[Ifeffit] Bug in Athena?

Scott Calvin SCalvin at slc.edu
Thu Nov 19 17:48:28 CST 2009

On Nov 19, 2009, at 2:59 PM, Matt Newville wrote:

> For this case, wouldn't it be better to measure the reference
> separately to determine the chemical shift, and not rely on the
> reference channel for this purpose?
> How often is the reference channel both noisy AND improved by merging?
> That would imply a transmission measurement
> that was poor due to low flux.  But if this is because the sample is
> thick as you suggest, the x-rays hitting the reference could be
> dominated by harmonics, and the reference data may just be bad, not
> noisy due to counting statistics.

It's a good point. But pick your poison. When I am trying to be  
careful about chemical shift, I don't trust that the mono won't just  
happen to skip a step between measuring the standard separately and  
measuring the sample. So I do both. I measure a standard in the sample  
channel, with a reference in the reference channel. I then leave the  
reference in the reference channel, and put my sample in. If the  
sample is a "reasonable" thickness for transmission, but a bit on the  
high side (say 2.3 absorption lengths), the photon count is down  
pretty far by the time it gets to the reference. The reference is also  
often the worst detector and amplifier that a line has, as the good  
stuff is used for I0, It, and If. So the reference channel may well  
have a considerable amount of random noise which can be improved by  

If that's the case, and if my sample appears to be suffering no beam  
damage (scans when aligned, lie on top of each other), then I align  
used the sample data. I then merge the sample data and the reference  
data. By comparing the sample to the reference and the previous scans  
where I measured the standard to the reference, I can see if there's  
been any energy shift between scans. As far as harmonics, this  
procedure should detect them. If the merged reference looks different  
from sample to sample (including the case where a standard was also in  
the sample channel), that suggests that there are issues with  
harmonics. If those issues move the first peak of the first  
derivative, I know they're going to affect my determination of  
chemical shift.  Also, if I get a nonzero chemical shift from this  
procedure for the standard, I know there's an issue. If not, they're  
not a problem.

The net result is that I have good confidence that I'm getting  
accurate chemical shifts, as loss of energy calibration, harmonics,  
and noise should all become evident by this procedure.

I'm not recommending this procedure over others; it's just what I do  
in some cases. But it doesn't seem like an unreasonable procedure to me.

--Scott Calvin
Sarah Lawrence College

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