July 2014 - Ifeffit - millenia.cars.aps.anl.gov

Athena crash report
by George Sterbinsky 05 Jul '14

05 Jul '14

Hello, I am running Athena 0.9.20 on OSX 10.8.5. Selecting the difference spectra tool from the drop-down menu causes Athena to crash and the following message to print to the terminal. Usage: Wx::ComboBox::GetClientData(THIS, n) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Athena/Difference.pm line 215, <F> line 339. I've tried this with several different projects and it appears to be general behavior. If I can provide any additional information please let me know. Thank you, George

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Re: [Ifeffit] Matthew Marcus Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

To: Matthew Marcus Hi Matthew, would you be able to send me the executable file and manual for PCA? My spectra files are in .dat form . Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 16:19, Teck Kwang Choo <teck.kwang.choo(a)monash.edu> wrote: > 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(a)millenia.cars.aps.anl.gov> wrote: > >> Send Ifeffit mailing list submissions to >> ifeffit(a)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(a)millenia.cars.aps.anl.gov >> >> You can reach the person managing the list at >> ifeffit-owner(a)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. Re: Principal Component Analysis (PCA) for XANES >> (fred.mosselmans(a)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(a)diamond.ac.uk> >> To: <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: >> < >> CF65047C5B0562499EAFF9FBBC542D64757859A1(a)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 >> >> -- >> This e-mail and any attachments may contain confidential, copyright and >> or privileged material, and are for the use of the intended addressee only. >> If you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> Any opinions expressed within this e-mail are those of the individual and >> not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in England >> and Wales with its registered office at Diamond House, Harwell Science and >> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 02 Jul 2014 08:33:25 -0700 >> From: Matthew Marcus <mamarcus(a)lbl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> Message-ID: <53B42645.5040005(a)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(a)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(a)gmail.com> >> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 >> Message-ID: >> <CAEq27Q2UkMuFScofU8w20jO= >> 7A34MkyKkimSgy5+h+7B_NCZ-w(a)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(a)millenia.cars.aps.anl.gov> >> wrote: >> >> > Send Ifeffit mailing list submissions to >> > ifeffit(a)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(a)millenia.cars.aps.anl.gov >> > >> > You can reach the person managing the list at >> > ifeffit-owner(a)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(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] spam on our mailing list >> > Message-ID: <53B2F08F.7000401(a)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(a)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(a)bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)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(a)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(a)monash.edu> >> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > Message-ID: >> > < >> > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)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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Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 5
by Teck Kwang Choo 03 Jul '14

03 Jul '14

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(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Principal Component Analysis (PCA) for XANES > (fred.mosselmans(a)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(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > CF65047C5B0562499EAFF9FBBC542D64757859A1(a)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 > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 02 Jul 2014 08:33:25 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: <53B42645.5040005(a)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(a)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(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 > Message-ID: > <CAEq27Q2UkMuFScofU8w20jO= > 7A34MkyKkimSgy5+h+7B_NCZ-w(a)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(a)millenia.cars.aps.anl.gov> > wrote: > > > Send Ifeffit mailing list submissions to > > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-owner(a)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(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] spam on our mailing list > > Message-ID: <53B2F08F.7000401(a)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(a)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(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)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(a)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(a)monash.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > > Message-ID: > > < > > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)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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Principal Component Analysis (PCA) for XANES
by Teck Kwang Choo 02 Jul '14

02 Jul '14

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

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4
by Abhijeet Gaur 02 Jul '14

02 Jul '14

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(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] spam on our mailing list > Message-ID: <53B2F08F.7000401(a)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(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)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(a)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(a)monash.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES > Message-ID: > < > CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q(a)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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Re: [Ifeffit] Principal Component Analysis (PCA) for XANES
by fred.mosselmans＠diamond.ac.uk 02 Jul '14

02 Jul '14

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 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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to use scattering path in different model or to construct a new model which is the combination of different simple compound
by ZHAN Fei 01 Jul '14

01 Jul '14

Dear all, I have a confusion.For instance,when I want to fit a simple which has Pt-O,Pt-S,Pt-N,Pt-Pt cordination shell;when can not find a compound with all same shell or can not find one with all suitable bond length,can I use different scattering path from different model to fit diffferent shell? and if do so atom may in different pot in feff ,are the phase and amplitude still transformable? Other choice is to use path-like object in demeter to construcr a more suitable distance scattering path,or construct a new cluster model according to several cif files, myself,which proticol is feasible or better ? sincerely zhanfei

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spam on our mailing list
by Bruce Ravel 01 Jul '14

01 Jul '14

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(a)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

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path contribution to fit in low R-space position, but the fit bond length is much longer than that
by ZHAN Fei 01 Jul '14

01 Jul '14

Dear all, I fit a Zn cluster which RDF has a peak little lower than Zn-S peak,and has a shoulder near Zn-O.This accords with my expection the cluster may have both Zn-S Zn-O bond.But after fit the Zn-O bond length is much larger than reff while it path contribution after fit did in low R.What's wrong with my fit?is it the big delro & delrs =0.7882? sincerely, zhanfei this is the fit log,and puc of fit and path contribution is attached Independent points : 8.0087891 Number of variables : 5 Chi-square : 2276.2312227 Reduced chi-square : 756.5273522 R-factor : 0.0023036 Measurement uncertainty (k) : 0.0002947 Measurement uncertainty (R) : 0.0004735 Number of data sets : 1 Happiness = 100.00/100 color = #D8E796 ***** Note: happiness is a semantic parameter and should ***** ***** NEVER be reported in a publication -- NEVER! ***** guess parameters: enot = 8.99859575 # +/- 1.30831421 [0] ssS = 0.01038392 # +/- 0.00062570 [0.00300] delrS = 0.01271583 # +/- 0.00971686 [0] ssO = 0.02806760 # +/- 0.00277795 [0.00300] delrO = 0.33252269 # +/- 0.01446304 [0] set parameters: amp = 0.85000000 OC = 0.01068708 Correlations between variables: delrs & enot --> 0.9345 delro & enot --> 0.8636 delro & delrs --> 0.7882 sso & enot --> -0.7422 delro & sso --> -0.6014 sso & delrs --> -0.5887 sss & enot --> 0.4980 delrs & sss --> 0.4803 sso & sss --> -0.4737 All other correlations below 0.4 ===== Data set >> CdSe-ZnS(Fe)-Zn << ==================================== : Athena project = C:\04-6-29wulizhu\Zn\athena.prj, 3 : name = CdSe-ZnS(Fe)-Zn : k-range = 3.000 - 10 : dk = 1 : k-window = hanning : k-weight = 1,2,3 : R-range = 1.15 - 3 : dR = 0.0 : R-window = hanning : fitting space = r : background function = no : phase correction = : R-factor by k-weight = 1 -> 0.01310, 2 -> 0.01474, 3 -> 0.02004 name N S02 sigma^2 e0 delr Reff R ========================================================================= O1.1 6.360 0.850 0.02807 8.999 0.33252 1.97800 2.31052 S7.1 3.600 0.850 0.01038 8.999 0.01272 2.34200 2.35472 name ei third fourth ========================================= O1.1 0.00000 0.01069 0.00000 S7.1 0.00000 0.00000 0.00000

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