Rigid bodies in a multibank GEM refinement

Ljmckinlay

Hi Topas forum,
I am having some trouble inserting rigid bodies into my GEM multibank sequential refinement. I have been using the tetrahedra macro: Tetrahedra(W1, O41, O44, O28, O25, 1.78, w1posx 0, w1posy 0, w1posz 0, w1angal, w1angbe, w1angga) (apologies this may not be the exact input I used as I have been trying a number of inputs and don't have access to topas right now), as well as a posted macro to a previous question that sets the position of the atom to the position of the central atom and keep recieving an error with 'pa not defined'. I have placed this in my strs 1 for the refinement because I want it to refine for all, I'm using topas v6 and havent yet gone about restraining the bond lengths of the refinement. I have only been using topas for a few days because of the scope of this project, apologies if I have missed something basic.

rigid-bodies-refinement.zip

318kB

johnsoevans

I'm guessing your problem was qa not pa. This is to do with the "rotate_about_axies" macro which spins the rigid body in the cell. Do you have that defined?
In general the issues with rigid bodies and tof come from having multiple strs and multiple xdds. It's often useful to start with a simple file (one xdd bank, one str) and to get that working before building up to the more complex fit.
You might also want to check your SWO model (Sc2(WO4)3 is a long time favourite of mine!). I only took a 2 second look, but It seems like you have a lot of sites defined. Do you have a P1 set of coordinates by mistake? If you calculate the density it will tell you.

Ljmckinlay

Hi John, I will see if I can get my rigid bodies working for one file and get back to you. The cell I have the inp file is the p21/a monoclinic (taken from Fe2Mo3O12 and adjusted), as this is at moderate pressure with low temperature runs as well. I will also try it for my orthorhombic at higher temperatures but refining the sites for the free atom monoclinic I have found to be tenuous at best without rigid bodies.

Ljmckinlay

I found the issue, when using the tetrahedra macro, the macro for setting the position to s0, does not work.
start_values_from_site didn't exist in my topas.inc folder, however all working now and thank you for your help.
macro Translate_with_site_start_values(s0, xc, yc, zc)
{
Translate(xc 0, yc 0, zc 0)
start_values_from_site s0
}