-rebox
This option forces the program to re-calculate the supercell vectors.
BEWARE: this option tries to provide a rectangular bounding box (so the box will NOT be correct for non-rectangular systems), and is very inaccurate. Do not trust it blindly: check the supercell vectors afterwards!
If you know the supercell parameters precisely, you may consider specifying them with the option -properties instead of the present one.
By default Atomsk uses the cell vectors read from the input file. If no cell vectors are found in the input file, then a warning is displayed and the present option is automatically called after reading the file (and before applying any other option). For instance, this is the case with the default XYZ format which does not contain any box vector.
atomsk system.gin -rebox xsf
This will read the file system.gin and re-calculate the supercell base vectors. The result will be output in system.xsf.
atomsk example.cfg -cut above 12 z -rebox xsf xyz
This will cut the system example.cfg above 12 Å along Z, and then re-calculate the supercell base vectors. The result will be output in example.xsf and example.xyz.