basis atoms

I have a crystal with orientations x 1 -1 1 ,y -1 1 2 and z -1 -1 0 and I want to rotate by a certain angle theta so I calculated the rotation matrix and then the novel orientations becomes x 0.9875 -0.9875 -1.0246, y 1.0246 -1.0246 1.975 and z -1 -1 0. I tried to add this new orientation using orient command but this gives error as they are not integers anymore so now I tried to make this using a1, a2 and a3 and basis atoms. So will I assign the new orientations to a1,a2 and a3 and if so what will be the values of the basis atoms if the structure is bcc?

Mohamed Hamza

As the lattice doc page explains, the basis atom positions are specified as fractions of
a,b,c. From the doc page:

The position vector
x of a basis atom within the unit cell is thus a linear combination of
the the unit cell’s 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
where bx,by,bz are the 3 values specified for the {basis} keyword.


So I tried to make this but the atoms in the lower region are not oriented probably, so what is wrong with the basis atoms of the bcc in the lower region

Make bicrystal, change orients to corresponding values for GB of interest

lattice bcc {lat_a} & orient x 1 -1 1 orient y -1 1 2 orient z -1 -1 0 create_atoms 1 region upper lattice custom {lat_a} a1 0.9875 -0.9875 -1.0246 a2 1.0246 -1.0246 1.975 a3 -1.0 -1.0 0.0 &
basis 0.0 0.0 0.0 &
basis 0.5 0.5 0.5

create_atoms 1 region lower

If you are specifying a1,a2,a3 directly, you probably shouldn’t
also use orient.