Re: [Ifeffit] Question about XAFS resolution
Hi Shoaib, On Wed, Jun 25, 2014 at 7:34 AM, Shoaib Muhammad mshoai...@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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Exchange Dirac Hara on Artemis
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 Token0 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 newvi...@cars.uchicago.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: ca+7esbrgvwpvatmbmccw+r3iazo0grcsd2zlj4ykbzu8tzw...@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 feff.inp Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Exchange Dirac Hara on Artemis
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 -- Bruce Ravel bra...@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Exchange Dirac Hara on Artemis
Siri, Runs for me with Feff6L.02 I see: Feff 6L.02 name: vanadium pentoxide formula: V2O_5 sites:V1,O1,O2,O3 refer1: wyckoff Vol 2, Ch V, p 184 notes:shifted by (0.25,0.25,0) Calculating potentials and phases... free atom potential and density for atom type0 free atom potential and density for atom type1 free atom potential and density for atom type2 overlapped potential and density for unique potential0 overlapped potential and density for unique potential1 overlapped potential and density for unique potential2 muffin tin radii and interstitial parameters phase shifts for unique potential0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... Rmax 6. keep and heap limits 0.000 0.000 Preparing neighbor table nfound nheap nheapx nscr 1000734 737 65.1542 2000938 946 65.5456 On Wed, Jun 25, 2014 at 2:45 PM, Siri V sirip...@uw.edu wrote: 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 Token0 Keyword unrecognized. See FEFF document -- some old features are no longer available. RDINP-2 What version of Feff is that? Anyone recognize that Feff 6.01l? --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
On 06/25/2014 02:31 AM, Badari Rao wrote: The new release is working fine in windows 7 64 bit. I was able to re-open a saved file. Thank you very much. Great! 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. Well, you are correct saying that it is surprising behavior for imported data to be lost if you save before having done a fit. I'll look into it. However, if you have done a lot of hard work, you have probably hit the fit button at least once. B -- Bruce Ravel bra...@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects
On 06/25/2014 04:03 PM, Bruce Ravel wrote: 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. Well, you are correct saying that it is surprising behavior for imported data to be lost if you save before having done a fit. I'll look into it. However, if you have done a lot of hard work, you have probably hit the fit button at least once. The situation where the data is lost if you save a project before doing a fit will be fixed in the next release. This afternoon, I have been working on setting up a computer to make a 32-bit build of Demeter. Once that is ready and tested, I will properly release 0.9.20. B -- Bruce Ravel bra...@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Exchange Dirac Hara on Artemis
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 bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: 53ab28c3.6090...@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 sirip...@uw.edu To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: CAGMtT44vT0pSEJdzcD33W5a37JT-72QCUZktkX2t7fvCLSE=u...@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 Token0 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 newvi...@cars.uchicago.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Exchange Dirac Hara on Artemis Message-ID: ca+7esbrgvwpvatmbmccw+r3iazo0grcsd2zlj4ykbzu8tzw...@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 -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140625/f57ff42f/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: feff.inp Type: application/octet-stream Size: 5265 bytes Desc: not available URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140625/f57ff42f/attachment-0001.obj -- ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Exchange Dirac Hara on Artemis
The recommendation is to update to a more recent version of Artemis with a version of Feff6.02: http://s3.amazonaws.com/demeter4xas/Demeter_Updater_for_Windows_0_9_18_2.exe --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
