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

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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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

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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.

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