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Today's Topics:
1. spam on our mailing list (Bruce Ravel)
2. Re: to use scattering path in different model or to construct
a new model which is the combination of different simple compound
(Bruce Ravel)
3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo)
4. Re: Principal Component Analysis (PCA) for XANES
(Amayri, Dr. Samer)
----------------------------------------------------------------------
Message: 1
Date: Tue, 01 Jul 2014 13:31:59 -0400
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] spam on our mailing list
Message-ID: <53B2F08F.7000401@bnl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi all,
Over the years we've done a pretty good job of keeping spam off this
mailing list. As you saw, one slipped through this afternoon. Hopefully
it was a one-time event and it will not be necessary to change the
friendly nature of security on the list.
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
------------------------------
Message: 2
Date: Tue, 01 Jul 2014 15:16:20 -0400
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] to use scattering path in different model or to
construct a new model which is the combination of different simple
compound
Message-ID: <53B30904.5030207@bnl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 07/01/2014 10:43 AM, ZHAN Fei wrote:
> 1 In the example,multiplet scattering path comes from two model
> respectively,if use path from different model in different shell's
> fit,there is risk of ignore important multiple path across models.Should
> construct a cluster ,run feff to ensure?
I don't completely understand the question, but I'll give it a try.
In the example of Shelly's paper, she had a situation where she
*couldn't* write a single feff.inp file. Her local environment was the
average of all possible ways that the uranyl ion could bond to biomass.
The uranyl binding disproportionated into a pH-dependent mixture of
carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to
write a feff.inp file for that. So her solution was to run Feff more
than once, picking and choosing paths that represented her best guess
for modeling the average bonding environment.
I think what you are really getting at, though, is whether it was right
for Shelly to use parts of Feff calculations on a crystals to model
something else. If you were to read up on the theory used in Feff, you
would find that the important thing is that the muffin tin radii of the
scatterers get calculated reasonably. Unless Shelly had a reason to
think that the interatomic distances in her biomass sample were VERY
different than in the crystals she used to run Feff, then the scattering
amplitudes and phase shifts were almost certainly computed quite well
enough.
> 2 I have confusion of the relationship pf N between single path and
> multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2
> respectively,instead 2 4 in paper.
I think Scott's explanation is correct. In real-space,
multiple-scattering theory, both ways around a three-legged path have to
be counted.
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage: http://xafs.org/BruceRavel
Software: https://github.com/bruceravel
------------------------------
Message: 3
Date: Wed, 2 Jul 2014 15:59:25 +1000
From: Teck Kwang Choo <teck.kwang.choo@monash.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES
Message-ID:
<CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Everyone,
Does anyone know what software I should use to perform a Principal
Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The
reason I need to use this technique is because I have a couple of reference
compound spectra but am not sure which of those I should use to fit my
unknown sample spectrum.
Any help is appreciated.
Thanks and kind regards.
Teck Kwang Choo
PhD Candidate
Department of Chemical Engineering
Room 225, Building 36
Monash University
Mobile No.: 04-11489904
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Message: 4
Date: Wed, 2 Jul 2014 07:22:08 +0000
From: "Amayri, Dr. Samer" <amayri@uni-mainz.de>
To: "'XAFS Analysis using Ifeffit'"
<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
Message-ID:
<AB4BA6D33C596041B4D27DC9FFD88F2D5B6E99D7@E14MDB-01.zdv.Uni-Mainz.DE>
Content-Type: text/plain; charset="utf-8"
Hallo Teck,
To get the Principal Component Analysis (PCA) program you can contact Dr. Andr? Ro?berg (rossberg@esrf.fr).
Heir some references related to ITFA:
Rossberg, A., Reich, T. & Bernhard, G. (2003). Analytical and Bioanalytical Chemistry 376, 631-638.
Scheinost, A. C., Rossberg, A., Marcus, M., Pfister, S. & Kretzschmar, R. (2005). Physica Scripta T115, 1038-1040.
Ikeda, A., Hennig, C., Rossberg, A., Tsushima, S., Scheinost, A. C. & Bernhard, G. (2008). Analytical Chemistry 80, 1102-1110.
Rossberg, A., Ulrich, K. U., Weiss, S., Tsushima, S., Hiemstra, T. & Scheinost, A. C. (2009). Environmental Science &
Technology 43, 1400-1406.
Breynaert, E., Scheinost, A. C., Dom, D., Rossberg, A., Vancluysen, J., Gobechiya, E., Kirschhock, C. E. A. & Maes, A. (2010).
Environmental Science & Technology 44, 6649-6655.
With best regards
Dr. Samer Amayri
From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Teck Kwang Choo
Sent: Wednesday, July 02, 2014 7:59 AM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES
Hi Everyone,
Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum.
Any help is appreciated.
Thanks and kind regards.
Teck Kwang Choo
PhD Candidate
Department of Chemical Engineering
Room 225, Building 36
Monash University
Mobile No.: 04-11489904
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