[Ifeffit] EXAFS

[Scott Calvin]

Hi Francisco,

I'll take a shot at some of these questions--I'm sure others will  
chime in as well.
On May 11, 2011, at 2:34 PM, Francisco Garcia wrote:

> Dear all,
>
> I tried computing K-edge chi(k) for a solvated metal ion. For each
> snapshot, I simply carved out a cluster of radius 6 Ang around the
> metal.
>
> 1. if I set RMAX to say 5.5 in feff.inp, the chi(k) plot looks totally
> different from the case where the RMAX line is commented out
> (particularly k>10). I thought RMAX is the largest metal-H or metal-O
> separation but I think I am wrong
>
RMAX is the longest half-path length to include in chi(k). For direct  
scattering paths, it is therefore the most distant scattering pair  
that is allowed to contribute. So your understanding of the meaning is  
essentially correct.

In FEFF7, the documentation says it defaults to 2.2 times the nearest  
neighbor if it is not included. So commenting out RMAX does not mean  
to include all paths! That could be responsible for a considerable  
difference in chi(k).

> 2. I dont quite understand why the number of paths increases
> (sometimes by a factor of 3) when I set RMAX as opposed to the case
> where I comment it out.

See above. If your nearest neighbor is at, say, 1.8 angstroms, then  
commenting out RMAX is equivalent to setting it to 3.96 angstroms.  
That's much less than 5.5, and explains the smaller number of paths.

>
> 3. From time to time I get warnings indicating that a water O-H
> distance is too short:
>
>   WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
>    atoms     5    7
>     5    0.14400    2.09700    1.16300
>     7    0.77400    2.67400    1.00800
>
> I tried setting FOLP to 0.8 for H but the warnings persist.

Don't worry about it. This FEFF warning doesn't really expect  
hydrogens, and so sometimes gives a warning for atoms that would be  
close if they were anything bigger, but are OK if one is a hydrogen.  
Looking at the coordinates it specifies in your example, the two atoms  
are about 1 angstrom apart--OK if one is a proton.
>
> 4. On what criteria are sigma2 and s02 chosen? They are not usually
> reported in published theoretical papers and I was wondering if they
> are arbitrary.

FEFF is not usually used for EXAFS on its own. Most people use a  
fitting program, such as Ifeffit, to optimize the values of S02 and  
sigma2 to provide the best fit. (Although S02 in particular is often  
fit for a known material, and then that value used.) When used in that  
way, FEFF should be run with S02 = 1 and sigma2 = 0 to avoid confusion.

>
> 5. Finally, is the chi(k) dependent of which version of FEFF is being
> used. I am asking this because the peak height of my FEFF6 chi(k) is
> slightly lower than that of published results using FEFF8.
>

Yes, they are slightly different. For EXAFS, they probably aren't  
different enough to affect the answers to your scientific questions  
much, though.

--Scott Calvin
Sarah Lawrence College

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