[Ifeffit] RE: XAFS 12
Wojciech Gawelda
wojciech.gawelda at epfl.ch
Thu Mar 4 03:44:53 CST 2004
Hi Bruce,
I wondered about the same thing but it seems like editors of Physica
Scripta are very reluctant to say anything. I tried repeatedly to send
e-mails to them asking about any approximation when the topical issue on
XAFS 12 will come out but I got no response. So it seems like we have to
patiently wait and check their web site from time to time.
I know it doesn't sound great...
Greetings,
Wojciech Gawelda
*********************************************************************
Wojciech Gawelda
Laboratoire de Spectroscopie Ultrarapide (LSU)
Institut des Sciences et Ingénierie Chimiques (ISIC),
Faculté des Sciences de Base (SB-BSP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
CH-1015 Lausanne-Dorigny, Switzerland
Tel.: +41 (21) 693 0452
Fax.: +41 (21) 693 0422
E-mail: wojciech.gawelda at epfl.ch
WWW: http://lsu.epfl.ch
*********************************************************************
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Subject: Ifeffit Digest, Vol 13, Issue 3
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Today's Topics:
1. references for fluorescence corrections (Grant Bunker)
2. XAFS12 (Bruce Ravel)
3. Chi^2-Map question (Norbert Weiher)
----------------------------------------------------------------------
Message: 1
Date: Tue, 2 Mar 2004 22:21:17 -0600 (CST)
From: Grant Bunker <bunker at biocat1.phys.iit.edu>
Subject: [Ifeffit] references for fluorescence corrections
To: ifeffit at millenia.cars.aps.anl.gov
Message-ID:
<Pine.LNX.4.44.0403022219160.32516-100000 at biocat1.phys.iit.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Greetings, All - I'll make another effort to get this by the ANL Spam
filters.
A references for fluorescence corrections can be found in Booth and
Bridge's paper
http://xxx.lanl.gov/abs/cond-mat/0306252
they have refs to earlier work also.
thanks - grant
On Tue, 2 Mar 2004 ifeffit-request at millenia.cars.aps.anl.gov wrote:
> Send Ifeffit mailing list submissions to
> ifeffit at millenia.cars.aps.anl.gov
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> or, via email, send a message with subject or body 'help' to
> ifeffit-request at millenia.cars.aps.anl.gov
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
> 1. Re: question about S02 (passive electron reduction factor)
> (Matt Newville)
> 2. *****SPAM***** references for self-absorption correction
> (Grant Bunker)
> 3. Correlations (Scott Calvin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 1 Mar 2004 12:16:38 -0600 (CST)
> From: Matt Newville <newville at cars.uchicago.edu>
> Subject: Re: [Ifeffit] question about S02 (passive electron reduction
> factor)
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>
<Pine.LNX.4.44.0403011211200.10753-100000 at millenia.cars.aps.anl.gov>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Hi Scott,
>
> First, I'm not sure how your message got tagged as Spam by Argonne's
> SpamAssassin (words or phrases selling drugs??? huh???), but that
> happens well before I can do anything about it. I've forwarded this
> message on as a false positive for spam. For better archiving, I
> also included the full message you sent below.
>
> > Good point. It is much more straightforward to check the uncertainty
than
> > the correlation to determine if that could be responsible for the
> > anomalous S02...so I should have said that Yu-Chuan should check the
> > uncertainty of the S02 parameter. If it is very large (say 0.8),
then
> > Ifeffit is in effect reporting that it cannot determine S02 well for
some
> > reason. At that point, I think it is helpful to see if there is a
high
> > correlation, since that may give a clue as to the reason for the
large
> > uncertainty.
>
> Knowing the correlations always helps. And stating a best-fit value
> without an uncertainty is dangerous (one might take an implicit
> uncertainty, which may not be what you mean).
>
> This is probably a bit off-topic from the original question (where
> I'd guess self-absorption to be the main issue,....), but let's
> consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/-
> 0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90.
> One could conclude from these that a true value of S02= 1.0 was
> reasonable. But in order to get to S02= 1.0, sigma2 has to go up to
> ~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80
> is also reasonable, but this implies sigma2 would drop to around
> 0.011. The correlation means that, although having either S02= 0.80
> OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND
> sigma2= 0.020 is much less likely.
>
> The correlation by itself says nothing about the likelihood of
> having a true value for S02 of, say, 0.5. There is a chance this
> can happen, but it's small because the uncertainty in S02 is 0.1.
> The correlation simply tells you how sigma2 would respond if S02
> were 0.5, but nothing more.
>
> > So this brings up a (possibly contentious) point. In their reporting
> > recommendations, the IXS suggests reporting high correlations,
> > particularly when they are between parameters that do not routinely
show
> > high correlations. What is the reason for this suggestion? I'm not
> > criticizing it...just looking for the rationale.
>
> It's hard to speak for the IXS, but I'd say that correlations are
> recommended to be reported because they're important statistics. The
> correlations, along with the best-fit values and uncertainties, help
> more fully describe the range of plausible results.
>
> It's generally well-known that the parameters (S02,sigma2) and
> (E0,R) are highly correlated for a single shell of a single data
> set, and the implications of these are generally understood, I
> think. Sometimes other variables are correlated, and some people
> even do complex fits with multiple data sets or generalized
> variables that are not the simple XAFS parameters ;). In these
> cases, it may not be obvious how the variables are correlated. I
> think the IXS committee was concerned about this, and so recommended
> reporting correlations in such cases. That seems sensible to me.
>
> --Matt
>
>
> > On Sat, 28 Feb 2004, Scott Calvin wrote:
> >
> > Matt,
> >
> > Good point. It is much more straightforward to check the uncertainty
than
> > the correlation to determine if that could be responsible for the
anomalous
> > S02...so I should have said that Yu-Chuan should check the
uncertainty of
> > the S02 parameter. If it is very large (say 0.8), then Ifeffit is in
effect
> > reporting that it cannot determine S02 well for some reason. At that
point,
> > I think it is helpful to see if there is a high correlation, since
that may
> > give a clue as to the reason for the large uncertainty.
> >
> > So this brings up a (possibly contentious) point. In their reporting
> > recommendations, the IXS suggests reporting high correlations,
particularly
> > when they are between parameters that do not routinely show high
> > correlations. What is the reason for this suggestion? I'm not
criticizing
> > it...just looking for th erationale.
> >
> > --Scott Calvin
> > Sarah Lawrence College
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST)
> From: Grant Bunker <bunker at biocat1.phys.iit.edu>
> Subject: [Ifeffit] *****SPAM***** references for self-absorption
> correction
> To: ifeffit at millenia.cars.aps.anl.gov
> Message-ID:
> <Pine.LNX.4.44.0403011343220.6220-100000 at biocat1.phys.iit.edu>
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> [score: 0.0000]
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> An embedded message was scrubbed...
> From: Grant Bunker <bunker at biocat1.iit.edu>
> Subject: references for self-absorption correction
> Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST)
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> ------------------------------
>
> Message: 3
> Date: Mon, 01 Mar 2004 16:00:16 -0500
> From: Scott Calvin <scalvin at slc.edu>
> Subject: [Ifeffit] Correlations
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <3.0.1.32.20040301160016.00b22028 at mail.slc.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Thanks, Matt. That clarifies a few things...in particular, I found the
> example you gave (quoted below) to be quite helpful.
>
> --Scott Calvin
> Sarah Lawrence College
>
> At 12:16 PM 3/1/2004 -0600, you wrote:
> >This is probably a bit off-topic from the original question (where
> >I'd guess self-absorption to be the main issue,....), but let's
> >consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/-
> >0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90.
> >One could conclude from these that a true value of S02= 1.0 was
> >reasonable. But in order to get to S02= 1.0, sigma2 has to go up to
> >~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80
> >is also reasonable, but this implies sigma2 would drop to around
> >0.011. The correlation means that, although having either S02= 0.80
> >OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND
> >sigma2= 0.020 is much less likely.
> >>
> >--Matt
> >
> >
>
>
> ------------------------------
>
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------------------------------
Message: 2
Date: Wed, 3 Mar 2004 09:17:53 -0500
From: Bruce Ravel <ravel at phys.washington.edu>
Subject: [Ifeffit] XAFS12
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200403030917.53970.ravel at phys.washington.edu>
Content-Type: text/plain; charset="us-ascii"
Hi folks!
Does anyone have any information on when the volume of Physica Scripta
containing the proceedings of the last XAFS conference will be
published? Is there at least a volume number yet?
Thanks,
B
--
Bruce Ravel -----------------------------------
ravel at phys.washington.edu
Code 6134, Building 3, Room 405
Naval Research Laboratory phone: (1) 202 767
2268
Washington DC 20375, USA fax: (1) 202 767
4642
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
------------------------------
Message: 3
Date: Wed, 3 Mar 2004 16:13:54 +0100
From: Norbert Weiher <weiher at chem.ethz.ch>
Subject: [Ifeffit] Chi^2-Map question
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Message-ID: <200403031613.54578.weiher at chem.ethz.ch>
Content-Type: text/plain; charset="iso-8859-1"
Dear Friends,
maybe some of you remember that I was implementing a chi^2 mapping
algorithm
using the IFEFFIT library. This is working now, and for the data
analysis of
the maps I would like to ask your opinion on the following problem:
I want to check with chi^2 maps if I can separate 2 shells, e.g. if a
peak is
comprising two O shells or only one. For this I take the one-shell fit,
half
the coordination number and then vary the distance of the shells against
each
other (all other values taking from the best single shell fit). If I
find two
contributions, I should see 2 mirror-symmetric minima centered at the
corresponding DR values, e.g. (0,-0.1) and (-0.1,0) if I work with the
same
reference.
These minima are separated by a saddle point which is more or less
pronounced.
In the case of some Fe complexes I simulated, it is clearly visible,
while
for my gold oxides, it is hardly seen but still there. If I take a
system
where I know there IS only one shell (e.g. Au metal) and do the map, I
find
no saddle point and correspondingly no 2 minima.
Does anyone know a relation between the height of a saddle point and the
physical significance of the map? I would be glad to learn more about,
but
the statistic books I know don't deal with such a problem (and I am
chemist
and not a mathematician)...
If you need an example, I can send you two slides of a recent talk which
explain this problem more in detail - just drop me a mail.
Cheers,
Norbert
--
Dr. rer. nat. Norbert Weiher (weiher at chem.ethz.ch)
Institute for Chemical and Bioengineering - ETH Hönggerberg
HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32
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