Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms"

Dear Matt, Dear Scott, Thank you very much for the detailed explanation on Delta E0 and S02. Now, things are becoming more clear to me. Best regards, Rana On 28.07.2010 19:00, ifeffit-request@millenia.cars.aps.anl.gov wrote:

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Today's Topics:

1. Re: Case of "nonequivalent multiple atomic sites of absorbing atoms" (Matt Newville) 2. Re: Case of "nonequivalent multiple atomic sites of absorbing atoms" (Scott Calvin) 3. Re: updating Athena in Windows 7 (Matt Newville)

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Message: 1 Date: Wed, 28 Jul 2010 06:46:24 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms" Message-ID: Content-Type: text/plain; charset=ISO-8859-1

Dear Rana,

Delta E0 is a shift in the Energy origin of k, that is where k=0. For the experimental data, this was chosen empirically (and so somewhat arbitrarily) from the measured data. For the FEFF calculation, it was chosen at the calculated absorption threshold (lowest available electronic level), but is known to not be perfect at this, especially in Feff6.

Though E0 is meant to be the absorption threshold, it is more important that the FEFF calculation and measured data agree. Because of this, Delta E0 is best left as an adjustable parameter in the analysis.

It is generally found that a single Delta E0 parameter is needed *per measured data set and per FEFF calculation*, because measured data can be shifted in energy and because each calculation can have a different definition of E0. It is possible to read the FEFF outputs and try to figure out how different these energies are and so set (not allow to float) the different E0 values. I believe this can work well, but it is not automated, and so not often used. In addition, usually one uses a different Delta E0 for each data set, but well-aligned data that re-use a FEFF calculation (say, data taken on the same system at different external conditions) can often get by with sharing a single Delta E0 parameter.

S02 is meant to express the incomplete overlap of the "passive electrons" in the absorbing atom. Removing the deep core electron can allow the other (L, M, N, O) electrons to relax slightly from their ground state. That relaxation reduces the overlap of the "initial" and "final" states of the transition that gives rise to XAFS, and so reduces the full effect. FEFF6 does not do a very good job of estimating this effect.

In practice, S02 can also mask other "amplitude issues", some theoretical (the inelastic losses that fold into the mean-free-path are not perfect) and some experimental (it is easier to mis-measure the amplitude than the phase of an oscillation). For XAFS, these experimental problems all tend to spoil the amplitude of the meaurement more than the phase: pin-holes in the sample, slight misalignment of the sample, over-absorption for fluorescence measurements, energy bandwidth of the incident beam and harmonic content of the incident beam.

The rule of thumb is that it is OK to use the same S02 for all samples of a particular absorbing atom. Many would add "measured at the same beamline" to that rule, so that effects of energy bandwidth and harmonic content are compensated.

Cheers,

--Matt

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Message: 2 Date: Wed, 28 Jul 2010 08:05:23 -0400 From: Scott Calvin To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms" Message-ID:<8295E519-0FC0-4D2C-8C33-944E9BF0F53D@slc.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi Rana,

Currently, S02 is usually described as being due to the relaxation of the other electrons in an atom when a core electron is removed, resulting in incomplete overlap of initial and final states. This appears to be a fairly good description, as careful experiments show good agreement with theoretical calculations based on this idea.

Note, however, that there could be some other contributors to S02. A photon could, in addition to exciting the core electron at the edge, also excite a valence electron.

There's a small thread on the transferability of S02 here:

http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01626.html

E0 is a tricky concept, in my opinion: it is the energy origin in the EXAFS equation. Perhaps a theorist can give me a pithy physical interpretation of what happens at that energy, but I don't know there needs to be anything; at k near 0, the path expansion is not convergent, so I'm not sure we should expect anything special to happen exactly at 0. In other words, it's not exactly the Fermi level or any other special energy.

E0 is dependent on oxidation state; it can shift by an electron volt or two when oxidation states vary.

Note that oxidation state is a simplistic measure of what's happening with the electron distribution in a material. Suppose fluorine is substituted for iodine in some material. Formally, the oxidation state of the atom they are bonded to is not changed by the substitution. But in reality, the electron distribution is different, and a small E0 shift would not be surprising.

I think the bottom line, then, is this:

S02 is completely transferable for the same element at multiple absorbing sites.

Delta E0 is transferable with some caution for the same element at multiple absorbing sites if the oxidation state is the same.

One other note: there's no rule that when trying constraints, you have to start unconstrained and add constraints to see the effect on the fit. With complicated systems like yours, it often pays to start with unrealistically simple constrains (not only E0's and S02's the same, but also sigma2's), and see if you're on the right track. Then look at the effect of relaxing constraints.

--Scott Calvin Sarah Lawrence College

On Jul 28, 2010, at 4:00 AM, Jatinkumar Rana wrote:

...

Dear Users,

Since long, i was trying to understand the physical meaning of term "Delta E0" and "S02" in EXAFS equation. I have little bit of idea about both of them. for example, S02 is element specific and it is transferable between samples (if we consider same absorbing atom).

However, I am not able to realize their importance in terms of their "physical meaning" as far as interaction of photoelectron is concerned. Therefore, it is difficult for me to understand their influence on EXAFS.

I am dealing with a case of "nonequivalent multiple atomic sites of absorbing atoms". It is quite obvious that in such kind of case no. of variables are more than no. of independent points and there is a need to constrain the parameters to solve such problems.

I have following questions :

How do i understand "Delta E0" and "S02" theoretically (in terms of photoelectron interaction) ?

Can i constrain "Delta E0" for all absorbing atomic site as same ? (my assumption : all absorbing atoms are at same oxidation level)

your comments and suggestions would be highly appreciated...

Best regards, Rana _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Message: 3 Date: Wed, 28 Jul 2010 07:37:52 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] updating Athena in Windows 7 Message-ID: Content-Type: text/plain; charset=ISO-8859-1

Hi Todd,

On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd wrote:

...

On Saturday, while starting up Athena, I was informed that there was an update to Athena available.? I tried installing the update but failed.? I am afraid this is due to some user permission issue in windows 7.? How can I try to reinstall the update and ensure that it works?

You can change the file current.dat in C:\Program Files\Ifeffit\config. It probably reads

013

right now, and you could change that to 012 or even lower. That will cause an update the next time ifeffit looks for updates, which only happens when one of the programs starts and if the time in Ifeffit\config\updater.ini is past. To force a check for updates the next time ifeffit runs, change updater.ini to read

timestamp = 0

In general, I believe this should work for Windows 7 (I have access to two Windows 7 64-bit machines, and all seems to be working on them, though I admit to not stressing them too much). So, as you say, I would also guess that the trouble you had was "only" permission issues. But, please let us know how it goes,

Sorry for the trouble,

--Matt

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