-separate <distance> <shift>
This option separates atoms that are too close to one another.
When two atoms are found closer than the specified <distance>, they are both pulled apart from each other by the given <shift>. The direction of the shift is along the vector joining the two atoms.
If the two atoms share exactly the same position (i.e. if their joining vector has a naught length), then the two atoms are moved along the Cartesian vector [1,1,1] (note that this has nothing to do with the crystal orientation).
The comparison of distances is based only on cores. If shells are present, both core and shell are moved by the same vector.
If a selection was defined (with the option -select) then the neighbor search is performed on all atoms, but only selected atoms are shifted.
By default atoms are not separated.
atomsk initial.cfg -separate 0.5 0.2 final.xyz
This will detect atoms that are closer than 0.5 Å, and move each of them by 0.2 Å apart from the other.