-disturb <dmax>
-disturb <dx> <dy> <dz>
This option applies a random translation vector to each atom. If only one value <dmax> is provided, then it is the maximum value of the displacement vector. If three values <dx>, <dy>, <dz> are provided, they correspond to the maximum displacement along each Cartesian direction.
The applied displacements follow a normal distribution function. They are adjusted so that there is no global translation of the system.
Note that this option attempts to generate random displacements along the cartesian X, Y and Z axis for each atom, therefore it is largely non-reproducible, i.e. starting from the exact same system and applying the present option will likely lead to different results.
After applying this option some atoms may not be inside of the simulation box, which can be fixed thanks to the option -wrap.
If some atoms have shells (in the sense of an ionic core-shell model), then both core and shells are shifted by the same vector.
If a selection was defined (with the option -select) then the perturbation is applied only to selected atoms.
By default the positions of atoms are not altered.
atomsk relaxed.xsf -disturb 1.0 disturbed.cfg
This will read the file relaxed.xsf and randomly move atoms, for a maximum of 1 Å. The new atom positions will be written to disturbed.cfg.
atomsk initial.xsf -disturb 250.0 -wrap amorphous.cfg
This will read the file initial.xsf and randomly move atoms for a maximum of 250 Å. Then the atoms that are out of the box will be wrapped back into the box. The resulting positions will be written to amorphous.cfg.
atomsk relaxed.xsf -disturb 1.2 1.2 0 disturbed.cfg
This will read the file relaxed.xsf and randomly move atoms, for a maximum of 1.2 Å along X and Y. Atoms will not be displaced along the Z direction. The new atom positions will be written to disturbed.cfg.