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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
-----Original Message-----
From: Roger M. Sullivan [mailto:smsulliv...@pams.ncsu.edu]
Sent: Sunday October 07, 2001 9:54 AM
To: rietveld_l...@ill.fr; sdpd...@yahoogroups.com
Cc: smsulliv...@pams.ncsu.edu
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
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