[Ifeffit] Theoretical value of S02 for different absorber

Rana, Jatinkumar Kantilal jatinkumar.rana at helmholtz-berlin.de
Thu Apr 5 13:08:03 CDT 2012


Dear Dr. Newville,

Thank you so much for your reply. Things are very much clear now.

With best regards,
Jatin
________________________________________
From: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of ifeffit-request at millenia.cars.aps.anl.gov [ifeffit-request at millenia.cars.aps.anl.gov]
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Subject: Ifeffit Digest, Vol 110, Issue 6

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Today's Topics:

   1. Re: Theoretical value of S02 for different absorber
      (Rana, Jatinkumar Kantilal)
   2. Results Reporting (John Farell)
   3. Re: Results Reporting (Bruce Ravel)
   4. Re: Theoretical value of S02 for different absorber
      (Matt Newville)


----------------------------------------------------------------------

Message: 1
Date: Thu, 5 Apr 2012 10:44:05 +0000
From: "Rana, Jatinkumar Kantilal"
        <jatinkumar.rana at helmholtz-berlin.de>
To: "ifeffit at millenia.cars.aps.anl.gov"
        <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber
Message-ID: <6FCB59A6A97E13429B863B7014B57E4B10E2E8 at didag1>
Content-Type: text/plain; charset="utf-8"

Dear Dr. Ravel,

Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02.

However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit.

For example,

S02 for Mn absorber

FEFF calculated                           0.94
Fitted value for my sample               ~0.75
Fitted value for various Mn-oxides       ~0.75
Other reported value from Mn fit         ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496)

S02 for Fe absorber

FEFF calculated                          ~0.94
Fitted value for Fe-foil                 ~0.70
Fitted value for various Fe-oxides       ~0.70
Reported value by calculation             0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1)


It is well known that S02 is a property of central absorbing atom and is considered to be constant between 0.7 - 1.0. However, in real world, S02 is affected by various systematic errors like thicker samples (in transmission), absorption by other elements in sample at given energy range and many more. These factors can suppress the amplitudes of EXAFS oscillations resulting in lower value of fitted S02 than it should be for a given absorber.

The reason I am so much curious about S02 is, if I know what should be (or should be considered) the value of S02 for a given absorber than I can possibly understand the reasons of fitted S02 being too low or too high. For instance, S02 and Sigma2 are highly correlated for first shell. So from fitted value of S02 and Sigma2 of first shell, I could possibly understand changes in local structure.

So I would like to put forward very simple but still confusing question that which value of S02 should be considered, FEFF calculated or the one obtained by fitting standards (either reference foils or reference compounds measured on same beamline) and why.

Many thanks in advance !!!

With best regards,
Jatin



-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request at millenia.cars.aps.anl.gov
Sent: Mittwoch, 4. April 2012 19:00
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 110, Issue 5

Send Ifeffit mailing list submissions to
        ifeffit at millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
        ifeffit-owner at millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Theoretical value of S02 for different absorber (Jatin Rana)
   2. Re: Theoretical value of S02 for different absorber (Bruce Ravel)


----------------------------------------------------------------------

Message: 1
Date: Wed, 4 Apr 2012 17:45:13 +0800 (SGT)
From: Jatin Rana <jatin_rana2002 at yahoo.com>
To: "ifeffit at millenia.cars.aps.anl.gov"
        <ifeffit at millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Theoretical value of S02 for different absorber
Message-ID:
        <1333532713.14873.YahooMailNeo at web193501.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear Ifeffit users,

Can anyone recommend a reference where I can get calculated value of S02 for various elements ? I would like to compare them with my fitted values.

Many thanks in advance !!

With best regards,
Jatin Rana
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Message: 2
Date: Wed, 4 Apr 2012 08:19:34 -0400
From: Bruce Ravel <bravel at bnl.gov>
To: Jatin Rana <jatin_rana2002 at yahoo.com>,      XAFS Analysis using Ifeffit
        <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber
Message-ID: <201204040819.35087.bravel at bnl.gov>
Content-Type: Text/Plain;  charset="iso-8859-15"

On Wednesday, April 04, 2012 05:45:13 am Jatin Rana wrote:
> Dear Ifeffit users,
>
> Can anyone recommend a reference where I can get calculated value of S02
> for various elements ? I would like to compare them with my fitted values.

http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation



--

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter


------------------------------

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Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov
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End of Ifeffit Digest, Vol 110, Issue 5
***************************************

________________________________

Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de



------------------------------

Message: 2
Date: 5 Apr 2012 04:59:55 -0000
From: "John Farell" <john_far at rediffmail.com>
To: "ifeffit at millenia.cars.aps.anl.gov"
        <ifeffit at millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Results Reporting
Message-ID: <20120405045955.8520.qmail at f4mail-235-118.rediffmail.com>
Content-Type: text/plain; charset="utf-8"

Hi..

Can you please explain me how to report the errors of EXAFS parameters like bond length, Co - ordination number, disorder etc. (Or how to obtain those errors ??)


with regards

John
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Message: 3
Date: Thu, 5 Apr 2012 09:31:09 -0400
From: Bruce Ravel <bravel at bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Results Reporting
Message-ID: <201204050931.09373.bravel at bnl.gov>
Content-Type: Text/Plain;  charset="iso-8859-15"

On Thursday, April 05, 2012 12:59:55 am John Farell wrote:
> Hi..
>
> Can you please explain me how to report the errors of EXAFS parameters like
> bond length, Co - ordination number, disorder etc. (Or how to obtain those
> errors ??)

This topic is discussed at length in the standard online resources for
EXAFS and for our software.

Ifeffit's error reporting is reasonably well explained in its
documentation.  See http://cars9.uchicago.edu/ifeffit/Documentation

Artemis reports all of Ifeffit's error reporting in the log file of
each fit.

Ifeffit uses a Levenberg-Marquardt, non-linear, least-squares
minimization.  Error bars and correlations are taken in the standard
manner form the covariance matirx, with the caveat that the error bars
are scaled assuming that the fit was good and that the measurement
uncertainty, epsilon, was incorrectly evaluated.  Thus, if you
actually like the fit, the error bars are scaled to the correct size.

I talk about all this at some length in my "Advanced Topics in EXAFS
Analysis" talk, atea.pdf at
https://github.com/bruceravel/XAS-Education/downloads


I am not really certain what you mean by "how to report" them.  I
usually say something like "<best fit> +/- <uncertainty>" for any
number I report.  If you use a lot of constraints in a fit, you will
need to do error propagation by hand -- neither Ifeffit nor Artemis
attempt to do error propagation.

B


--

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter


------------------------------

Message: 4
Date: Thu, 5 Apr 2012 09:22:11 -0500
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber
Message-ID:
        <CA+7ESbq3ZivZob3nwqTV261m=HzDE53=o+F-iuRCbShSTOHQNA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Jatin,

On Thu, Apr 5, 2012 at 5:44 AM, Rana, Jatinkumar Kantilal
<jatinkumar.rana at helmholtz-berlin.de> wrote:
> Dear Dr. Ravel,
>
> Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02.
>
> However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit.
>
> For example,
>
> S02 for Mn absorber
>
> FEFF calculated ? ? ? ? ? ? ? ? ? ? ? ? ? 0.94
> Fitted value for my sample ? ? ? ? ? ? ? ~0.75
> Fitted value for various Mn-oxides ? ? ? ~0.75
> Other reported value from Mn fit ? ? ? ? ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496)
>
> S02 for Fe absorber
>
> FEFF calculated ? ? ? ? ? ? ? ? ? ? ? ? ?~0.94
> Fitted value for Fe-foil ? ? ? ? ? ? ? ? ~0.70
> Fitted value for various Fe-oxides ? ? ? ~0.70
> Reported value by calculation ? ? ? ? ? ? 0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1)
>
>
> It is well known that S02 is a property of central absorbing atom
> and is considered to be constant between 0.7 - 1.0. However, in real
> world, S02 is affected by various systematic errors like thicker
> samples (in transmission), absorption by other elements in sample at
> given energy range and many more. These factors can suppress the
> amplitudes of EXAFS oscillations resulting in lower value of fitted
> S02 than it should be for a given absorber.

Yes, that is all correct. You don't mention it explicitly, so I'll
also remind you that energy resolution also couples closely with S02
(especially if you're not carefully investigating energy resolution)
and poorer-than-ideal resolution would also tend to make S02 lower
than the "theoretical" value, which takes into account only the
passive electron effect.  Taken together, these could easily explain
why you see values closer to 0.7 than 0.9.


> The reason I am so much curious about S02 is, if I know what should
> be (or should be considered) the value of S02 for a given absorber
> than I can possibly understand the reasons of fitted S02 being too
> low or too high. For instance, S02 and Sigma2 are highly correlated
> for first shell. So from fitted value of S02 and Sigma2 of first
> shell, I could possibly understand changes in local structure.

Yes, this is why it is often recommended to measure a "standard" (a
sample with well-constrained first shell coordination) so that an S02
that includes many of the above effects (notably, energy resolution)
can be determined.

> So I would like to put forward very simple but still confusing
> question that which value of S02 should be considered, FEFF
> calculated or the one obtained by fitting standards (either reference
> foils or reference compounds measured on same beamline) and why.

The latter.   It still might miss some effects that are
sample-specific (pinholes, over-absorption), but it does include
beamline-related effects that the calculation does not account for.

Cheers,

--Matt



------------------------------

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Ifeffit at millenia.cars.aps.anl.gov
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End of Ifeffit Digest, Vol 110, Issue 6
***************************************

________________________________

Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de




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