[Ifeffit] fitting a specific k range
newville at cars.uchicago.edu
Thu Dec 5 23:29:26 CST 2013
On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin <scalvin at sarahlawrence.edu> wrote:
> 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.
It's reasonable to question whether the threshold for such a warning
is too conservative or to suggest (better yet, issue a pull request
for) a fix for a particular feature. Saying (as you did) that turning
the warning off "usually one of the first things" you teach students
seems counterproductive. To be clear, you did not teach them to
change the default value of reff_margin. I would have said Mend it,
don't End it. Perhaps the rule should be (Reff+0.5)*1.1? But this
was not your suggestion. Your suggestion was to ignore the rule.
If you are relying on these codes for your work, and teaching others
to use them, and find things you don't like or could be improved, it
is your responsibility to provide constructive, specific feedback and
fixes to the actual code. Yes, I actually do mean you, Scott. This
would be the perfect place for you to contribute. See
> 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.
I cannot tell if you are joking. It is, of course, to prevent one
from including paths (say, the second and third shells with variable
parameters when the R range being fit (say the first shell) will not
allow those variables to alter the fit. Having such variables can
grossly distort the fit and will generally prevent good error bars
from being calculated. I agree that it's not so much the presence of
Paths well beyond Rmax as it is the presence of variables that only
affect Paths outside the fitting range. But that is much harder to
automatically detect, and the case described above is a likely way to
get into that situation. Having a warning about this is vastly
preferable to not having such a warning.
The details of the thresholds may be tweaked, but you didn't complain
about the details of the rules, but the existence of the rule itself.
Perhaps your view is that this rule is just always wrong and not worth
fixing, but I think many of us would disagree with you.
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