We have investigated, by the Monte Carlo simulation, spin systems which represent moments of arrayed magnetic nanoparticles interacting with each other only by the dipole-dipole interaction. In the present paper we aim the understanding of finite size effects on the magnetic nanoparticles arrayed in hexagonal columns cut out from the close-packing structures or from those with uniaxial compression. In columns with the genuine close-packing structures, we observe a single vortex state which is also observed previously in finite two-dimensional systems. On the other hand in the system with the inter-layer distance set 1 / sqrt(2) times of the close-packing one, we found ground states which depend on the number of layers. The dependence is induced by a finite size effect and is related to a orientation transition in the corresponding bulk system.
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