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

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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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

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Exchange Dirac Hara on Artemis
by Siri V 26 Jun '14

26 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

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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.

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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

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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

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