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

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 >

1 0

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

1 0

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

4 5

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

1 0

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

01 Jul '14

Hi, I recommend you to try eM Client! My eM Client for Windows is: - Free MS Outlook, Outlook Express and Thunderbird replacement - Fully integrated with GMail, Hotmail, Yahoo and many others - Super fast and easy to use - Integrated with Facebook and Skype Visit www.emclient.cz for more information Do not know Alexandre dos Santos Anastacio? If you do not know Alexandre dos Santos Anastacio, you can safely ignore this email - your details have not been disclosed to anymore. It is likely that another user wanted to refer some friends and entered your email address by mistake.

1 0

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

1 0

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

3 5

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 >

2 1

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

1 0

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

1 0

32 Windows installer for testing
by Bruce Ravel 26 Jun '14

26 Jun '14

Hi all, I just built a 32 bit version of the Demeter installer: https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_(… If you have a 32 bit Windows machine, could you give this a try and report back to the list? If you could do a bit more than just fire up the programs, that would be helpful. I think it works, but it would be reassuring to know that it works for someone else besides me. Thanks in advance, 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

2 3

Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Bruce Ravel, Thank you for your quick reply. If my problem is using Artemis, do you mean I should not use Run Feff under Artemis [Feff] Atoms and Feff, if I want to incorporate Exchange 1 0 0? My other approach was running the feff.inp on feff6 and have it calculate all the paths with Exchange 1 0 0. Is this the solution you have in mind? However, when I am in Artemis 0.9.13, I cannot find the option for Artemis to pull those pre-calculated paths into the project file. Kind regards, Siri --------------------------------------------------------- Message: 3 Date: Wed, 25 Jun 2014 15:53:39 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <53AB28C3.6090208(a)bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 06/25/2014 03:45 PM, Siri V wrote: > > - open this data file in Artemis 0.9.13 and ^^^^^^ There's your first problem. B --------------------------------------------------------- Message: 2 Date: Wed, 25 Jun 2014 12:45:00 -0700 From: Siri V <siripunt(a)uw.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CAGMtT44vT0pSEJdzcD33W5a37JT-72QCUZktkX2t7fvCLSE=UQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Dr. Matt Newville, Thank you for your quick reply and attention to my inquiry. I have change the exchange card so that it has only 3 numbers: EXCHANGE 1 0 0. Please find attached the input file, feff.inp. To replicate my error, please: - open this data file in Artemis 0.9.13 and - refer to Artemis [Feff] Atoms and Feff - click Run Feff You should see the following error report: Feff executable: C:\strawberry\c\bin\feff6.exe) Feff 6.01l exchange exchange Token 0 Keyword unrecognized. See FEFF document -- some old features are no longer available. RDINP-2 ********** Feff calculation finished at 2014-06-25T12:40:41 Kind regards, Siri ---------------------------------------------------- Message: 2 Date: Wed, 25 Jun 2014 07:18:42 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CA+7ESbrgvWpVATmbMCCW+R3iAzO0gRcsD2zLj4YKbzU8TZwy_Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Siri, Hmm, not sure -- running feff6L with exchange 1 works for me. The exchange card only takes 3 numbers (index v_real v_imag). If you're still having troubles, please send a complete input file, plain text format, or the complete project file. Sending the full plain text of the output you get would be helpful too. In general: Please don't send screenshots -- they're too hard to read and don't tell the whole story. We're willing to help, but it's very hard for us to guess what might be going on with a partial story. --Matt

2 1

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Badari Rao 25 Jun '14

25 Jun '14

Dear Sir, The new release is working fine in windows 7 64 bit. I was able to re-open a saved file. Thank you very much. However, there is one more problem happening. When I re-open a previous file and simply press on save and then close it (I did not do anything else at all), all the data is lost. My file size which was 179KB, reduced to 1KB and when I re-opened it, there was nothing stored in it. There is no problem if I do more fitting and then save the data. This is a minor problem but a dangerous as one might lose all his hard-work done in fitting the data. @Matt Newville: I had included a dataset while creating the sample file, but strangely only the Feff input file was stored. I guess the dataset is not saved until we actually run a fit. Also, the problem of not being able to re-open saved project was not only with an empty fits, but also with files with actual fits in them. However, this has been resolved with the new release https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_p…. <https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_p…> -- Thanks & Regards, 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.

2 2

Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Matt Newville, Thank you for your quick reply and attention to my inquiry. I have change the exchange card so that it has only 3 numbers: EXCHANGE 1 0 0. Please find attached the input file, feff.inp. To replicate my error, please: - open this data file in Artemis 0.9.13 and - refer to Artemis [Feff] Atoms and Feff - click Run Feff You should see the following error report: Feff executable: C:\strawberry\c\bin\feff6.exe) Feff 6.01l exchange exchange Token 0 Keyword unrecognized. See FEFF document -- some old features are no longer available. RDINP-2 ********** Feff calculation finished at 2014-06-25T12:40:41 Kind regards, Siri Message: 2 Date: Wed, 25 Jun 2014 07:18:42 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: <CA+7ESbrgvWpVATmbMCCW+R3iAzO0gRcsD2zLj4YKbzU8TZwy_Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Siri, Hmm, not sure -- running feff6L with exchange 1 works for me. The exchange card only takes 3 numbers (index v_real v_imag). If you're still having troubles, please send a complete input file, plain text format, or the complete project file. Sending the full plain text of the output you get would be helpful too. In general: Please don't send screenshots -- they're too hard to read and don't tell the whole story. We're willing to help, but it's very hard for us to guess what might be going on with a partial story. --Matt

3 2

Re: [Ifeffit] Question about XAFS resolution
by Matt Newville 25 Jun '14

25 Jun '14

Hi Shoaib, On Wed, Jun 25, 2014 at 7:34 AM, Shoaib Muhammad <mshoaibce(a)gmail.com> wrote: > > Dear Matt Newville, > > Sorry to disturb you by asking one question, hopefully you will mind it. Asking on the ifeffit mailing list is generally better. I am CCing this reply to that list. > I often see that resolution XAFS spectrum of K-edge and especially pre-edge is good for > 3d transition metal but comparatively 4d transition metal XAFS spectra and its pre-edge > spectrum is poor. Is it due to low energy resolution at higher energy level at synchrotron > source or something related with electronic transitions? because as far I understand > pre-edge in 3d transition metal is due to 1s-3d and 4d metals is 1s-4d. > The energy resolution is a convolution of monochromator energy resolution and natural line-width of the core electronic level. Generally speaking, for K edges below 10 keV or so, Si(111) and the core-level widths are comparable, ranging from ~0.5eV to 2 eV. Both the mono resolution and core-width increase with energy, but the core-width increases quadratically and so tends to dominate at higher energies (say, above 20 keV). Core level widths for L3 edges are about 2x that of K edges, so that this term almost always dominates for L3 edges. > I am student in Sungkyunkwan University (Korea) and a beginner of XAFS. Cheers, --Matt

1 0

Exchange Dirac Hara on Artemis
by Siri V 25 Jun '14

25 Jun '14

Dear Dr. Matt Newville, Thank you for your reply. I was able to run the FEFF calculation on Artemis (Demeter 0.9.13), before I included the card below: EXCHANGE 1 0.0 0.0 -1 [image: Inline image 2] I received an error as follow: [image: Inline image 3] I am not sure what I did wrong, should I refer to the EXCHANGE card differently? Please kindly advise, Best regards Siri ---------- Forwarded message ---------- From: Matt Newville <newville(a)cars.uchicago.edu> Date: Mon, Jun 23, 2014 at 12:44 PM Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hi Siri, On Mon, Jun 23, 2014 at 2:21 PM, Siri V <siripunt(a)uw.edu> wrote: > Dear ifeffit members, > > I would like to inquire whether the Feff's Exchange card (Dirac Hara) is > supported on Artemis fitting program. > Yes. You can edit the feff input file and change the exchange card (or other cards) before running the calculation. --Matt

2 1

Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
by Badari Rao 24 Jun '14

24 Jun '14

Hello Sir, I wanted to report that I am facing the same problem as the one faced by Mengling Stuckman (dated: Wed, 19 Mar 2014 11:53:10 -0700.) It does not appear to be problem with the operating system because I am facing the same problem in systems with windows 7 as well as windows xp. I have tried a fresh install on a new system with windows 7 os, and the same problem occurred. Even a simple artemis file in which I have just imported and saved the processed file from athena cannot be re-opened in artemis. Kindly sort out the problem. I have attached one sample artemis file which is giving the problem and also the demeter log file from %APPDATA%\demeter. <https://www.mail-archive.com/search?l=ifeffit%40millenia.cars.aps.anl.gov&q…> 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.

4 6

Exchange Dirac Hara on Artemis
by Siri V 23 Jun '14

23 Jun '14

Dear ifeffit members, I would like to inquire whether the Feff's Exchange card (Dirac Hara) is supported on Artemis fitting program. Kind regards, Siri University of Washington

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 17
by madhusmita sahoo 22 Jun '14

22 Jun '14

Respected Dr. Bruce, I am looking forward to the updated version with the correction. Regards Madhusmita Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 21 June 2014 22:30, <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: Ifeffit Digest, Vol 136, Issue 11 (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Jun 2014 17:47:31 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11 > Message-ID: <53A4ABF3.4070901(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Well, not only was the shift vector not working, it seems I had somehow > neglected to even implement it in Demeter! It's amazing what can go > unnoticed and for how long. > > This will be fixed in the next release. Thank you, Madhusmita, for > bringing this to my attention. > > B > > > On 06/18/2014 09:38 AM, Bruce Ravel wrote: > > On 06/18/2014 07:52 AM, madhusmita sahoo wrote: > >> Contd- Crystallographic input for a structure having screw axis and > >> co-ordinates shifted by certain amount > >> Dear sir, > >> herewith I am attaching two input files. The first one with the name > >> wyckoff .inp generates The first co-ordination sphere at 1.9465 angstrom > >> with degenracy of 6. > >> According to crystal structure data anatase structure should have 4 > >> oxygens at 1.9339 angstrom and 2 oxygens at 1.9796 angstrom. > >> So, I tried with the crystal input from the latest PDF-4+2013 > >> database(attaching the PDF as word file for your ref. > >> That ( inp file - attached)eventually generates the required > >> co-ordination sphere with 4 oxygen at 1.3964( as against the XRD data of > >> 1.9339) and 2 oxygen at 1.8925(aginst the XRD data from PDf-4+2013 of > >> 1.9796 angstrom) > > > > You seem to be asking about Atoms' use of the shift vector. > > Specifically, you seem to be asking whether the shift vector is > > working correctly. > > > > If so, that appears to be a legitimate question and the answer appears > > to be /no/. Sigh.... I will look into it and try to have that fixed > > in time for the next release. > > > > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 17 > **************************************** >

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11
by madhusmita sahoo 20 Jun '14

20 Jun '14

Contd- Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount Dear sir, herewith I am attaching two input files. The first one with the name wyckoff .inp generates The first co-ordination sphere at 1.9465 angstrom with degenracy of 6. According to crystal structure data anatase structure should have 4 oxygens at 1.9339 angstrom and 2 oxygens at 1.9796 angstrom. So, I tried with the crystal input from the latest PDF-4+2013 database(attaching the PDF as word file for your ref. That ( inp file - attached)eventually generates the required co-ordination sphere with 4 oxygen at 1.3964( as against the XRD data of 1.9339) and 2 oxygen at 1.8925(aginst the XRD data from PDf-4+2013 of 1.9796 angstrom) Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 13 June 2014 22:30, <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: Scattering paths in XANES calculations (Bruce Ravel) > 2. Re: Crystallographic input for a structure having screw axis > and co-ordinates shifted by certain amount (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Jun 2014 15:42:22 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Scattering paths in XANES calculations > Message-ID: <539A029E.4050609(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 06/12/2014 10:07 AM, Stefanie Roese wrote: > > But now I fail at getting the plots with the Energy at the x-axis and > > the normailzed mu at the y-axis likle Bruce did it in his talk. Which > > program was used there? Athena? And how can I get the > > energy/mu-information out of my feffnnn.dat files to compare to the > > total spectrum? I think I am quite close to the solution, but it does > > not work. > > Stefanie, > > The R-space figures were made using Artemis. I fit the Fe foil data > using the version of Feff6 that comes with Artemis, then plotted the > data and the path relevant to each slide. > > The energy plots were made using Athena back in the early days of Feff8 > (which were also the early days of Athena!). The plots show Fe foil > data and (if I remember correctly) column 4 of the xmu.dat file that was > one of the output files from Feff of that vintage. I imported the data > and the xmu.dat file into Athena to make those plots. The calculation > is offset downwards a bit using the y-axis offset in Athena. > > To answer Matthew's question: interesting? Not sure I'd go that far...! > Here's the link: > > > > https://speakerdeck.com/bruceravel/a-practical-introduction-to-multiple-sca… > > 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: Thu, 12 Jun 2014 15:49:56 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Crystallographic input for a structure having > screw axis and co-ordinates shifted by certain amount > Message-ID: <539A0464.1090102(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Madhusmita, > > Regarding the first question, I am not clear what the problem is. I > grabbed the crystal data for anatase from Matt's website: > > http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp > > and imported it into Artemis. I certainly don't know what the > interatomic distances for anatase should be off the top of my head, but > what Atoms produced from that input data certainly seems reasonable. If > you think there is a problem, you are going to need to explain it in a > way that I can reproduce easily on my own computer. > > Regarding the second question, the vector specified in the box labeled > "Shift vector" will be added to each site *before* any calculation is made. > > B > > On 06/12/2014 01:45 AM, madhusmita sahoo wrote: > > Dear Members, > > > > I would like to know, > > > > *Q1)* If there is a screw axis in the system, like the anatase phase of > > TiO2, whose space group is I41/amd, how should I enter that in the > > atoms for feff calculation. Kindly tell me which is the correct way. > > > > When I entered 141(the space group number) and I41/amd, both generated > > separate set of atomic positions. > > > > The older version of artemis, now the new one(latest version), both > > generates different set of atomic position with the same > > crystallographic input, i.e if I enter 141(or I41/amd) in place of space > > group and run atoms, it generates two different set of co-ordinates in > > Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same. > > > > *Q2)* And when co-ordinates is shifted by certain amount, do we have to > > enter that in the shift vector as well as while defining the (x y z) > > of a particular site. Or I should just enter the shift vector and > > define the co-ordinates at its usual position ( I feel this one is > > correct). > > > > For example in anatase crystal structure the co-ordinates are shifted > > by (0,0.25,-0.125). > > > > So, the inputs can be > > > > For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, > > z= 0 and O (scatterer) x= 0, y=0, z=0.20806 > > > > (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= > > -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally > > > > both should give the same result. But it gives different set of atomic > > positions. > > > > Even the same input in different version of artemis is yielding > > different results(in Artemis 0.8.012 and in Demeter 0.9.18) . > > > > I am confused about how atoms work in artemis. I request you to > > elucidate the correct method. > > > > Warm wishes > > > > Madhusmita > > > > India > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > -- > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 11 > **************************************** >

2 2

Postdoctoral position in Yeshiva University and Brookhaven National Laboratory
by Anatoly I Frenkel 20 Jun '14

20 Jun '14

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunity. Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2014. The project title is: "Characterization of structure, diffusion mechanism and optoelectronic properties of doped colloidal semiconductor nanocrystals." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II for X-ray spectroscopy and Center for Functional Nanomaterials for electron microscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods and their applications to nanomaterials, and experience with in situ characterization methods. Working knowledge of Raman spectroscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

1 0

Use of the 3rd and 4th Parameter
by Michael Kömm 16 Jun '14

16 Jun '14

Hello, I'm trying to make an EXAFS analysis on the Structure of Tb in a borogermanate glass System. The reference is an .cif of Terbium-Gallium-Garnet (TGG). I expect some disorder caused to working in glass. Therefore I would like to use the 3rd and/or the 4th parameter. I tried to set a guess parameter to evaluate those parameters. Could you tell me a reasonable value for these parameters? The 3rd only varies a little bit around its guessed value (+- 0.01) and if I try to do the same with the 4th parameter no fit at all takes place. The errors in the GDS-window are exactly 0.00000 with no fit taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) and the R-factor of the fit is way over the top (>10^20). I've chosen a value of 0.5 for the 3rd and the 4th parameter just to see if they're working and I was only doing a quick first shell fit with the surrounding oxygen-shell. Please can somebody tell me how to deal with this problems. Thanks a lot for your time and efford. Sincerly yours, Michael Kömm

3 2

Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Ah okay. I think now I get it. Is it correct that in the mu(E) spectrum you plot the total spectrum in blue and in red you chose different fms-radii like 2.5, 3.0, 4.1 to get the XANES spectrum for different shells? Or are the red curves another varied FEFF parameter? Thanks so much for your support! Stefanie

2 1

Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Dear Bruce, thanks for your answer! My problem is how to get the E/mu information for each single scattering path. If I get it right, the xmu.dat contains the sum of all scattering paths. This is the blue curve in your talk. But there are also the spetra for the first,s econd, third,... path at page 11 in red. I think the information comes from the feff0001.dat. feff0002.dat and so on. But these files do not contain mu! Or do I understand it wrong? I have no data to fit, just the FEFF calculations. Is there any possibility to get the XANES spectrum of all paths and the XANES spectrum of every single path to compare how the single paths influence the complete spectrum? Thanks! Stefanie

2 1