Discussions on setting up Rigid Bodies in GSASVia Rietveld Mailing ListAlso refer to: "Ian Swainson's Fireside Guide to Rigid Bodies in GSAS" |
To: rietveld_l@ill.fr, sdpd@yahoogroups.com From: "Roger M. Sullivan" [smsulliv@pams.ncsu.edu] Date: Sun, 07 Oct 2001 13:54:11 -500 Reply-To: sdpd@yahoogroups.com Subject: [sdpd] (unknown) Greetings All, Please help me with insertion of rigid bodies in GSAS. I have been using Ian Swain's guide (for which I am very grateful) at: http://www.ccp14.ac.uk/ccp/web-mirrors/ian-swainson/fireside_fuide_to_rigid_bodies.pdf My difficulty is knowing the proper input to orient my rigid bodies. I chose a local cartesian coordinate system such that x//a z//axb y//(axb)xc and placed the origins at the atom which is always 0 0 0 in vector input (central atom in r.b. type 1, bent L-M-L; central atom of r.b. type 2 tetrahedral ML4) so my cartesian vectors are oriented with respect to the fractional coordinate system of the monoclinic cell (b unique). When I enter zero angles I seem to be getting a random orientation. Also why are there six rotation angles? Are these related to the six unique elements of the transformation matrix between the cartesian coordinate system and the fractional monoclinic coordinate system? Further background on the problem. I am trying to solve a structure from powder diffraction data. I know the structure of some similar materials and have tried both EXTRA/SIRPOW and ESPOIR to generate models for refinement. I believe I have the proper fragements (this is also supported by MAS NMR data), and a roughly correct orientation in the unit cell from ESPOIR (using HKL, Fobs generated by EXTRA). I wish to try and refine the orientation of the bent and tetrahedral fragments as rigid bodies. Roger M. Sullivan Department of Chemistry, Box 8204 North Carolina State University Raleigh, NC 27695-8204 Phone: 919.515.8924 FAX: 919.515.8909 smsulliv@pams.ncsu.edu |
To: rietveld_l@ill.fr, sdpd@yahoogroups.com From: "Swainson, Ian - NRC" [ian.swainson@nrc.ca] Date: Tue, 9 Oct 2001 10:15:41 -0400 Subject: RE: [sdpd] (unknown) Hi Roger, I'm afraid the short notes were designed to be talked around, so they are an annotated set of handouts on the absolute basics: not sure how well they work as a "stand alone" document. I have to confess to only ever having done relatively simple RBs myself, but you always need to start with an _orthogonal_ Cartesian system for your molecule (at least I believe this to be a requirement). I wasn't sure from your description whether you had done that or not. The closest example in my short notes (I think) to your situation would be (ND4)2PdCl6, however the notes are not as detailed on that one. Suffice it to say that the tetrahedra/octahedra I used can be set up basically irrespective of the crystal frame. It is only when you do the insertion (e.g. I 1 1 etc...) that your orthogonal RB axes become linked to your crystal axes via the transforms you describe. This is probably the "random" orientation you describe. I am not sure if it is a typo in your message, or my short notes, but Z (not Y) // axb and Y (not Z) //(axb)xa not (axb)xc. Apologies if that is my fault. I will check to see. So for a std monoclinic system (I'm thinking while I'm typing so please check!) , X//a, Z//axb (i.e. 1/c*) and Y//(1/c*)x a which would be b, I think. You should therefore be able to relate your XYZ orthogonal Cartesian description to a,b,1/c* of the crystal frame (The examples I have done, I have not had to worry too much about the intial orientations too much. I have actually found that for simple molecular crystals, if you damp everything, GSAS actually manages to find the correct orientation for you, once you start refining(!) However, that probably depends heavily on the complexity of the problem.) As to 6 angles: I think Bob Vondreele once told me that three XYZ rotations are provided for an initial guess and three more to refine (see how wrong you were!). I have only ever used three for everything. Hope this is some help. Ian Ian Swainson Neutron Program for Materials Research, NRC Chalk River Labs, Stn 18 Chalk River, ON, K0J 1P0 CANADA Tel: +1 613 584 8811 ext 3995 Fax: +1 613 584 4040 |
Date: Tue, 09 Oct 2001 09:40:13 -0600 From: Allen Larson [aclarson@concentric.net] To: rietveld_l@ill.fr Subject: Re:[sdpd](unknown) Re: 6 rotations in GSAS rigid bodies I might insert a word or two here concerning rigid bodies in GSAS. The reason for 6 rotations angles in GSAS is to provide flexibility to molecules such as nitro methane permitting refinement of rotations of the methyl and nitro groups about an axis that goes through the molecule origin. Three rotation angles are used to orient the complete rigid group and the other three are available to allow up to secondary groups rotation about axes that go through to group origin. In general you should not be using them for most rigid bodies. Since much of the design work on GSAS rigid bodies was done about 30 years ago (10 to 15 years before I met Bob Von Dreele), it might be worth while to rethink some of the details again. Allen C. Larson |