Hi Peng,
On Sat, Oct 2, 2021 at 2:50 AM Peng Liu
Dear IFEFFIT members,
I am sorry to bother you again. I asked about S02 selection for the first major revision. I just received the second revision. The reviewer is not satisfied with one S02 value for all our samples. "
1. I am still not satisfied with selected SO2 value (it is set to 0.85). SO2 is not transferable between different samples and detection methods. It is not possible to use a value obtained from different compound using transmission measurement mode to completely different other compound measured using fluorescence mode. One method to fix SO2 value is to measure diluted solution (to avoid self-absorption) of reference material in fluorescence mode. Other is to use multiple spectra fitting for all samples of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2 parameter is the same for all samples.
At the same time I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for measurements in fluorescence mode. "
We do get the S02 from a similar reference material measured in transmission mode, and our samples were all measured in fluorescence mode. It is not possible to measure the diluted reference material in fluorescence mode in one or two months. If you could give me some suggestions, that would be great.
It is always challenging to know what to do when a reviewer insists on being wrong. Well, I guess it is even more challenging when they turn out to be right. ;). Many different sample preparation and measurement effects can suppress the overall XAFS amplitude. There are "theoretical/calculational" terms: a) the relaxation of passive electrons to the core-hole that gives S02. b) the photo-electron mean-free-path. that are expected to be "atomic only" and so will not vary with measurement mode or sample-to-sample (mean-free path might be affected by samples smaller than a few mean-free path lengths, but the evidence for this is incomplete). But, the calculations for these (at least from "easily run XAFS calculations'') terms are imperfect and may need adjusting to completely match experimental spectra. For simplicity, we tend to adjust S02 but not the mean-free-path. There is also an amplitude term that may vary beamline-to-beamline (or even between beam runs) but not between samples or measurement mode: c) the actual energy resolution of the beamline. This could be compensated by adjusting either the mean-free-path term or S02. Again, we typically just adjust S02. In my experience, adjusting the mean-free-path ("Ei" in ifeffit/Artemis/Larch) is not any better than folding this into S02. I'll also say that for the very common situation of "Si(111) monochromator at a beamline intended for XAFS" especially in the common 5 to 20 keV range, that spectral resolutions tend to be pretty close to one another. And there are terms that can reduce the amplitude that can vary from sample-to-sample, and some of these are different depending on the measurement mode. d) pinhole effects, important for transmission mode. e) over-absorption for fluorescence mode. f) detector saturation effects for fluorescence mode measured with pulse-counting, energy-dispersive detectors. g) edge step from normalization, where slowly varying backgrounds can be different for collection mode. That is, if you have avoided or corrected for "d", "e", "f", and "g", then S02 will be transferable between samples, at least those measured with the same beamtime to account for "c". All that said, I would expect the reviewer may be correct when saying "I am confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6.", especially if that is a main conclusion of the work. It appears to me that the reviewer may not be convinced that effects "e" and "f" were completely avoided or compensated. That is, claiming that the uncertainty in coordination number is less than 1 (and claiming that CN of 7 and 6 are significantly different) would require special attention and confidence that the sample-dependent factors were carefully addressed. For example, if two transmission measurements give CN of 7.1 and 6.9 (say with fitting uncertainty of 1) and a sample measured in fluorescence measurement gives CN of 5.6 +/- 1, I think it would be fair to suspect that the effects "e", "f", and "g" could be influencing that difference. If those effects are large, then you may need to convince the gentle reader and the not-so-gentle reviewer that corrections are done appropriately. Hope that helps, --Matt