-cut <above|below> <d> <normal>
This option allows to "cut" a system, i.e. remove atoms that are above or below a given plane.
The parameters for this option are the following:
The position <d> is usually given in Å. It is also possible to give it with respect to the box dimensions with the keyword BOX and an operation (see this page).
The <normal> can be one of 'x', 'y', 'z' (referring to cartesian axes), or a crystallographic direction defined by its Miller indices [hkl], or [hkil] for hexagonal systems (see how to specify Miller indices). If the crystallographic orientation of the system is defined (e.g. through the option -properties) then the Miller indices are considered with respect to that orientation. Otherwise the orientation assumed is X=[100], Y=[010], Z=[001].
If some atoms have shells (in the sense of an ionic core-shell model), it is the position of the core that is compared to <d>. When an atom is removed, both its core and shell (and auxiliary properties if any) are removed.
If a selection was defined (with the option -select) then only the selected atoms are removed.
Note that this option does not change the supercell parameters. In other words, it results in a void region where atoms have been removed.
By default the system is not cut.
atomsk system.gin -cut above 0.5*BOX z xsf
This will read the file system.gin, and delete all atoms that are above the plane placed at half the height along Z. The result will be output to the file system.xsf.
atomsk initial.gin -cut below 2.4 x -cut above 40 x final.xyz
This will read the file initial.gin, delete all atoms that have an X coordinate smaller than 2.4 Å or greater than 40 Å. The result will be output in the file final.xyz.
atomsk final.xyz -cut below 2.4 x initial.gin -cut above 40 x
Same as the previous example. Note that each option must be followed by its parameters, but input and output files can be placed in any order.
atomsk final.xyz -cut below 14 [011] initial.gin -cut above 40 [1-10]
This will read the file initial.gin, delete all atoms that are closer than 14 Å along the [011] direction, and those more far away than 40 Å along [110].
atomsk final.xyz -cut above 40 [1-210] initial.gin -cut above 40 [1-10]
This example illustrates the use of Miller indices for hexagonal systems. In this case, atoms that are above 40 Å along the [1210] direction will be deleted.