-cut <cutdirection> <cutdistance> <cutplane>
This option allows to "cut" a system, i.e. to output only part of its atoms. In this option, a plane is defined by its normal (which can only be X, Y or Z axes) and its distance from the origin; then atoms can be deleted above or below that plane.
The parameters for this option are the following:
This option does not change the size of the box. In other words, it will result in a void region where atoms have been removed.
If you want to cut above (or below) a plane that is not aligned with X, Y or Z, then you can first rotate the system to align the direction you want with an axis, then cut the system, and finally rotate it back to its original orientation.
pikashu system.gin -cut above 5 z xsf
This will read the file system.gin
, and delete all atoms that are above the plane placed along Z at 5 Å from the origin. Th result will be output to the file system.xsf
.
pikashu initial.gin -cut below 2.4 x final.xyz
This will read the file initial.gin
, and delete all atoms that are below the plane placed along X at 2.4 Å from the origin. The result will be output in the file final.xyz
.
pikashu -cut below 2.4 x final.xyz initial.gin
Same as the previous example. Note that the block "-cut below 2.4 x
" cannot be broken, but input and output files can be placed in any order.