. For the case, when i have very limited amount of sample that i can not cover 1sq.cm area, you, Matt and others have given very very clear explanation about possible solutions and the probable effects on data quality. I am really very thankful to all of you for sharing your experience and expertise. My last post was with reference to the case when i have enough powders (i.e., reference oxide compounds). It is just to be ensured that i am doing things 100% exactly in a same way it has to be done. With best regards, Jatin -- Jatinkumar Rana Yes, Jatin, the procedure you described is fine. There is no "right" way to make samples, although there are many wrong ways. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
To my mind, when considering sample preparation the important thing is not so much the "right" thickness, as knowing the effects to guard against as the thickness deviates toward the thin or thick side. As transmission samples become thicker, the problem of "unwanted" photons becomes more severe. Those photons may be harmonics, photons scattered into the It detector, or photons from the tails of the resolution curve of the monochromator. As transmission samples become thinner, uniformity becomes more of an issue. If you play with the equations, you'll see that if your sample is a mixture of regions that have a thickness of 1.0 absorption lengths and regions that have a thickness of 2.0 absorption lengths, the spectrum is less distorted than if it is a mixture of 0.5 and 1.0 absorption lengths. So if a sample is on the thick side, it is particularly important to guard against harmonics in the beam and scattered photons. If it is on the thin side, it is particularly important to guard against nonuniformity. To put it another way, problems are synergistic. With a well- conditioned beam, a uniform sample, and linear detectors, the thickness almost doesn't matter (within reason)--at a modern beamline, a total absorption of even 0.05 or 4.0 will work. But as each of those conditions deviates from the ideal, distortions become much more severe. There's an old joke about someone on a diet going in to a fast food joint and asking for a double bacon cheeseburger, a large fries...and a diet Coke. In XAFS measurements, that attitude actually kind of works, because of the synergies I just discussed. Personally, I trust my ability to condition the beam and minimize scattering more than I trust my ability to make a uniform sample, so I lean a little toward the thicker side. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 22, 2010, at 5:13 AM, Welter, Edmund wrote: Dear Jatin, the optimum mued of 2.x is not just derived by simple photon counting statistics. As Matt pointed out, for transmission measurements at a synchrotron beamline in conventional scanning mode this is seldom a matter. Nevertheless, one should avoid to measure subtle changes of absorption at the extreme ends, that is, transmission near 0 % or 100 %. In optical photometry this is described by the more or less famous "Ringbom plots" which describe the dependency of the accuracy of quantitative analysis by absorption measurements (usually but not necessarily in the UV/Vis) from the total absorption of the sample. This time the number is only near to 42, the optimum transmission is 36.8 % (mue = 1). So, to achieve the highest accuracy in the determination of small Delta c (c = concentration) you should try to measure samples with transmissions near to this value (actually the minimum is broad and transmissions between 0.2 and 0.7 are ok). In our case, we are not interested in the concentration of the absorber, but we are also interested in (very) small changes of the transmission resp. absorption in our samples. Or, using Bouger, Lambert Beer's law, in our case mue (-ln(I1/I0) is a function of the absorption coefficient (mue0). The concentration of the absorber and the thickness (d) of the sample are constant. -ln(I1/I0) = mue0 * c * d But then: If the optimum is a mue between 0.35 and 1.6 why are we all measuring successfully (ok, more or less ;-) using samples having a mue between 2 and 3? ...and 0.35 seems desperately small to me! Maybe sample homogeneity is an issue? Cheers, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Transmission EXAFS sample
On 21.11.2010 19:00, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: 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 ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Transmission EXAFS sample (Jatinkumar Rana) 2. Re: Transmission EXAFS sample (Scott Calvin) -- Message: 1 Date: Sun, 21 Nov 2010 11:44:25 +0100 From: Jatinkumar Rana To:ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Transmission EXAFS sample Message-ID:<4ce8f809.3040...@helmholtz-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 20.11.2010 19:00,ifeffit-requ...@millenia.cars.aps.anl.gov wrote: 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 ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Transmission EXAFS sample (Scott Calvin) 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) -- Message: 1 Date: Fri, 19 Nov 2010 10:30:37 -0800 From: Scott Calvin To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Transmission EXAFS sample Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Jatin, Matt covered most of what I would say, but I'll add a few comments of my own. I'm not sure how you arrived at the conclusion that you have only a few percent of what you need--you must be assuming a sample area somehow. I have frequently made transmission measurements on samples where I only had a few milligrams available. Generally, I did it by spreading it on a layer of tape as well as I could and then folding the tape over and over again--sometimes to make as many as 16 layers. (Of course, that many layers is not advisable if you're below 6 keV or so, as the absorption of the tape itself would kill the signal). Even if there are lots of pinholes because you can't cover the tape effectively, 16 layers from folding will make them cancel out fairly well. I can then narrow the beam a bit to match the size of my sample. Flux isn't really the issue here, so I don't even need a focussed beamline--I can just narrow the slits. Two other tips: 1) Realize that even with a tiny amount of sample that much of it won't end up on the tape. The process of brushing on tape is designed to separate the small grains from the big ones, with only the small ones ending up on tape. Allow that to happen! 2) You can sometimes get a second piece of tape to have some sample on it by putting it sticky side down on your mortar and peeling it back. A thin layer of dust from the sample will stick to the tape, and give you a little more absorption and a bit more of a uniform distribution. If you stack that with the primary piece of tape and then fold a few times, you may end up in pretty good shape, as long as you're not operating at a low enough energy so that all the layers of tape are a problem.. This procedure doesn't give me the best data I've ever seen, but it's often not bad. --Scott Calvin Sarah Lawrence College On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: Dear Jatin, The idea that the optimum absorption length (mu*t) for transmission experiments is 2.3 assumes that the errors in the measurement are due to counting statistics of the x-rays. For any synchrotron experiment, the number of x-rays in the transmission chamber is high enough that the noise from counting statistics is rarely significant. This means that using a value of 2.3 is really not that important. The more important issues are a) having a uniform sample. b) not having (mu*t) so high that higher-order harmonics dominate the transmission measurement. For transmission measurements, it's difficult to overstate the importance of a uniform sample. For an ideal thickness, I would say that the better rules of thumb than mu*t = 2.3 are to aim for an edge step of 0.1 to 1.0, and a total absorption less than 3.0. If you only have enough material for an edge step as low as 0.02 (as you imply), then measuring in fluorescence or electron emission is probably a better choice. S
Re: [Ifeffit] Transmission EXAFS sample
Dear Jatin, the optimum mued of 2.x is not just derived by simple photon counting statistics. As Matt pointed out, for transmission measurements at a synchrotron beamline in conventional scanning mode this is seldom a matter. Nevertheless, one should avoid to measure subtle changes of absorption at the extreme ends, that is, transmission near 0 % or 100 %. In optical photometry this is described by the more or less famous "Ringbom plots" which describe the dependency of the accuracy of quantitative analysis by absorption measurements (usually but not necessarily in the UV/Vis) from the total absorption of the sample. This time the number is only near to 42, the optimum transmission is 36.8 % (mue = 1). So, to achieve the highest accuracy in the determination of small Delta c (c = concentration) you should try to measure samples with transmissions near to this value (actually the minimum is broad and transmissions between 0.2 and 0.7 are ok). In our case, we are not interested in the concentration of the absorber, but we are also interested in (very) small changes of the transmission resp. absorption in our samples. Or, using Bouger, Lambert Beer's law, in our case mue (-ln(I1/I0) is a function of the absorption coefficient (mue0). The concentration of the absorber and the thickness (d) of the sample are constant. -ln(I1/I0) = mue0 * c * d But then: If the optimum is a mue between 0.35 and 1.6 why are we all measuring successfully (ok, more or less ;-) using samples having a mue between 2 and 3? ...and 0.35 seems desperately small to me! Maybe sample homogeneity is an issue? Cheers, Edmund Welter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit Digest, Vol 93, Issue 16
On 21.11.2010 19:00, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: 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 ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Transmission EXAFS sample (Jatinkumar Rana) 2. Re: Transmission EXAFS sample (Scott Calvin) -- Message: 1 Date: Sun, 21 Nov 2010 11:44:25 +0100 From: Jatinkumar Rana To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Transmission EXAFS sample Message-ID:<4ce8f809.3040...@helmholtz-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 20.11.2010 19:00, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: 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 ifeffit-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Transmission EXAFS sample (Scott Calvin) 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) -- Message: 1 Date: Fri, 19 Nov 2010 10:30:37 -0800 From: Scott Calvin To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Transmission EXAFS sample Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Jatin, Matt covered most of what I would say, but I'll add a few comments of my own. I'm not sure how you arrived at the conclusion that you have only a few percent of what you need--you must be assuming a sample area somehow. I have frequently made transmission measurements on samples where I only had a few milligrams available. Generally, I did it by spreading it on a layer of tape as well as I could and then folding the tape over and over again--sometimes to make as many as 16 layers. (Of course, that many layers is not advisable if you're below 6 keV or so, as the absorption of the tape itself would kill the signal). Even if there are lots of pinholes because you can't cover the tape effectively, 16 layers from folding will make them cancel out fairly well. I can then narrow the beam a bit to match the size of my sample. Flux isn't really the issue here, so I don't even need a focussed beamline--I can just narrow the slits. Two other tips: 1) Realize that even with a tiny amount of sample that much of it won't end up on the tape. The process of brushing on tape is designed to separate the small grains from the big ones, with only the small ones ending up on tape. Allow that to happen! 2) You can sometimes get a second piece of tape to have some sample on it by putting it sticky side down on your mortar and peeling it back. A thin layer of dust from the sample will stick to the tape, and give you a little more absorption and a bit more of a uniform distribution. If you stack that with the primary piece of tape and then fold a few times, you may end up in pretty good shape, as long as you're not operating at a low enough energy so that all the layers of tape are a problem.. This procedure doesn't give me the best data I've ever seen, but it's often not bad. --Scott Calvin Sarah Lawrence College On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: Dear Jatin, The idea that the optimum absorption length (mu*t) for transmission experiments is 2.3 assumes that the errors in the measurement are due to counting statistics of the x-rays. For any synchrotron experiment, the number of x-rays in the transmission chamber is high enough that the noise from counting statistics is rarely significant. This means that using a value of 2.3 is really not that important. The more important issues are a) having a uniform sample. b) not having (mu*t) so high that higher-order harmonics dominate the transmission measurement. For transmission measurements, it's difficult to overstate the importance of a uniform sample. For an ideal thickness, I would say that the better rules of thumb than mu*t = 2.3 are to aim for an edge step of 0.1 to 1.0, and a total absorption less than 3.0. If you only have enough material for an edge step as low as 0.02 (as you imply), then measuring in fluorescence or electron emission is probably a better choice.
