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

Re: [Ifeffit] How to distinguish whether the coordination
by Michael Weir 07 Jul '14

07 Jul '14

Hi Matt and Zhan, I think this is the point where adding another approach would be very useful. In my limited experience, XAFS was much more powerful when combined with other techniques to eliminate potential models. We also needed to use our "chemical sense". Is there a reason you would suspect Se, Ge, Ga, or any of the other elements in your material? Could you use your beamline to look for these elements by a quick scan of one of their stronger transitions? If there is a full coordination shell, detecting the other element this way is feasible. However, as someone else mentioned recently, dopants would be much more difficult to detect. Is there another analytical technique you could use to narrow down the possible elements in your system? I hope that answering those questions helps you answer your question about the system. Also, thank you Bruce, Matt, Scott and others for the very useful discussions on this list. Michael Weir Hi Zhan, On Mon, Jul 7, 2014 at 3:40 AM, ZHAN Fei <zhanfei(a)ihep.ac.cn> wrote: > Hi Matti? > Thanks for your attention and patience. > The back fourier transform of the specific peak (use window)of Chi(R) > gives the amplitude,donated by amp_bft?As in previous mails,I ask whether > the compare the amp_bft and the amplitude of specific Z number element can > determine the Z. > Sorry, I'm not sure I understand this. I didn't understand the figure you attached in your earlier mail. Generally speaking, I find back-transformed data to be not very useful -- making any sense of these requires very well isolated shells of atoms. The amplitude of the back-transformed chi(k) (is that what you mean by amp_bft??) has many contributions, and is not simply f(k). It will have Z dependence, but it will have other dependencies too. > And thanks for telling me the useful trick using the total phase shift of > the specific element. > > > The discrepancy between R and Rphcor is below,the Zn and Br is close to > Se(the best fit)'s 0.013, > Yes, Ge actually gives the closest match, and Se the second closest match, and I left Ga out of the test. I would probably say that anything closer that 0.015 Ang (and, really, maybe 0.02 Ang) is pretty darn close. So the phase-correction approach appears to be (in this case) not as sensitive to Z as the reduced chi-square, but does provides a check on self-consistency. The fits with Zn and Rb are noticeably worse than the fit with Se... hence Z +/- 3 or perhaps 5 seems like a reasonable rule of thumb, and sometimes one might be able to do better. > should the enot also be important criterion in this trick?and dose the > plus or minus of enot indicate the lighter or higher element relative to > the specific coordination shell? > Well, an E0 shift > 10 eV probably indicating that something is off .... but that could be just the selection of E0 for the experimental data. I wouldn't put much meaning of the absolute value of E0 though for any single fit. "a bond valence sum can be an independent check on the consistency of N, > R, and valence",can your give the ref. paper of this method? Thanks > > http://en.wikipedia.org/wiki/Bond_valence_method The idea is that N, R, and valence are not independent. --Matt --

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Multiple phases in samples
by Dien.Li＠srs.gov 07 Jul '14

07 Jul '14

Hi, All "Assuming" there are multiple phases in one sample, saying, U on goethite, U on organic matter, and uraninite, how to fit the EXAFS data using Artemis? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Chris, I am facing the same problem in both windows xp (32 bit) as well as windows 7 (64 bit) operating systems. Dear Matt, These two problems are not file specific since I have confirmed it with many files and also with different systems. (windows xp as well as windows 7). Dear Bruce, Thank you for taking note of the problem. - Badari

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Demeter-devel MacPorts Athena issues & work-around
by Margaret Hinkle 07 Jul '14

07 Jul '14

Dear OS X Users, First let me thank Frank Schima for fixing the issues with Artemis and ATOMS with his new demeter-devel Macports download -- I (and all Mac users) greatly appreciate it! I thought I would bring two issues with Macports Athena to your attention... FYI, I am using Mac OS X Mavericks v. 10.9.4, with an Intel processor. I followed the directions found here today to delete the old version of demeter and download the new one: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04404.ht… Issue 1. With the new demeter-devel Macports download, Athena freezes upon opening. Opening up Athena via Terminal brought up perl5.16 -- I could see the GUI, the Tip of the Day, and the Athena startup box, but the system just froze. I had to force quit every time, getting the following notice in my Terminal: 'Terminated: 15'. I had a feeling it was an issue with the Tip of the Day popping up, so I edited the Athena.pm file (in the UI folder), and edited line 197 from ‘$app->show_tip if Demeter->co->default('athena', 'tips');’ TO ‘$app->show_tip if Demeter->co->default('athena', 'tip');’ (honestly, I don't know enough about this code to be able to give it a real option that would turn off the Tip of the Day as the default, so I just hoped this would make the program give me general error in the GUI but that Athena could still load). Luckily, my not-fix fix worked. I get an error every time I open it, but after clicking 'OK', Athena behaves just like normal. I hope you can use this information to provide a real fix to the problem! Issue 2. I can only load data files into Athena if there are no headers of any sort -- commenting out each header line with a # or % does not work. When I try to load in a .dat file with a commented-out header, I get the following error message in Terminal: 'At line 436 of file iff_show.f Fortran runtime error: End of record' followed by Athena quitting itself. This is an issue with both the regular Macports demeter download and the demeter-devel download. These data files loaded in just fine to the old iXAFS version of Athena, and on a PC. Is there a plugin I should be using in the Demeter versions? If I delete the header, or load it in from a .prj file, everything works just fine. So it is not huge issue, as I do have a work around. Thank you, Frank, for the new version of Demeter, and thank you all for any thoughts you have on Issue 2. Best regards, Margaret Anne ------------------------------------ Margaret Anne G. Hinkle Ph.D. Candidate Earth and Planetary Sciences Washington University in St. Louis Rudolph Hall Campus Box 1169 1 Brookings Drive St. Louis, MO 63130 email: mhinkle(a)eps.wustl.edu website: aqgeochem.wustl.edu

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Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7
by Badari Rao 07 Jul '14

07 Jul '14

Dear Sir, I am facing two problems while handling files in Athena. First of all, when I freshly open Athena and import a file, it gives some kind of warning, which says can't locate Encoding/FixLatin/XS.pm in @NIC.. etc. I have attached a screenshot of the warning message. However, I could continue with my work without any problem, and importing more files did not give this warning. The second problem, which is a major one is that I am not able to use the "align data" option. Whenever I select my data and click on "align data", the software crashes and closes. kindly look into this issue. I would also like to mention that both these bugs were not present in the earlier version: Demeter 0.9.20_pre5. Thanking You, -- Yours Sincerely, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science. [image: Inline image 2]

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How to distinguish whether the coordination element is heavy or light
by ZHAN Fei 07 Jul '14

07 Jul '14

Dear all, when I try to solve my question{[Ifeffit] path contribution to fit in low R-space position, but the fit bond length is much longer than that},I find a method from Prof.Calvin to distinguish whether coordination shell is composed by light or heavy element: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2007-December/007983.html A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen. But I still don't know ,why it works. Thanks for your patience, Sincerely, zhanfei

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Athena crash report
by George Sterbinsky 04 Jul '14

04 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

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