-center <index>
This option shifts all atoms so that the atom with the given <index> is at the center of the box.
If <index>=0 or "com", then all atoms are shifted so that the center of mass is at the center of the box.
By default the system is not centered.
atomsk initial.cfg -center 23 final.xsf
This will read the file initial.cfg and shift all atoms so that the atom #23 is exactly at the center of the cell. The result will be output to the file final.xsf.
atomsk initial.cfg -center com final.xsf
This will shift atoms so that their center of mass is at the center of the box.