RE: Instrumental resolution function
Matt, The one time I tried to model tube tails with widely available software was in Fullprof and the approach was to include extra wavelengths in the profile. In case you would like to get a good understanding of the fundamental parameters approach, see Cheary, Coelho and Cline's paper in the NIST journal (I can dig up a copy sometime if you're interested) Also, seeing as you're in OR, I'm about to get rid of an old RU-200 rotating anode generator (rotating anode and tank, perhaps water chiller; no diffractometer, etc)(a long time ago it was used on an R-Axis II, has been dormant for about 10 years) - you may have it for free if you're willing to show up at OSU with a truck with a tailgate lift and cart it away. Let me know if you're interested. Alex Y ___ Dr. Alexandre (Alex) F. T. Yokochi Associate Professor of Chemical Engineering Laboratory for innovative Reaction Engineering for Materials and Sustainability (iREMS lab) School of Chemical, Biological and Environmental Engineering Oregon State University Corvallis, OR 97331 - 2702 -Original Message- From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of Matt Beekman Sent: Monday, September 16, 2013 9:10 AM To: 'Peter Y. Zavalij'; 'Alan Coelho'; mariomac...@tux.uis.edu.co; rietveld_l@ill.fr Subject: RE: Instrumental resolution function Alan, Peter, Would you mind briefly elaborating on the procedure used to "fit tube tails?" I personally have only used GSAS for Rietveld refinement, and other than adding another phase(s) with slightly different lattice parameter(s) I am not sure I understand how you would account for the additional wavelengths in the beam. Many thanks in advance! Matt -- Matt Beekman, Ph.D. Assistant Professor of Physics Department of Natural Sciences Oregon Institute of Technology 3201 Campus Drive Klamath Falls, OR 97601 Tel: 541-885-1940 Fax: 541-885-1849 Email: matt.beek...@oit.edu Web: http://www.oit.edu/faculty-staff/home-pages/natural-science/matt-beekman -Original Message- From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of Peter Y. Zavalij Sent: Monday, September 16, 2013 6:11 AM To: Alan Coelho; mariomac...@tux.uis.edu.co; rietveld_l@ill.fr Subject: RE: Instrumental resolution function I do exactly the same - fit tube tails using LaB6 standard and use the parameters (usually w/o fitting) in all other refinements. Although tube tails fitting helps a lot it's not perfect. Peter Zavalij -Original Message- From: Alan Coelho [mailto:alancoe...@bigpond.com] Sent: Sunday, September 15, 2013 10:05 PM To: Peter Y. Zavalij; mariomac...@tux.uis.edu.co; rietveld_l@ill.fr Subject: RE: Instrumental resolution function Hi Peter, Mario I happen to have a Ni filter, Cu, LaB6 pattern that has a very similar look to the one sent by Mario. Probably best to look at the 21.35 degrees 2Th peak. The Ni filter cut-off occurs at 20.6 degrees 2Th, the satellite group is hard to see due to the low angle and hence compression of the emission profile. What made sense in the pattern was to fit Tube tails. Across the whole patter the Rwp was reduced by 2.1% where Tube tails was considered and the fit at the shoulders was good. Cheers Alan -Original Message- From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of Peter Y. Zavalij Sent: Monday, 16 September 2013 10:55 AM To: mariomac...@tux.uis.edu.co; rietveld_l@ill.fr Subject: RE: Instrumental resolution function Hi Mario, The shoulder you observe is what's left from "white" after it is cut off by beta-filer. You could check the absorption edge of Ni and it is right at the shoulder you observe. Peter __ Peter Zavalij X-ray Crystallographic Center University of Maryland College Park, MD 20742 Phone/Fax: (301)405-1861 http:/www.chem.umd.edu/crystallography -Original Message- From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of mariomac...@tux.uis.edu.co Sent: Sunday, September 15, 2013 6:08 PM To: rietveld_l@ill.fr Subject: Instrumental resolution function Dear All, I am calculating the corresponding instrumental resolution function of our Bruker diffractometer which is operating in Bragg-Brentano geometry with Cu radiation, using a nickel filter and LynxEye detector. The calculation is carried out by the Rietveld analysis of the LaB6 (660b) NIST-standard. We observed the Kbeta peaks, but also some shoulders in the left part of the peaks. We have some ideas about this but taking into account that I'm not an actual expert, your comments will be very important to me. In the attached file, I send an image to make a better illustration of my doubts. Thanks in advance for your help. Best Regards, Mario A. Macías Universidad Industrial de Santander Bucaramanga-Colombia. ++ Please do NOT attach files to the whole list
RE: [sdpd] Re: Are restraints as good as observations ?
Hi all, I have been following the tennis match going on here, and I'll point out what Brian Toby said again - use the data you have to fit what you can. When my work strongly focused on this I too used to be stuck on the fact that macromolecular crystallographers can use ultra-low resolution data... until I figured out they're not doing the same thing as people doing large small molecule work. So on the reliability of structures, how reliable is a DFT optimized structure... I know that theoreticians can calculate and optimize almost anything, which does not mean the result has any bearing on reality. Is it a result that was DFTized more reliable than a poorly converging result based on experimental data from a fit? And if you want to discuss the philosophy of restraints/constraints, we were not the ones that invented Tikhonov regularization and Levenberg-Marquardt fitting - sometimes when fitting a Jacobian with a poor quality number it is the only way to approach a stable solution... Alex Y ___ Dr. Alexandre (Alex) F. T. Yokochi Associate Professor of Chemical Engineering Laboratory for innovative Reaction Engineering for Materials and Sustainability (iREMS lab) School of Chemical, Biological and Environmental Engineering Oregon State University Corvallis, OR 97331 - 2702 -Original Message- From: s...@yahoogroups.com [mailto:s...@yahoogroups.com] On Behalf Of Leonid Solovyov Sent: Thursday, August 01, 2013 4:33 PM To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Subject: Re: [sdpd] Re: Are restraints as good as observations ? >What information capacity ? The fact is that imposing the expected >values you obtain a similar fit. This tells you that you cannot >discuss your unrestrained "information", because it is unreliable. > Information is something you may discuss reliably. > The only possible discussion about P3-O14 = 1.72(3)A is to say that >it is very probably strongly overestimated. After THIS unrestrained refinement one CAN discuss RELIABLY ALL interatomic distances including P-O, K-O, K-P, K-K and P-P, as well as angles, orientations etc., WITHIN THEIR UNCERTAINTIES that are also estimated RELIABLY according to the EXPERIMENTALLY DETERMINED deviations of the unrestrained P-O distances. After the restrained refinement NOTHING can be discussed RELIABLY since neither the values nor their uncertainties are determined EXPERIMENTALLY. After the unrestrained refinement one can state RELIABLY that the structure is DETERMINED with definite precision and, thus, discuss its features, compare it with other experimentally determined structures within their uncertainties, make more or less definite conclusions etc. After the restrained refinement one can only state that a hypothetical structure model is proposed and NOTHING can be concluded or discussed RELIABLY. Don't you see the difference??!! Determination = reliable experimental evaluation + reliable estimation of uncertainties. Now I probably understand your "colleagues". *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: Armel Le Bail To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Sent: Friday, August 2, 2013 12:40 AM Subject: Re: [sdpd] Re: Are restraints as good as observations ? > All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s > that are around 0.03 A in average. Further improvements seem possible, but it > will require more time and efforts. > > So, one more example of underestimated information capacity of powder data > and overestimated necessity of restraints. What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained "information", because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. Such are powder results for complex cases. Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant. Best Armel [Non-text portions of this message have been removed] Yahoo! Groups Links <*> To visit your group on the web, go to: http://groups.yahoo.com/group/sdpd/ <*> Your email settings: Individual Email | Traditional <*> To change settings online go to: http://groups.yahoo.com/group/sdpd/join (Yahoo! ID required) <*> To change settings via email: sdpd-dig...@yahoogroups.com sdpd-fullfeatu...@yahoogroups.com <*> To unsubscribe from this group, send an email to: sdpd-unsubscr...@yahoogroups.com <*> Your use of Yahoo! Groups is subject to:
FwD: Re:
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Instrumentla design
Hello everyone, Here is a general question for anyone that has pertinent information or just cares to give some input. Basically, here at Oregon State we have, coexisting in one lab, an INEL PSD detector set up for a horizontal line focus and a Rigaku rotating anode generator set for a vertical line focus (for thin films, etc, work). For quite some time I have been musing on the possibility to hook both up in order to give me a primary beam with higher intensity in the instrument we use for variable temperature experiments. Unfortunately, most powders refuse to defy gravity and stick conveniently to a vertical sample holder (well, one could stuff it into a capillary, of course) and, thus, what I am considering doing is using a monochromator at 45 degrees with the horizontal to give me a horizontal line. This should work fine (in theory). Preliminary experiments with lots of wire and duct tape and geiger counters shows things in practice do work out. My question then is, has anyone here done this (possibly one of you chaps that get to play at synchrotrons)? If you have, can you share your experiences (successes, failures, caveat with the design, etc.)? If you haven't and you think you have some insight please also fell free to share (as if you weren't going to anyway...). Some secondary concerns: On the use of a concentrating crystal monochromator - how advisable is it to cut the crystal so as to concentrate the diffracted beam vs. leaving the s.v. perfectly normal to the crystal's face? So you know, right now we're using Ge 111 crystals cut so 111 is perpendicular to the surface. Works ok. Or, how much do you know of the monochromating, etc, properties of total reflectance or multi-layered mirror systems? Would I be able to get a parallel and as monochromatic incident beam out of one of these set-ups as with a monochromator? And, of course, would the one order of magnitude increase in cost be worth the gains. Finally, concerning polarization corrections and other such parameters. In such programs as Fullprof and GSAS, I believe the assumption is that the primary, monochromated and diffracted beams all lie on one plane. However, this will no longer be the case and we'll need to worry with cross polarization terms, etc. Is there any software that will take goffy geometries into account (or is there a way to do this in the above mentioned packages?). I could, of course, choose to ignore the polarization corrections, in which case the displacement parameters will take care of absorbing the errors. Such a solution would be one of last resort and would set my fur on edge - not a good solution, of course. Well, thank you all in advance for all the profound insights I'm, certain to get in response. AlexY P.S.- You'll notice that I refrained from using y'all in that last sentence there even though that is one of my favourite words I learnt in Texas. P.P.S.- If you think I'm kidding about the fur bit, you've evidently never seen my swimming era unshaved, untapered photographs. P.P.P.S.- If you think I'm not making much sense, I just came back from the dentist to have a filling replaced. It's either the chemicals that still have an effect or the amalgam's mercury finally got to my brain. Or maybe I'm just naturally crazy, which my wife seems to believe. Dr. Alexandre F. T. Yokochi Director, X-ray Crystallographic Facilities Department of Chemistry Oregon State University Corvallis, OR 97331-4003 Ph# (541) 737-6724 Email: [EMAIL PROTECTED] Fax# (541) 737-2062 Web Page: crystal.chem.orst.edu/~alexy
