[Ifeffit] Ifeffit Digest, Vol 137, Issue 5

Teck Kwang Choo teck.kwang.choo at monash.edu
Thu Jul 3 01:19:48 CDT 2014


Thanks everyone for the suggestions! I will give Six pack a go first since
I have that software. If that doesn't work, I'll send another message.

I wish you all a pleasant day.

Teck Kwang Choo
PhD Candidate
Department of Chemical Engineering
Room 225, Building 36
Monash University
Mobile No.: 04-11489904


On 3 July 2014 01:33, <ifeffit-request at millenia.cars.aps.anl.gov> wrote:

> Send Ifeffit mailing list submissions to
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> Today's Topics:
>
>    1. Re: Principal Component Analysis (PCA) for XANES
>       (fred.mosselmans at 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 at diamond.ac.uk>
> To: <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
> Message-ID:
>         <
> CF65047C5B0562499EAFF9FBBC542D64757859A1 at 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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>
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>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 02 Jul 2014 08:33:25 -0700
> From: Matthew Marcus <mamarcus at lbl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
> Message-ID: <53B42645.5040005 at 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 at 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 at gmail.com>
> To: ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4
> Message-ID:
>         <CAEq27Q2UkMuFScofU8w20jO=
> 7A34MkyKkimSgy5+h+7B_NCZ-w at 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 at millenia.cars.aps.anl.gov>
> wrote:
>
> > Send Ifeffit mailing list submissions to
> >         ifeffit at 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 at millenia.cars.aps.anl.gov
> >
> > 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
> > 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 at bnl.gov>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: [Ifeffit] spam on our mailing list
> > Message-ID: <53B2F08F.7000401 at 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 at 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 at bnl.gov>
> > To: XAFS Analysis using Ifeffit <ifeffit at 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 at 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 at 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 at monash.edu>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES
> > Message-ID:
> >         <
> > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q at 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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/afc4cff2/attachment-0001.htm
> > >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Wed, 2 Jul 2014 07:22:08 +0000
> > From: "Amayri, Dr. Samer" <amayri at uni-mainz.de>
> > To: "'XAFS Analysis using Ifeffit'"
> >         <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
> > Message-ID:
> >         <
> > AB4BA6D33C596041B4D27DC9FFD88F2D5B6E99D7 at 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 at 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 at millenia.cars.aps.anl.gov [mailto:
> > ifeffit-bounces at 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 --------------
> > An HTML attachment was scrubbed...
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> > >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> > End of Ifeffit Digest, Vol 137, Issue 4
> > ***************************************
> >
>
>
>
> --
> Dr. Abhijeet Gaur
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> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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>
> End of Ifeffit Digest, Vol 137, Issue 5
> ***************************************
>
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