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

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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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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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 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

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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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