-deform <direction> <ε> <ν>
-def <direction> <ε> <ν>
This option allows to apply a uniaxial stress or strain to a system.
The user has to provide the direction of deformation, the applied strain, and the Poisson's ratio of the material. The program deforms the material in the given direction according to the applied strain, and deforms it in the other directions according to Poisson's ratio. The command-line parameters of importance are:
This transformation should result in an uniaxial stress: the stress should be non-zero in one direction, and should be zero in the other directions (that is, if Poisson's ratio is specified correctly).
In order to apply an uniaxial strain (i.e. elongate only one dimension), set Poisson's ratio to zero.
In order to apply an anisotropic deformation one can use this option three times along the three axes, using ν=0 and different values of ε (see example 3 below).
In order to apply the same deformation in all directions, set the Poisson's ratio value to -1. This can be useful, for instance, to deform a system according to its thermal expansion coefficient α, in which case one should use ε=αT, where T is the target temperature.
If a selection was defined (with the option -select) then the deformation applies only to selected atoms, and the box is not deformed.
For shear strain one can use the option -shear. In order to apply stress one can use the option -stress.
By default the system is not deformed at all.
atomsk initial.cfg -deform x 0.06 0.3 final.xyz
This will elongate the system initial.cfg by ε=6% along X, applying a Poisson's ratio of 0.3 along the other axes; this is equivalent to uniaxial stress. The result will be output into final.xyz.
atomsk initial.cfg -def y 2.5% 0.0 final.xyz
This will apply an uniaxial strain (Poisson's ratio is 0) of 2.5% along Y to the system unitcell.cfg. The result will be output into final.xyz.
atomsk initial.cfg -def x 1% 0 -def y -0.76% 0 -def z -0.73% 0 final.xyz
This example uses the option "-deform" three times to apply different deformations along the three axes (Poisson's ratio is always zero). This is equivalent to anisotropic axial deformation.
atomsk initial.cfg -def x 0.003 -1 final.xyz
This will apply a tension of 0.3% in all directions, thus mimicking the effects of a thermal expansion coefficient α=10-5 K-1 at a temperature T=300 K.