thin film with surface reactions

[Taquansoho]

I am interested in modeling a 3D system, which is open in one direction (i.e. has a surface along +/-z), allowing for surface reactions (i.e. adsorption/desorption + surface diffusion) to occur. I guess, if my system size is 20 along all three directions, I will just have to block PBC for all (x,y,20,n) sites and use these sites specifically for surface reaction processes. Any suggestions how to go about doing this, say for a two-site unit-cell ?