-swap <id1> <id2>
-swap <x|y|z> <x|y|z>
This option swaps the positions of the two atoms of the given indices, or swaps the two given Cartesian axes.
Swapping atoms means that their positions are exchanged. If shells (in the sense of an ionic core-shell model) and/or auxiliary properties are defined, then they are also swapped.
Swapping Cartesian axes means that the two given vectors of the box are exchanged. For instance, exchanging the Cartesian axes X and Y would result in the following transformation (where H is the old vector and H' the new one):
H'(1,1) = H(2,2)
H'(1,2) = H(2,1)
H'(2,1) = H(1,2)
H'(2,2) = H(1,1)
The corresponding coordinates of atoms are also exchanged (i.e. following the same example, the coordinates X and Y of each atom are exchanged).
By default no atom is swapped.
atomsk initial.cfg -swap 530 1065 final.xsf
This will read the file initial.cfg, and exchange the positions and all properties of atoms 530 and 1065. The final result will be written into final.xsf.
atomsk initial.cfg -swap X Y final.xsf
This will read the file initial.cfg, and exchange the Cartesian axes X and Y. The final result will be written into final.xsf.