[Ifeffit] fitting a specific k range
scalvin at sarahlawrence.edu
Thu Dec 5 16:56:06 CST 2013
I love the warnings Artemis gives! They're not just for novices--they often catch when I've made a dumb mistake somewhere. I praise them, defend them, and generally think Bruce has done a wonderful thing by having them.
The out of range default warning, however, I find counterproductive and confusing to novices. There are two reasons for my opinion (and it is, of course, my opinion--as Bruce points out, if others differ, they can set the defaults differently.) One has to do with the kind of example I mentioned earlier. Here's the other reason:
The default behavior is to warn if there is a path beyond 1.1 times the top of the range, correct? (It's kind of a pain for me right now to fire up the most recent version of Artemis, so I can't actually easily confirm that at the moment.) The default R-max is, if I recall correctly, 3.0 angstroms. Thus, by default, a warning is generated if there is a path above 3.3 angstroms in the list.
But, as we know, the path list uses distances which are half path lengths, while the Fourier transform range is in terms of the conjugate variable to k. For edges around the third row of the periodic table, the peaks corresponding to a path tend to show up about 0.3 to 0.5 angstroms lower in the Fourier transform than their half path-length. And, of course, that's just the peak--the path has significant amplitude a bit below (and above) that.
So, a novice user fires up Artemis, imports her data, and uses atoms to generate a feff file. Because she's appropriately thoughtful about what she's doing, she looks at what the unfitted paths of the FEFF calculation look like. She sees the fitting range goes up to 3 angstroms, and then selects all the paths that contribute significant amplitude to that range. That might include a path with a half path length of 3.4 angstroms. She then runs a fit--and Artemis gives her a warning that something may be wrong.
At that point, she could stick to her guns and tell the fit to continue. Since that's going to happen with pretty much every fit she runs, it becomes very tempting not to read the warning each time, but just dismiss it. And at that point, if there's a highly useful warning, she'll miss it.
Or, she could decide that she's the novice, and what she's doing isn't that unusual, so maybe she shouldn't be including that path at 3.4 angstroms, and take it out. She is now getting distorted results, because she's leaving out a path that has significant amplitude in the region.
I think, not just from personal preference, but also from a consideration of what is best for people learning to use the software, that the warning is set too conservatively. And I'm not even clear what misstep it's trying to prevent.
Sarah Lawrence College
On Dec 5, 2013, at 2:32 PM, <fred.mosselmans at diamond.ac.uk> <fred.mosselmans at diamond.ac.uk> wrote:
> What I find reassuring about Bruce's warnings is they allow you to think properly about what you are doing. Fortunately, unlike Chris, I am not of a size where I have to worry about falling down rabbit holes, unless American rabbits are much bigger than English ones.
> I would commend Matt's original question as it opened a debate with 3 of the mainstays of the list. That may not have been the intention but it makes interesting reading for us mailing list voyeurs.
> Sent from Samsung tablet
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