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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)
----------------------------------------------------------------------
Message: 1
Date: Wed, 28 Jul 2010 06:46:24 -0500
From: Matt Newville<newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of
absorbing atoms"
Message-ID:
<aanlktikm-ufmhua8tpoq3ja7xr0bc+xxfpwfsh75r...@mail.gmail.com>
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
------------------------------
Message: 2
Date: Wed, 28 Jul 2010 08:05:23 -0400
From: Scott Calvin<scal...@slc.edu>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of
absorbing atoms"
Message-ID:<8295e519-0fc0-4d2c-8c33-944e9bf0f...@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
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------------------------------
Message: 3
Date: Wed, 28 Jul 2010 07:37:52 -0500
From: Matt Newville<newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] updating Athena in Windows 7
Message-ID:
<aanlktinxbx3acxugdn5xzcajmuk5gwcyftb9n-6yv...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Todd,
On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd<tmon...@sandia.gov> 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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End of Ifeffit Digest, Vol 89, Issue 19
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