Thanks for the responses. Seems like it is a problem without a simple solution, especially after the experiment has already been performed. When my users rerun the samples, I'll have to make sure they are very careful.
In terms of the question about fitting the Hephaestus reference, when you plot it in Hephaestus it only shows out to ~50eV, but when you save the data file the data goes out much further. You can see from the plots I had included that the data goes out past k=10 A^-1. Neil -----Original Message----- From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Wednesday, July 27, 2016 4:09 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 161, Issue 39 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.gov_mailman_listinfo_ifeffit&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=fTJzaojqXXInhR2RY8yBfnPci8s-rax9ReQ5rZat51M&e= 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: determining reasonable fitting parameters (Matthew Marcus) 2. Re: determining reasonable fitting parameters (Bruce Ravel) 3. Re: determining reasonable fitting parameters (Matthew Marcus) 4. Re: determining reasonable fitting parameters (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jul 2016 13:39:03 -0700 From: Matthew Marcus <mamar...@lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <c2c71f99-44d9-f17f-ab52-399f53d8b...@lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed I'm not sure I get your point about ion-chamber response. Shouldn't that normalize out in post-edge spline? If the I0 chamber gets less sensitive as a function of energy, then the post-edge background rises by the same amount as the wiggles get bigger, so it divides out. Similarly for probe-depth effects, depending on concentration. Another couple of possible sources of amplitude error: 1. The model for the pre-edge background is inaccurate, so that its extrapolation to the EXAFS region is incorrect. For instance, if there's a lot of elastic scatter getting into the fluorescence detector, then the pre-edge is curved, and if you model that with a straight line fitted near the edge, them you'll be off far from the edge. Similarly, in a long transmission scan, both pre- and post-edge are curved. My background-sub program has simple models for thse shapes which aren't perfect but help. This effect is really hard to control for because you have no real way to know what the 'right' answer is, most of the time. 2. Overabsorption will definitely reduce the amplitude of the wiggles, and I'm surprise Bruce didn't menntion it. It looks much like pinhole effect. Harmonics do similar things as well in transmission. I still haven't heard how you do EXAFS analysis using the short spectrum from Hepheastus. mam On 7/27/2016 1:23 PM, Bruce Ravel wrote: > On 07/27/2016 03:53 PM, Neil M Schweitzer wrote: >> Thanks to everyone for all the previous responses to my emails, I've >> learned a lot in the few weeks I've been on this list! I was hoping >> to build off of the last point Bruce made in message 3 below by >> asking another question. I am fitting a CeO2 reference from paths >> generated by feff from a cif file. Since this is my starting point, I >> made SO2 the same for every path (and used the coordination numbers >> from the cif file). If I am generating what looks to be a reasonable >> fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to >> tell me? Am I doing something wrong in my initial background >> subtraction in Athena? >> >> I'm asking about the background subtraction because I recently >> discovered that there is a CeO2 reference provided in Hephaestus. I >> exported the data, and tried to fit it in Artemis using a similar >> methodology I used for my own sample, and I got an even lower SO2. So >> I don't think the small SO2 value is an artifact of the way the >> experiment was run (although I might be wrong, I wasn't present when >> the data was actually collected). The observed difference seems real >> because the magnitude of the signal in E-space, k-space, and R-space >> is lower for the Hephaestus sample compared to my experimental sample >> (see attached image... One note, I'm not sure why the signals are off >> set in the Energy plot. The Eo's are the same, and if I plot the >> spectra together in E-space alone, they are not offset. Maybe a >> bug?). > > I don't remember much about the provenance of that CeO2 spectrum. I > don't remember how calibration was done (or even if it is reliable). > I don't remember much about the sample -- it was a pellet, but I have > no way of knowing if it was homogeneous or even if the particles were > of the size reported. > > I guess what I am trying to say is this -- if you trust your CeO2 > measurement, you should have more faith in that (or the one Matthew > just sent) than in the one from Hephaestus. > > As for your S02 question, here's some of the standard litany: > > + the mean free path used by feff was too long. > > + S02 and sigma^2 are highly correlated. > > + you did a lousy job normalizing the data (although it sure doesn't > look that way from your picture). > > + your sample had a lot of pinholes. > > + there is some source of loss in CeO2 that is neglected in Feff > (which is, practically speaking, the same as the mean free path > comment). You could try fixing S02 and floating an Ei parameter. > Or floating both S02 and Ei, although they will be highly > correlated. > > + There is also an energy response to the ionization chambers at such > a low energy -- that is, the absorption of the gas in the detector > is weaker at the end of the spectrum than at the beginning. In > fluorescence, that serves to attenuate the edge0step-normalized > spectrum in a way that looks like an enhancement to sigma^2. But > it's an attenuation, which could show up in S02. > > I should mention that in my favorite teaching example -- FeS2 -- by > the end of the lecture I have a S02 of something like 0.69. And I > just walk away from the lecture at that point :) The reason I do so is > that all the rest of the parameters are defensible and I chalk the > small S02 up to one of the points above (along with some enthusiastic > hand waving -- usually it's time for coffee or lunch by the time I've > finished the FeS2 demo!). > > B > > ------------------------------ Message: 2 Date: Wed, 27 Jul 2016 16:45:26 -0400 From: Bruce Ravel <bra...@bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <e0a93edf-8a8b-97a5-aa14-f595fc385...@bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:39 PM, Matthew Marcus wrote: > I'm not sure I get your point about ion-chamber response. Shouldn't > that normalize out in post-edge spline? Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does not do a functional (or energy dependent) normalization by default in the way you are suggesting. > If the I0 chamber gets less sensitive as a function of energy, then > the post-edge background rises by the same amount as the wiggles get > bigger, so it divides out. Similarly for probe-depth effects, > depending on concentration. Another couple of possible sources of > amplitude error: > 1. The model for the pre-edge background is inaccurate, so that its > extrapolation to the EXAFS region is incorrect. > For instance, if there's a lot of elastic scatter getting into the > fluorescence detector, then the pre-edge is curved, > and if you model that with a straight line fitted near the edge, > them you'll be off far from the edge. Similarly, in > a long transmission scan, both pre- and post-edge are curved. My > background-sub program has simple models for thse > shapes which aren't perfect but help. This effect is really hard > to control for because you have no real way to know > what the 'right' answer is, most of the time. > > 2. Overabsorption will definitely reduce the amplitude of the > wiggles, and I'm surprise Bruce didn't menntion it. It looks > much like pinhole effect. Harmonics do similar things as well in > transmission. My brain is really tiny and it's getting to be late in the afternoon here. It's amazing that many bullet points actually made it into the email! B -- Bruce Ravel ------------------------------------ bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_home_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=CLGK4SlRApN605gvlt2z7d5JRA2pjQzyGrKlMAZAFR0&e= Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=T9lLAQDmJODoEAvgTvbnoE24yE0m9GeGDV-QHGTgnHU&e= Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_demeter_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=WLNEeyBYvGHNsVvtMhUdPJCWK2FdLnMzBI4zMOWd9oQ&e= ------------------------------ Message: 3 Date: Wed, 27 Jul 2016 13:56:41 -0700 From: Matthew Marcus <mamar...@lbl.gov> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <3ee04494-5113-2994-3d96-e9e5bd2eb...@lbl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine does (mu(E(k))-spline(k))/spline(k), which I guess has its own problems - any wiggles driven in the spline will multiply the EXAFS. I haven't seen any effect from this, though. Maybe the right thing is (mu(E(k))-spline(k))/smooth(E(k)) where smooth is a smooth post-edge background such as a polynomial or spline with fewer knots than the subtraction spline or even a tensioned spline. I'd be willing to bet that this refinement will make no detectable difference, especially if you do the reference data the same way. I've found that you can do the most amazingly bogus things and get away with it as long as you do them equally to your reference and unknown, especially if the reference is very similar to the unknown. Of course, you can't rely on that. mam On 7/27/2016 1:45 PM, Bruce Ravel wrote: > On 07/27/2016 04:39 PM, Matthew Marcus wrote: >> I'm not sure I get your point about ion-chamber response. Shouldn't >> that normalize out in post-edge spline? > > Athena edge-step normalizes (i.e. normalizes by a constant) by default. It > does not do a functional (or energy dependent) normalization by default in > the way you are suggesting. > >> If the I0 chamber gets less sensitive as a function of energy, then >> the post-edge background rises by the same amount as the wiggles get >> bigger, so it divides out. Similarly for probe-depth effects, >> depending on concentration. Another couple of possible sources of >> amplitude error: >> 1. The model for the pre-edge background is inaccurate, so that its >> extrapolation to the EXAFS region is incorrect. >> For instance, if there's a lot of elastic scatter getting into >> the fluorescence detector, then the pre-edge is curved, >> and if you model that with a straight line fitted near the edge, >> them you'll be off far from the edge. Similarly, in >> a long transmission scan, both pre- and post-edge are curved. My >> background-sub program has simple models for thse >> shapes which aren't perfect but help. This effect is really hard >> to control for because you have no real way to know >> what the 'right' answer is, most of the time. >> >> 2. Overabsorption will definitely reduce the amplitude of the >> wiggles, and I'm surprise Bruce didn't menntion it. It looks >> much like pinhole effect. Harmonics do similar things as well in >> transmission. > > My brain is really tiny and it's getting to be late in the afternoon here. > It's amazing that many bullet points actually made it into the email! > > B > > ------------------------------ Message: 4 Date: Wed, 27 Jul 2016 17:08:58 -0400 From: Bruce Ravel <bra...@bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] determining reasonable fitting parameters Message-ID: <a632df68-e115-cda0-3ace-4c066230b...@bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 07/27/2016 04:56 PM, Matthew Marcus wrote: > Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.? Mine > does (mu(E(k))-spline(k))/spline(k), which I guess has its own > problems Exactly. Both solutions have problems. The potential for trouble with "/const" seems less severe to me and easier to support (in the sense of supporting the use of a software package). So that's why Athena does what she does. B -- Bruce Ravel ------------------------------------ bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_home_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=CLGK4SlRApN605gvlt2z7d5JRA2pjQzyGrKlMAZAFR0&e= Software: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bruceravel&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=T9lLAQDmJODoEAvgTvbnoE24yE0m9GeGDV-QHGTgnHU&e= Demeter: https://urldefense.proofpoint.com/v2/url?u=http-3A__bruceravel.github.io_demeter_&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=WLNEeyBYvGHNsVvtMhUdPJCWK2FdLnMzBI4zMOWd9oQ&e= ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.gov_mailman_listinfo_ifeffit&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=fTJzaojqXXInhR2RY8yBfnPci8s-rax9ReQ5rZat51M&e= Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia.cars.aps.anl.gov_mailman_options_ifeffit&d=CwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=oD5QfHEvBMM5YYrnfMF2YrJNX5aSKvlIRGd2B3iC9kQ&m=me9NMsJZQ49OCIWDVSMQ8TFLVLnHpw-OGYb2AvDyU48&s=b2awR0WPvycGR7oWC9OeoKFcelAARwiV__fV1V-xSm0&e= ------------------------------ End of Ifeffit Digest, Vol 161, Issue 39 **************************************** _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
