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-requ...@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-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@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 <bra...@bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: [Ifeffit] spam on our mailing list > Message-ID: <53b2f08f.7000...@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 ------------------------------------ bra...@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 <bra...@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: <53b30904.5030...@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 ------------------------------------ bra...@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.c...@monash.edu> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > cahxrqwdt2lvasbvbuu7hmag0owcc9u8fkbchzdamyw14-uy...@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" <ama...@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: > < > ab4ba6d33c596041b4d27dc9ffd88f2d5b6e9...@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 (rossb...@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-boun...@millenia.cars.aps.anl.gov [mailto: > ifeffit-boun...@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... > URL: < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/41d07580/attachment.htm > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit@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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