Re: [Ifeffit] Problem with importing projects from ATHENA into ARTEMIS
Hi Alexander, I think you may not alone in having this issue. You should be using normalized chi(k) in Artemis, but I don't think Artemis would be reading chi(k) from the project file incorrectly Perhaps there is something strange about how you're doing the normalization? Or perhaps it is just a question of what k-weighting is being used for the plot. Unfortunately, the PNGs I see have been cropped and don't show the labels of the axes. I'm sending this to the Ifeffit mailing list, where you'll probably get a more complete answer. On Mon, Apr 7, 2014 at 9:57 AM, Britz, Alexander alexander.br...@xfel.eu wrote: Dear Mr. Newville, I came across a problem when I import an ATHENA project after normalization into ARTEMIS. Maybe you could tell me who to contact about this problem. Let me try to explain it in few words: I normalize my EXAFS data in ATHENA and safe it a s a .prj file. When I open the .prj file in ARTEMIS I noticed, that the amplitude of some oscillations have changed. When I save the chi(k) as .txt, this problem does not occur. When I open the chi(k) text file in ARTEMIS, the normalization and the amplitude of the oscillations are exactly the same as in ATHEN. I have attached a .png file for the EXAFS in k-space. It is the same .prj file, one time opened in ARTEMIS, one time in ATHENA. To be more specific, the amplitude of the oscillation at k=3 is -1.4 and -1.6, respectively. Thank you very much for your help in advance! Best regards from Hamburg, Alexander Alexander Britz European XFEL GmbH alexander.br...@xfel.eu Tel. +49 (0)40 8998-6986 Fax +49 (0)40 8998-1905 www.xfel.eu/de Postadresse: Notkestraße 85, 22607 Hamburg Sitz: Albert-Einstein-Ring 19, 22761 Hamburg Geschäftsführer: Prof. Dr. Massimo Altarelli, Dr. Claudia Burger Registriert als European X-Ray Free-Electron Laser Facility GmbH beim Amtsgericht Hamburg, HRB 65 -- --Matt Newville newville at cars.uchicago.edu 630-252-0431 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Problem with importing projects from ATHENA into ARTEMIS
There are a number of known problems with the current version of Artemis. It's pretty much impossible for me to troubleshoot without examples being posted to the mailing list. B On 04/07/2014 11:17 AM, Matt Newville wrote: Hi Alexander, I think you may not alone in having this issue. You should be using normalized chi(k) in Artemis, but I don't think Artemis would be reading chi(k) from the project file incorrectly Perhaps there is something strange about how you're doing the normalization? Or perhaps it is just a question of what k-weighting is being used for the plot. Unfortunately, the PNGs I see have been cropped and don't show the labels of the axes. I'm sending this to the Ifeffit mailing list, where you'll probably get a more complete answer. On Mon, Apr 7, 2014 at 9:57 AM, Britz, Alexander alexander.br...@xfel.eu wrote: Dear Mr. Newville, I came across a problem when I import an ATHENA project after normalization into ARTEMIS. Maybe you could tell me who to contact about this problem. Let me try to explain it in few words: I normalize my EXAFS data in ATHENA and safe it a s a .prj file. When I open the .prj file in ARTEMIS I noticed, that the amplitude of some oscillations have changed. When I save the chi(k) as .txt, this problem does not occur. When I open the chi(k) text file in ARTEMIS, the normalization and the amplitude of the oscillations are exactly the same as in ATHEN. I have attached a .png file for the EXAFS in k-space. It is the same .prj file, one time opened in ARTEMIS, one time in ATHENA. To be more specific, the amplitude of the oscillation at k=3 is -1.4 and -1.6, respectively. Thank you very much for your help in advance! Best regards from Hamburg, Alexander Alexander Britz European XFEL GmbH alexander.br...@xfel.eu Tel. +49 (0)40 8998-6986 Fax +49 (0)40 8998-1905 www.xfel.eu/de Postadresse: Notkestraße 85, 22607 Hamburg Sitz: Albert-Einstein-Ring 19, 22761 Hamburg Geschäftsführer: Prof. Dr. Massimo Altarelli, Dr. Claudia Burger Registriert als European X-Ray Free-Electron Laser Facility GmbH beim Amtsgericht Hamburg, HRB 65 -- 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] D-Atoms program, common positions and occupancies
Hi Moneed, Bruce is a busy fellow. I doubt he has time to double-check every user's input file. Let's go through some steps that might help you. What reference are you using for CdSe crystal structure? What are (is) the Se positions (position) supposed to be in that structure with the P63mc symmetry?... the Cd positions (position)? What are they in your input file? Only one unique atom should be specified for a given symmetry position that has more than one symmetry-related atom in the unit cell. More generally, how much do you understand about crystal structures and symmetry? If the answer is not much, taking a course on such would be beneficial, or even reading about it in some standard inorganic or solid state chemistry texts. regards, Robert On 4/5/2014 4:54 AM, Moneeb Shatnawi wrote: Dear Bruce Ravel, Hello, I am Moneeb Shatnawi from the University of Jordan. I have a question and I appreciate your help in advance. I have installed the Demeter program (version 0.9.18) and I tried to use your (D)Atoms program using the attached input files. When I try to run atoms, I get a warning message stating that two sites generate one or more common positions and their occupancies sum to more than 1. (attached also the warning message that I got). If I ignore this warning message and try to run FEFF, the program crashes. When I change the space group to P 1 (as indicated by the message) , the program runs well. My question is, could you please figure out the problem with these input files, so that I can run them with the correct space group? Thank you so much in advance, Moneeb ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 9700 S. Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 ph 630-252-0580 fax ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
