[Ifeffit] restraints in larch

Fri Oct 5 00:54:00 CDT 2018

Hi,

Thought I'd give my two cents before the experts chime in... I'm only a
grad student right now though so make what you want out of it. I also
haven't touched Larch for a while now since I got my xafs (Larch) functions
working in python several months ago.

First off though, ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5) ran
without throwing an error in Larch for me... (See screenshot near the
middle of this email) So I don't think anyone can really help without more
details, but I want to comment on some things:

   1. The first thing is that you're missing a vary = True in the statement
   for ntot1. Since the default value for vary is False according to the
   website, I would add that in if you actually wanted it to be fitted for
   during the fitting process (
   https://xraypy.github.io/xraylarch/fitting/parameters.html).
   2. In addition, when you run ntot1 = param(expr='nO1+nO2', min=5.0,
   max=8.5), are nO1 and nO2 pre-defined? If not the computer's not going
   to know what to make of those variables.
   3. I'd recommend something along the lines of:

nO1 = param(7.0, min=5, max=7, vary=True)
nO2 = param(1, vary=True),
ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5, vary=True)

I just tested this on my machine and it didn't throw any errors. (Though it
also didn't throw any errors without the 2 fixes I recommended...):

[image: Screen Shot 2018-10-05 at 12.55.59 AM.png]

I didn't think to check when I took that screenshot but with that line, the
vary is in fact set to false:

larch> ntot1.vary

False

In terms of the errors on error calculation --

   1. What's the reduced chi-sq? What do you mean by very small? In physics
   you want that to be as close to one as possible. Though in xafs the reduced
   chi-sq apparently is typically around 100-1000 so I'm confused as to what
   you mean by "small". Also, if you're having issues with errorbars to begin
   with, I wouldn't trust the chi-sq since that calculation relies on how
   big the errorbars are. If the errors are NAN, who knows what the
   computer would do to divide those numbers...
   2. What do you mean by "errors are not reported"? After the fit, it's
   returned in feffit.residual, or something along those lines (
   http://cars9.uchicago.edu/xraylarch/fitting/results.html#fitting-results-sec)...
   I haven't actually used this myself, so I can't say more.
   3. *(Just a comment...)* I don't know if this would help but my physics
   professor didn't let me trust the reduced chi-sq and gof values I was
   getting until I found out how the errors were calculated. By default,
   the errors are calculated by assuming that the noise is white in R-space
   and that there's no signal at high-R, so the "signal" near your rmax is
   the noise. (
   http://cars9.uchicago.edu/xraylarch/xafs/utilities.html#_xafs.estimate_noise,
   second to last paragraph)

Hope this was at least somewhat helpful,
----------
Hanyu (Alice) Zhang
*Master's in Materials science | 2019*

Research in utilizing XAFS to match current theory of metallic glasses to
experimental data

*Academic achievements:*

*MASMC
<https://en.wikipedia.org/wiki/Missouri_Academy_of_Science,_Mathematics_and_Computing>/NWMSU
<https://www.nwmissouri.edu/>:* Associate of Science, 2014
*CWRU <http://case.edu/>:* Bachelor's of Science in Engineering Physics
<http://physics.case.edu/undergraduate-programs/undergrad-degree-programs/bsdegree-engrphys/>
, 2018
*Honors societies*: National Society of Collegiate Scholars | Tau Beta Pi
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*Other interests:*

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subscribers) | Saturday Vlogs <http://bit.ly/AliceZhang>

On Thu, Oct 4, 2018 at 8:04 PM Barbara Etschmann <
barbara.etschmann at monash.edu> wrote:

> Hello
>
> I'm trying to use larch to refine the coordination of Y in solution. I
> need to use 2xO paths to fit the first shell and would like to restrain the
> total coordination to be between 5.5 and 8.
>
> I can apply the constraint to each nO, but not the total, i.e.
> nO1 = param(7.0, min=5, max=7, vary=True),
> nO2 = param(1, vary=True),
>  but
> ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5)
> does not work.
> How can I restrain the total coordination?
>
> Also, having some problems with the gofs and errors - the chi square is
> rather small and often the errors are not reported and it is not clear why.
>
> Thanks
> Barb
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