To design a versatile simulation tool, we use periodic boundary conditions to create rectangular simulation box for structures with non-rectangular unit cell. An extended neighbor list is created from atoms of the translated rectangular boxes within the chosen cutoff. When looping over the unique atoms of the framework in the surface sampling, this neighbor list is restrained to a shorter neighbor list to be used in the interaction energy calculation, like in most molecular simulation algorithms. To evaluate the effect of the neighbor list, we tested the final implementation without the implementation of the neighbor list, and the simulation runs for 12.6 s instead of 0.34 s (37 times slower) without altering the accuracy. This shows that the implementation of an efficient neighbor list is a key point in our algorithm.