-dislocation <disloctype> <dislocline> <b> <poisson> <pos1> <pos2>
or
-disloc <disloctype> <dislocline> <b> <poisson> <pos1> <pos2>
This option allows to insert a straight edge or screw dislocation in the system.
The user has to provide the following parameters:
dislocline
; for edge dislocations it will be normal to dislocline
in the order of rotation X, Y, Z (e.g. if dislocline=Y
then the Burgers vector will be along Z); if you want to orient the Burgers vector in the other direction then you can rotate the system by 90 degrees around dislocline
;dislocline
, by order of rotation X, Y, Z (e.g. if dislocline=Y
then pos1
will be the position along Z and pos2
along X). The coordinates pos1
and pos2
can be specified in Å or as fractional coordinates (pikashu
will detect it automatically).In the case of an edge dislocation, new atoms are inserted in the system and then atomic displacements are applied. So beware that this option changes the total number of atoms in the system. Due to these displacements, the supercell vectors are also a bit elongated in the direction of the Burgers vector -it is recommended that you check them afterwards.
Inserting a screw dislocation conserves the number of atoms as well as the cell vectors.
Note that b
can take negative values. This can be useful for instance if you want to insert dislocations of opposite Burgers vectors in the same supercell.
Beware that pikashu
does not "automagically" find the Burgers vector, so you have to provide a very precise value of b
. Neither does the program find the "best" position for the dislocation center: if you specify a position pos1, pos2
that exactly matches an atom position you may end up with unrealistic displacements, so you may have to play around with the dislocation coordinates to obtain proper results. As usual, don't trust a program blindly -check your system before running any simulation, specially when building systems with dislocation(s).
Default is <b> = 0 (i.e. no dislocation is introduced at all).
pikashu initial.cfg final.xyz -dislocation screw z 3.2 0.33 0.5 0.5
This will read initial.cfg
and insert a screw dislocation in the middle of the supercell (because pos1=pos2=0.5), with the dislocation line along Z, with a Burgers vector of 3.2 Å, using a Poisson's ratio of 0.33. The result will be output to final.xyz
.
pikashu initial.cfg final.xyz -disloc screw z 3.2 0.33 0.25 0.5 -disloc screw z -3.2 0.33 0.75 0.5
This will read initial.cfg
and insert two screw dislocations of opposite Burgers vectors, the first one at (0.25;0.5) and the second at (0.75;0.5). The result will be output to final.xyz
.
pikashu unitcell.xyz dislocation.xsf -expand 30 2 20 -disloc edge y 2.8 0.28 30 40.2
This will read unitcell.xyz
, expand it to form a 30x2x20 supercell, and then insert an edge dislocation which line will lie along Y, with a Burgers vector of 2.8 Å, using a Poisson's ratio of 0.28, and the center of the dislocation will be placed at 30 Å along Z and 40.2 Å along X. The result will be output to dislocation.xsf
.