As discussed before the atomic positions are input with the key ATOMS. One option has thus far not been mentioned: the possiblity to redefine the local coordinate frame of an atom.
ATOMS {type of coordinates}
{n} atomname coordinates {F=fragment} {Z=xx yy zz} {X=xx yy zz}
...
end
Except for the z= option all aspects have been examined already before.
z=xx yy zz
defines a reorientation
of the local atomic z-axis; it is interpreted as a direction vector
with components (xx,yy,zz) pointing away from the atom. In the local,
reoriented frame the local atomic x-axis will be rotated to the plane defined
by the directions of the molecular z-axis and the local atomic
z-axis.
This feature can be used only for single-atom fragments (otherwise it is
ignored). Its purpose is to give more flexibility in the analysis of the final molecular orbitals in terms of the
atomic orbitals. In such a case it may be very helpful to redefine the
orientation of say the p-orbitals of an atom. For instance, you may orient all p-orbitals towards the origin by specifying for each atom
z= -x -y -z (with x,y,z the coordinates of that atom).
By default the local and molecular z-axes are identical.
x=xx yy zz
defines a reorientation
of the local atomic x-axis; it is interpreted as a direction vector
with components (xx,yy,zz) pointing away from the atom. Together with the z vector this defines
the xz plane. The y axis is then given by the vector product z * x.
This is used for analysis (see orientation of the z-axis).
