Dear experts,
I am interested in calculation of Peierls stress for screw dislocations in bcc metals. In this respect I was going through examples of lammps-10Aug15.
There for the NEB simulation of vacancy hopping in silicon crystal, there is a file final.sivac . Can you please let me know what does this file inform and how this file is generated?
I am asking this question as I want to find out how to input the final position of the screw dislocation for my simulation. The final position of the dislocation would be in the adjacent Peierls valley position to the initial position of the dislocation in a Peierls valley.
Thanking you,
Best regards,
Krishnendu
Dear experts,
I am interested in calculation of Peierls stress for screw dislocations in bcc metals. In this respect I was going through examples of lammps-10Aug15.
There for the NEB simulation of vacancy hopping in silicon crystal, there is a file final.sivac . Can you please let me know what does this file inform and how this file is generated?
Like the other final.* files in the neb folder, it contains the positions of the atoms that have moved during the mechanism. The position of these atoms will be interpolated by the NEB.
It can be generated by any tools, script, etc. But not directly with lammps.
Julien
Dear Julien,
Thank you for your kind reply. In the in.neb.sivac script there is the following comment and command:
"
initial minimization to relax vacancy
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
"
So, I guess this command is to relax the initial vacancy.
If the final.* file gives the final position of the vacancy, the relaxation step should also be done for the final position before running the NEB. But there is no relaxation step for the final position of the vacancy in the script. Please let me know how to relax the final.* position.
I am asking this question because it may also arise when I do my Peierls barrier calculation for screw dislocation in bcc metal. I can create the screw dislocation through isotropic elastic displacement solution in two boxes where the dislocations are positioned in adjacent Peierls valley. If one of them is the initial.* file which I can relax using the above mentioned comment. But how to relax the other dislocation which would be my final.*?
Thanking you,
Sincerely,
Krishnendu
Dear Julien,
Thank you for your kind reply. In the in.neb.sivac script there is the following comment and command:
"
initial minimization to relax vacancy
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
"
So, I guess this command is to relax the initial vacancy.
If the final.* file gives the final position of the vacancy, the relaxation step should also be done for the final position before running the NEB. But there is no relaxation step for the final position of the vacancy in the script. Please let me know how to relax the final.* position.
I am asking this question because it may also arise when I do my Peierls barrier calculation for screw dislocation in bcc metal. I can create the screw dislocation through isotropic elastic displacement solution in two boxes where the dislocations are positioned in adjacent Peierls valley. If one of them is the initial.* file which I can relax using the above mentioned comment. But how to relax the other dislocation which would be my final.*?
I don’t exactly know why the example is build like that… Maybe it should be run several time by commenting some lines?
Anyway, the usual way to perform a NEB is with 3 simulations:
- 1 minimization of the initial config.
- 1 minimization of the final config.
- 1 NEB with initial and final relaxed config.
Note that there are other (more complex?) NEB schemes as described in the documentation (free end, …) which do not requires relaxed intial/final config.
Julien
Thanking you,
Sincerely,
Krishnendu
Dear experts,
I am interested in calculation of Peierls stress for screw dislocations in bcc metals. In this respect I was going through examples of lammps-10Aug15.
There for the NEB simulation of vacancy hopping in silicon crystal, there is a file final.sivac . Can you please let me know what does this file inform and how this file is generated?
Like the other final.* files in the neb folder, it contains the positions of the atoms that have moved during the mechanism. The position of these atoms will be interpolated by the NEB.
It can be generated by any tools, script, etc. But not directly with lammps.
Julien
I am asking this question as I want to find out how to input the final position of the screw dislocation for my simulation. The final position of the dislocation would be in the adjacent Peierls valley position to the initial position of the dislocation in a Peierls valley.
Thanking you,
Best regards,
Krishnendu
–
Dr. Krishnendu Mukherjee,
Principal Scientist,
CSIR-NML,
Jamshedpur.
–