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## Option: cut

#### Syntax

`-cut <above|below> <d> <normal>`

#### Description

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:

- above|below: this keyword decides if it is the atoms above or below the plane that are removed.
- d: distance from the origin of the axis where the cut plane is placed, in angströms (Å).
- normal: direction perpendicular to the plane of cut; can be x, y, z, or a crystallographic direction (see below).

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.

#### Default

By default the system is not cut.

#### Examples

- `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.

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