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Today's Topics:
1. Re: Principal Component Analysis (PCA) for XANES
(fred.mosselmans@diamond.ac.uk)
2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus)
3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur)
----------------------------------------------------------------------
Message: 1
Date: Wed, 2 Jul 2014 07:48:29 +0000
From: <fred.mosselmans@diamond.ac.uk>
To: <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
Message-ID:
<CF65047C5B0562499EAFF9FBBC542D64757859A1@EXCHMBX01.fed.cclrc.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Dear Teck,
ITFA does transformation factor analysis as well, if you just want to do PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use.
https://home.comcast.net/~sam_webb/sixpack.html
cheers
Fred
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------------------------------
Message: 2
Date: Wed, 02 Jul 2014 08:33:25 -0700
From: Matthew Marcus <mamarcus@lbl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
Message-ID: <53B42645.5040005@lbl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 software package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software .
If you can't get at it there, I can send the executable and manual.
mam
On 7/1/2014 10:59 PM, Teck Kwang Choo wrote:
> 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
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
------------------------------
Message: 3
Date: Wed, 2 Jul 2014 21:03:17 +0530
From: Abhijeet Gaur <abhijeetgaur9@gmail.com>
To: ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4
Message-ID:
<CAEq27Q2UkMuFScofU8w20jO=7A34MkyKkimSgy5+h+7B_NCZ-w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Teck Kwang Choo,
For PCA analysis you can use SixPack
data analysis package by Dr. Sam Webb available at
https://home.comcast.net/~sam_webb/sixpack.html.
Also you can use Dmeter by Dr Bruce Ravel
available at http://bruceravel.github.io/demeter/.
With best wishes
Dr Abhijeet Gaur
On Wed, Jul 2, 2014 at 12:52 PM, <ifeffit-request@millenia.cars.aps.anl.gov>
wrote:
> Send Ifeffit mailing list submissions to
> ifeffit@millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
> ifeffit-request@millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner@millenia.cars.aps.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> 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
> -------------- next part --------------
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> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/41d07580/attachment.htm
> >
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
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>
> End of Ifeffit Digest, Vol 137, Issue 4
> ***************************************
>
--
Dr. Abhijeet Gaur
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