Hello everybody,

I have an issue concerning rigid bodies which I am sure someone can come up with a better solution for.
I very often have structures that require a rigid or semi-rigid tetrahedron to be modelled.

Commonly I do this by defining the tetrahedron with the macro using the point_for_site definition.

Here is an example of a tetrahedron sitting on special position ..m:

' Tetrahedra(B1, H21, H22, H23)
rigid
point_for_site B1
' point_for_site H13 ux = -0.816496580927726 r; uy = 0.4714045207910317 r; uz = -r/3;
point_for_site H13 ux = 0.816496580927726 r; uy = 0.4714045207910317 r; uz = -r/3;
point_for_site H11 uy = -0.942809041582063 r; uz = -r/3;
point_for_site H12 uz = r;
' point_for_site A1 ux = 0.1; uy = 0; uz = 0;

Translate_point_amount(B1, -) operate_on_points "B* H* A*"

rotate 90.0 qa 1
rotate 30.0 qb 1
rotate @ 188.96804`_1.73326 qc 1
' Rotate_about_points (90, B1, A1, "H11 H12 H13")

Translate_point_amount(B1, +) operate_on_points "B* H* A*"

translate
ta @ 0.91324`_0.00088 min = Val-.5/Lpa; max = Val+.5/Lpa;
tb @ 0.97969`_0.00103 min = Val-.5/Lpb; max = Val+.5/Lpb;
tc 0.25 min = Val-.5/Lpc; max = Val+.5/Lpc;
start_values_from_site B1

prm r 1.13997`_0.00682_LIMIT_MIN_1.13 min 1.13 max 1.15
' prm !r 1.08

This macro is excellent for general positions but as most users I am having trouble with the special ones.
I can get around this quite well by rotating the tetrahedron manually until atoms are reproduced by the corresponding symmetry operations correctly, due to the convention between internal kartesian coordinates of the rigid body and the crystallographic axes.

for the above give example on ..m

rotate 90.0 qa 1
rotate 30.0 qb 1
rotate @ 188.96804`_1.73326 qc 1
' Rotate_about_points (90, B1, A1, "H11 H12 H13")

here I have rotated 90° around a followed by 30° around b. Rotation around c is undefined due to ..m.

Now this works, but gets really tedious really quickly when you have many different .inp files to write or sub- supergroups to check. Especially in monoclinic systems this approach is not very good.

Is there any way, in TOPAS Academic, that allows you to basically just place a rigid body on a special whyckoff site and let TOPAS do the rest? An example where this is done would be FOX, which we use for structure solution.

On another note, is there an editor that can transform .cif files into .inp syntax for TOPAS?

I greatly appreciate any advice which makes writing the rigid-body easier and quicker, as an inexperienced TOPAS academic user I find it really hard to find anything on this.

Thanks a lot to everyone!!

Pascal