The setup in your script file indicates that an atomic layer of W (110) surface is calculated. In the primitive unit cell of W(110) surface, each atomic layer contains only two atoms. But there are fours atoms in your script file, and so some of them will be overlapped due to the periodicity.
unit_cell=[[1.414*a, 0.0, 0.0],
[0.0, a, 0.0],
[0.0, 0.0, b]]*Angstrom
here b stands for the thickness of vacuum, 1.414*a and a are the lattice constants of W(110) surface in the xy plane. Maybe 10 is enough for b.
my_cell=PeriodicAtomConfiguration(
super_cell_vectors=unit_cell,
elements=2*[Tungsten],
fractional_coordinates=[(0.0,0.5,0.0),(0.5,0.0,0.0)]
)