Initial position generation

It depends what you mean by 'crystals'. LIGGGHTS is a granular extension of LAMMPS, but essentially all you would need to define is a box simulation region, and fix the x-y plane as a wall (this will act as your slab). Then define another region the length and width of your simulation region, and some thickness (probably relatively thin if you are looking to place crystals directly on the slab). To deposit crystals randomly you can just use the 'fix deposit' command. This randomly places atoms according to a seed that you set in the command. As for 'crystals' you are going to have to look at supported atom types to see if you can place the atoms you require