You mean packing in a solid or stacking of ions in the gas phase?

Both are possible, but different kinds of code are optimal for it.

Jürgen Weippert in solid state

OK, then you certainly need a DFT package which can operate under periodic boundary conditions. Here you can check which ones offer that option:

https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software#Quantum_chemistry_and_solid-state_physics_characteristics

Once you have familiarized yourself with the handling in your package of choice (which is probably the biggest piece of work here), you proceed essentially like in your molecular calculation: make a guess structure and optimize it. Since you already have an optimized structure of the main molecule, at least that part is already done and can be pasted into your start guess.