Hello,
I have problems understanding an example in the SIESTA manual and placing a
molecule at a specified place on a surface. The slab is defined in Cartesian
coordinates, the molecule as a Z-matrix. The example on page 35 of the manual
(3.1) looks like this:
%block Zmatrix
molecule
2 0 0 0 xm1 ym1 zm1 0 0 0
2 1 0 0 CC 90.0 60.0 0 0 0
2 2 1 0 CC CCC 90.0 0 0 0
2 3 2 1 CC CCC 0.0 0 0 0
...
fractional
3 0.000000 0.000000 0.000000 0 0 0
3 0.333333 0.000000 0.000000 0 0 0
...
xm1 etc. are the Cartesian coordinates of the first atom. But with respect to
what are the angles and the dihedral of the next two atoms defined? From trying
it out, it seems like atom 2 is in y-direction, and the first angle gives a
rotation within the xy plane. Can this be changed?
If I want the molecule in a specific position, I presumably have to include
three surface atoms in the definition of the molecule, but if these have to
fulfil the above criteria, I end up with a not very intuitive orientation of the
system. Is there a way to specify the orientation of the first few atoms, or to
specify their z-matrix coordinates wrt atoms in the Cartesian block?
Thanks in advance,
Herbert
--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532
