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

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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Alexandre dos Santos Anastacio invites you to eM Client
by Alexandre dos Santos Anastacio 01 Jul '14

01 Jul '14

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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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Solid AuCl EXAFS fitting – big N
by Sin Yuen Chang 30 Jun '14

30 Jun '14

Dear all, I have questions on the EXAFS fitting of a spectrum of solid AuCl. I find this quite important to resolve because AuCl is so widely used in the literature as a standard reference compound. I obtained the spectrum from the 2013 XAS workshop in Diamond Light Source. It is one of the reference spectrum in the cyanobacteria tutorial. The XANES in the spectrum looks similar to previously published XANES of AuCl. Lengke, M. F. et al., Can. J. Chem. 85: 651-659 (2007) Each Au in the compound has two Cl atoms attached to it, as seen in the crystal structure below. So I fitted the spectrum using two scattering paths: (i) the Au-Cl single scattering, and (ii) the forward through absorber (Au-Cl- -Cl-Au) multiple scattering path. In the fitting model, I fixed So2 (or amp) at 1. The variables that I used for the paths are: (i) N, drcl, sscl, dele; (ii) N = 2, drcl*2, sscl*2, dele. One would expect N to be 2, or perhaps even a little lower because amp = 1 is quite high, but instead, I get N = 2.35, significantly higher than expected. Reduced chi-square : 1706.6480592 R-factor : 0.0222459 guess parameters: N = 2.34968550 # +/- 0.18385678 [1.00000] dele = 0.82469594 # +/- 0.86953191 [0] drcl = -0.02909926 # +/- 0.00608062 [0] sscl = 0.00349927 # +/- 0.00072012 [0.00300] set parameters: amp = 1.00000000 Fixing the coordination number N at the expected value of 2 leads to unrealistically high amp values, as one would expect because of the strong correlation between the two parameters. Next, I tried adding the third and fourth cumulant terms to perhaps account for anharmonic vibrations. The variables for the two paths are now: (i) N, drcl, sscl, dele, third, fourth; (ii) N = 2, drcl*2, sscl*2, dele, third*2, fourth*2. amp was still fixed at 1. But that doesn’t seem to improve matters much, N is similar to the value found without cumulants. Reduced chi-square : 1114.1247832 R-factor : 0.0106796 guess parameters: N = 2.32392798 # +/- 0.21444748 [1.00000] dele = -2.54795042 # +/- 1.27479319 [0.82470] drcl = -0.07137580 # +/- 0.01429137 [-0.02910] sscl = 0.00338118 # +/- 0.00154424 [0.00300] third = -0.00056160 # +/- 0.00017873 [0] fourth = -0.00000155 # +/- 0.00003392 [0] set parameters: amp = 1.00000000 So I have two questions here: 1. Why is the EXAFS amplitude overall so high? The only possibility I can come up with is that the material is actually a mixture of AuCl3 and AuCl. The bond lengths are very similar and it is well known that AuCl is quite unstable in aqueous solution. I have seen the conversion of [AuCl2]- in solution to Au(III) in my own XAFS experiments. 2. I have tried to include a Au-Au first shell scattering path. But there doesn’t seem to be evidence for Au-Au scattering in the data. If the sample was pure crystalline AuCl, the first Au shell would be at 3.2 Å from the absorber, but I cannot fit such a path to the data. So I am wondering whether the AuCl spectrum is unreliable... Given how many times AuCl XANES has been published before, has anyone else perhaps run into this problem? Has anyone perhaps measured solid AuCl under exclusion of moisture and air, or several times as a function of time to assess beam damage? Does anyone perhaps have suggestions what else may explain the high EXAFS amplitudes and the absence of Au-Au scattering…? Attached are the Athena, Artemis and .cif files. I used Demeter 0.9.18 with perl 5.012003 and using Ifeffit 1.2.11d on Windows 7. Thank you for your attention. Best wishes, Sin-Yuen, Chang PhD Student School of Chemical Engineering and Analytical Science The University of Manchester

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pre-release for Demeter 0.9.20 (Bruce Ravel)
by madhusmita sahoo 28 Jun '14

28 Jun '14

One more problem is there, when i am saving the data in atoms and reopening it, the Z co-ordinate of Ti site is getting changed from -0.125 to 0.875 automatically. Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 28 June 2014 17:23, madhusmita sahoo <krushna.chem(a)gmail.com> wrote: > > On 27 June 2014 22:30, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > >> pre-release for Demeter 0.9.20 (Bruce Ravel) > > > I have tried the 64 bit version of Demeter 0.9.20. Initially when i > entered all the details for anatase, it gave the required paths. But when i > pressed first hit button it showed perl has stopped working. so i cancelled > and it got closed. after that when i am trying to run atoms I am not > getting the required paths. rather I am facing the same old problem of > having 6 oxygen atoms in the first co-ordination instead of 4 and 2 oxygen > atoms at different R( i.e 1.9339 and 1.9796). Attaching the input file and > the generated paths. > > Regards > Madhusmita Sahoo, > SO/C,TFCS/SND/MSG(22171) > Indira Gandhi Centre for Atomic Research, > Kalpakkam, Tamilnadu >

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Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 27
by madhusmita sahoo 28 Jun '14

28 Jun '14

On 27 June 2014 22:30, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > pre-release for Demeter 0.9.20 (Bruce Ravel) I have tried the 64 bit version of Demeter 0.9.20. Initially when i entered all the details for anatase, it gave the required paths. But when i pressed first hit button it showed perl has stopped working. so i cancelled and it got closed. after that when i am trying to run atoms I am not getting the required paths. rather I am facing the same old problem of having 6 oxygen atoms in the first co-ordination instead of 4 and 2 oxygen atoms at different R( i.e 1.9339 and 1.9796). Attaching the input file and the generated paths. Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu

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pre-release for Demeter 0.9.20
by Bruce Ravel 27 Jun '14

27 Jun '14

Hi All, As I said yesterday, I now have trial versions of Demeter 0.9.20 available for both 64 and 32 bit Windows machines. I am happy with how both are working and I think they address all the issues that have come up in recent days. 64 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… 32 bit: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… List of changes for this version: https://github.com/bruceravel/demeter/blob/master/Changes.org Assuming I don't hear of any problems, I will make a formal release sometime next week and update the website. Cheers, 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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