Hi Youzhao,
Indeed as you guessed the atom_index is simply the number of the atom in the list of atoms in the geometry. So the example you constructed:
geometry units au
O 0.00000000 0.00000000 0.00000000 atom_index 1
H 0.00000000 1.43042809 -1.10715266 atom_index 2
H 0.00000000 -1.43042809 -1.10715266 atom_index 3
end
is correct.
Best wishes,