[Ifeffit] Bond length and Coordination number problems from EXAFS

Robert Gordon ragordon at alumni.sfu.ca
Tue Feb 21 13:02:45 CST 2017


Hi Fuxiang,

How much background do you have in EXAFS fitting? Have you taken a course?
Do you have access to a good EXAFS primer book (e.g. Grant Bunker's or 
Scott Calvin's)?

/1) Which is better, to refine only the first shell or more shells. /
/    The results seems to be quite sensitive on the selection of 
kmin/kmax and Rmin/Rmax, I cannot judge when can get reliable results 
(base on chi?) /

In general, I would take a kmin that is above the edge and away from any 
white line because background
removal in those areas (white line, or on the rising edge) is suspect. I 
would take a kmax that avoids data that cannot be distinguished from 
noise. I picked Rmax on the high side to isolate the 1st peak in the FT. 
I picked Rmin based on the magnitude of the 1st Feff shell and a need to 
get enough R-range to do a 6
parameter fit. It was a nervous choice since too low an Rmin could bring 
in unwanted artifacts. What it
comes down to is: do the choices allow a sufficient amount of data for 
use in fitting; and are
they defensible in review.

What I considered good fits were based in part on looking for where 
chi^2 is a minimum and
in part from inspection of the results - were the results consistent 
with a basic understanding
of how atom-atom distances should manifest. You applied this as well 
when you initially wrote
and noted your fit was giving Pd-Pd distances shorter than Pd-Ni, and 
you questioned that.

As for fitting higher shells, what is the problem you are trying to 
answer? Is the Pd distribution
statistical or showing evidence of clustering? The higher shells are 
weak and have multiple scattering
as well as back-scattering paths. The error in just the first shell Pd 
content is large, owing to the
strong correlation with the mean-square-relative-displacement. I would 
expect this to also be
problematic in higher shells - more so. So, can you build a defensible 
argument based on a first
peak analysis? Is taking more data an option (going to higher k with 
less noise)? This was just
the Pd data. How consistent is the Ni data fit?

/2) You used Rmax=2.56, while Rpd is 2.68, not sure if there's 
any contradict /

The sine term in the EXAFS equation is sin(2kR+delta). What is delta?
Did you measure reference foils for Ni and Pd? Where does the first peak 
manifest
in the |FT(k^n * chi(k))| - at what R-value? By how much is the peak 
shifted from the
crystallographic distance for the different standards?
/
/
/3) For the Nni and Npd, you change them manually and check the chi 
values during fitting, is that right?/

Correct. Try this yourself. I suggest you tabulate and plot them so you 
can see
the different subsidiary minima and maxima and how the fit results vary 
between them. Perhaps use
a broad range to get a sense of what a global minimum might be.

Please note: The questions I have posed are intended to stimulate 
thinking and need not warrant
a response.

Another curious note: If you look at the chi(k)'s for the 1st shell Feff 
paths, they are almost
180 degrees out of phase at higher k...a suppressing effect that could 
make it difficult to
study higher concentration mixtures.




cheers,
-R.

On 2/21/2017 6:22 AM, Fuxiang Zhang wrote:
> Hi, Robert,
> Thank you very much for the help. Based on the nominal composition, 
> there should have more than one Pd atoms in the 1st shell and both the 
> R values you got are reasonable.
> I still have some questions about the fitting
> 1) Which is better, to refine only the first shell or more shells.
>     The results seems to be quite sensitive on the selection of 
> kmin/kmax and Rmin/Rmax, I cannot judge when can get reliable results 
> (base on chi?)
> 2) You used Rmax=2.56, while Rpd is 2.68, not sure if there's 
> any contradict
> 3) For the Nni and Npd, you change them manually and check the chi 
> values during fitting, is that right?
>
> Thanks again
>
> Fuxiang
>
>
>
> On Tue, Feb 21, 2017 at 3:30 AM, Robert Gordon <ragordon at alumni.sfu.ca 
> <mailto:ragordon at alumni.sfu.ca>> wrote:
>
>     Hi Fuxiang,
>
>     I tried fitting just the first shell in your data:
>     kmin 3.5  kmax 11.775
>     Rmin 1.25  Rmax 2.56
>
>     I used just Pd-Ni and Pd-Pd single scatter paths with one
>     amplitude, one E, 2 delR's and 2 sigma-squareds
>     for a 6 parameter fit.
>
>     I didn't let Nni or Npd vary in a fit, but did change them between
>     fits. I get what seems to be
>     a double minimum yielding similar chi values as I varied Nni+Npd = 12
>     i.e. Npd in the range 1.6 - 1.8   or Npd 2.0 - 2.2 yielded similar
>     values
>     Another minimum occurs near 2.4 but sig^2-pd is getting larger
>     than seems plausible.
>
>     I did not try changing Ranges or windows to see if that would
>     smooth out the oscillations in the fit
>     versus relative N values
>
>     amp ~ 0.7 (ok...but I didn't normalise the data or compare with Pd
>     or Ni foils)
>     delEo  -7 (which seems large)
>     Rni  2.54            Rpd 2.68   (both a bit small but would need
>     to compare to Ni and Pd foil fits for systematic error in fitting)
>     ssni  0.0050(2)    sspd   0.010(3)   (error bars from correlation
>     with changing N - strong correlation
>     between Npd and sspd)
>
>     This is not consistent with your model, since it has more than 1
>     Pd in the 1st shell.
>     The R-values (apart from not having checked reference foils) are
>     within reason for what one
>     would expect from sums of atomic radii.
>
>     Hope this helps get you pointed in the right direction as you
>     refine your model.
>
>     cheers,
>     Robert
>
>
>
>
>     On 2/20/2017 10:57 AM, Fuxiang Zhang wrote:
>>     Dear All,
>>     I met a problem in fitting my sample. The sample is a very
>>     simple crystalline Ni (fcc) with minor Pd. I measured both the
>>     K-edge of Ni and Pd and fit with a 55 randomly distributed
>>     cluster model (from calculations). The model suggested that there
>>     are 1 Pd in the first and second-shell, 6-Pd in the 3rd-shell and
>>     2-Pd in the 4th shell. I have attached the FPJ file here, can
>>     anyone help me to have a look.
>>
>>     1. In fitting the K-edge of Pd, most paths are single scattering,
>>     but I always get a shorter Pd-Pd length than Pd-Ni, even I tried
>>     to include all the paths. Not sure if I made any mistakes in the
>>     path parameters settings.
>>
>>     2. If including the minor contribution paths, I use the same
>>     parameters for the path: @Ni1.1 Ni1.1@ (acute triangle) and the
>>     path: @N1.1 Ni1.1@ (obtuse triangle), as well as
>>     single scattering path @Ni1.1 at . I know there's a problem (though
>>     no much effect on the results), but don't know how to set the
>>     first two paths' parameters
>>
>>     3. If the result is correct, which may suggest there is no Pd in
>>     the 1st-shell, but how to fit the coordination number of Pd is a
>>     problem. Since Pd is only 1/12 in the first shell, while
>>     the uncertainty of CN from EXAFS fitting is pretty large. Does it
>>     make a sense to refine the CN?
>>
>>     FPJ file is attached
>>
>>     Thank you very much
>>
>>     Fuxiang Zhang
>>
>>
>>     _______________________________________________
>>     Ifeffit mailing list
>>     Ifeffit at millenia.cars.aps.anl.gov
>>     <mailto:Ifeffit at millenia.cars.aps.anl.gov>
>>     http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>     <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
>>     Unsubscribe:http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>     <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit>
>     _______________________________________________ Ifeffit mailing
>     list Ifeffit at millenia.cars.aps.anl.gov
>     <mailto:Ifeffit at millenia.cars.aps.anl.gov>
>     http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>     <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
>     Unsubscribe:
>     http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>     <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/20170221/85883b35/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ojogemeemnkoodpj.png
Type: image/png
Size: 34424 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170221/85883b35/attachment-0001.png>


More information about the Ifeffit mailing list