Since the ab initio structures are periodic in all 3 directions, do the atoms are the atoms at the bottom of the slab also exposed to the vacuum on the top? To better illustrate my question, here’s an illustration of a catalyst + adsorbate system from the paper:
I drew the main simulation box, everything outside is a periodic image.
Consider the black atom at the bottom - I drew a cutoff radius around it. Since the boundary conditions are periodic, is my understanding correct that this black atom at the bottom of the slab is also exposed to the vacuum?