CP2K is optimized for periodic calculations, and those are the default. Still it is possible to perform other kinds of calculations. First an important thing to note is, that by convention the cell goes from 0 to h, not from -h/2 to h/2. Thus if you want to put a cluster at the center of the cell you need to put it in h/2 not in 0. This can be done automatically using the FORCE_EVAL/SUBSYS/TOPOLOGY/CENTER_COORDINATES option. For certain Poisson solvers this is recommended to ensure an electron density of zero on the non-periodic faces of the cell.

The periodicity of the neighbor list, and thus of the gaussian collocation/integration is controlled by the keyword FORCE_EVAL/SUBSYS/CELL#PERIODIC.

The Poisson solver (electrostatics) is controlled in the section FORCE_EVAL/DFT/POISSON. The possible Poisson solvers are chosen with the POISSON_SOLVER keyword. Note, that not all solvers support all periodicities.

The periodicity of the Poisson solver (electrostatics) is set in FORCE_EVAL/DFT/POISSON#PERIODIC, and the Poisson solver chosen should support it. In most cases the periodicity settings of the Poisson solver and the subsystem should be identical.