[Ifeffit] restraints in larch
Barbara Etschmann
barbara.etschmann at monash.edu
Thu Oct 11 20:34:34 CDT 2018
Hi Hanya
The fit looks reasonable. Tried changing the initial guess a bit, now it
produces errors but the gofs are still odd. Fitting 2<k<10 & 1<R<3. The
same data, fitted with the same parameters & restraints fits as well with
HORAE but with a reduced chi square of 225.
[[Statistics]]
nvarys, npts = 6, 588
n_independent = 16.279
chi_square = 0.000793878
reduced chi_square = 7.72339e-05
r-factor = 0.01890
Akaike info crit = -149.624
Bayesian info crit = -144.885
delrO1 = 0.133098 +/- 0.011100 (init= 0.150000)
delrO2 = -0.460833 +/- 0.024223 (init= -0.440000)
[image: Sol3_20C.png]
A new wrinkle - can only do one fit with this version of larch (0.9.40),
then have to close and open it again in order to be able to run another
fit. Tried running larch (0.9.40) on a windows7 virtual machine - it does
not work at all. Will try it on a real PC asap.
Thanks
Barb
On Tue, 9 Oct 2018 at 04:39, Hanyu Zhang <hxz269 at case.edu> wrote:
> Hi Barbara,
>
> Looking at this data I don't think Larch found a fit... Try overlaying a
> plot of your fit with your data and see if the fit was any good.
>
> I'd check the assumptions again and change the initial guesses around.
> Since this is a multi-dimensional fit, the initial guesses could change the
> results quite a bit. A small chi_sq in physics typically means that the
> errorbars on the data is too big, though I don't know how that would factor
> into XAFS... Where's your cutoff for the R-value when you're fitting? If
> it's at a R where you are still expecting data, that might be the issue (?)
>
> ----------
> 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
> <http://www.tbp.org> | Pi Mu Epsilon <http://pme-math.org/>
>
> *Other interests:*
>
> *Clubs*: Case Origami Circle | Case Rocket Team
> <http://caserocketteam.org> | CWRUbotix <http://cwrubotix.case.edu/> | Case
> Physics and Astronomy club | Math club
> *YouTube*: Chinese Operations Lead, Veritasium <http://veritasium.com> (5M
> subscribers) | Saturday Vlogs <http://bit.ly/AliceZhang>
>
>
>
> On Sun, Oct 7, 2018 at 5:56 PM Barbara Etschmann <
> barbara.etschmann at monash.edu> wrote:
>
>> Hi Matt and Hanyu
>>
>> Thanks - the latest version of larch runs wrt
>> ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5, vary=True)
>>
>> However, still getting odd gofs/errors:
>> [[Statistics]]
>> nvarys, npts = 6, 390
>> n_independent = 11.186
>> chi_square = 0.00080359
>> reduced chi_square = 0.000154956
>> r-factor = 0.01850
>> Akaike info crit = -94.7257
>> Bayesian info crit = -92.2378
>> ....
>>
>> delrO1 = 0.132140 +/- unknown (init= 0.150000)
>> delrO2 = -0.446980 +/- unknown (init= -0.500000)
>> enot = -4.125159 +/- unknown (init= 0.000000)
>> nO1 = 7.000000 +/- unknown (init= 7.000000)
>> nO2 = 0.929177 +/- unknown (init= 1.000000)
>> ntot1 = 7.929177 +/- unknown = 'nO1+nO2'
>> ssO1 = 0.006499 +/- unknown (init= 0.003000)
>> .....
>> (Please ignore the large init value.)
>>
>> Running on a Mac 10.13.3.
>> Happy to send the script & output.
>> Thanks
>> Barb.
>>
>>
>>
>>
>>
>>
>> On Fri, 5 Oct 2018 at 23:02, Matt Newville <newville at cars.uchicago.edu>
>> wrote:
>>
>>> Hi Hanyu, Barbara,
>>>
>>>
>>> On Fri, Oct 5, 2018 at 12:55 AM Hanyu Zhang <hxz269 at case.edu> wrote:
>>>
>>>> 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 <http://www.tbp.org> | Pi Mu Epsilon <http://pme-math.org/>
>>>>
>>>> *Other interests:*
>>>>
>>>> *Clubs*: Case Origami Circle | Case Rocket Team
>>>> <http://caserocketteam.org> | CWRUbotix <http://cwrubotix.case.edu/> | Case
>>>> Physics and Astronomy club | Math club
>>>> *YouTube*: Chinese Operations Lead, Veritasium <http://veritasium.com> (5M
>>>> 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?
>>>>>
>>>>>
>>> I think that should work. But I can also believe it doesn't ;). It
>>> may require a recent version of Larch (0.39 or 0.40 and really lmfit).
>>> I'll try to verify that over the next couple of days.
>>>
>>>
>>> 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.
>>>>>
>>>>
>>>
>>> Hm, not sure. Can you post an example?
>>> Cheers,
>>>
>>> --Matt
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20181012/225c050b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Sol3_20C.png
Type: image/png
Size: 165617 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20181012/225c050b/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2018-10-05 at 12.55.59 AM.png
Type: image/png
Size: 122637 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20181012/225c050b/attachment-0003.png>
More information about the Ifeffit
mailing list