# Problem with heating a non-periodic bicrystal to a certain temperature

Dear all lammps-users:

As the title mentioned, my problem is about heating a non-periodic bicrystal to a certain temperature.

Firstly, i constructed a bicrystal system with boundary condition(bc) 'p s p'(i.e. two free surfaces at the top and bottom of the bicrystal, and one grain boundary between two grains), and the dimensions for each direction are X-dimen=33.39, Y-dimen=70.4, Z-dimen=33.39.
Secondly, "displace_atoms","fix box/reax" and "minimize" commands are used to enforce the bicrystal to reax to get a local minimum grain boundary energy, undoubtedly these commands will cause the chang of Y-dimen for non-periodic bc, and that is just why atoms arrangement of the bicrystal with minimun gb energy is slightly different from the initiallly constructed bicrystal.
Thirdly, i dumped the bicrystal with minimun gb energy and heated it to a certain temperature by the "fix nvt" command, then the problem came.
By observing atoms structure of the bicrystal visualized by the 'ATOMEYE', i found the grain boundary and the two free surface gradully disappeared with the process of heating, and finally there was no boundry in the bicrystal system, but this kind of phenomenon does not happen if i set the bc of the bicrystal as 'p p p'. So i think it is the non-periodic boundary condition in Y-direction causing the problem, is that ture? If yes, then how can i heat the bicrystal with bc 'p s p' without appearance of boundaries? Could anyone give me some ideas about this problem?

Dear all lammps-users:

As the title mentioned, my problem is about heating a non-periodic bicrystal to a certain temperature.

Firstly, i constructed a bicrystal system with boundary condition(bc) 'p s p'(i.e. two free surfaces at the top and bottom of the bicrystal, and one grain boundary between two grains), and the dimensions for each direction are X-dimen=33.39, Y-dimen=70.4, Z-dimen=33.39.
Secondly, "displace_atoms","fix box/reax" and "minimize" commands are used to enforce the bicrystal to reax to get a local minimum grain boundary energy, undoubtedly these commands will cause the chang of Y-dimen for non-periodic bc, and that is just why atoms arrangement of the bicrystal with minimun gb energy is slightly different from the initiallly constructed bicrystal.
Thirdly, i dumped the bicrystal with minimun gb energy and heated it to a certain temperature by the "fix nvt" command, then the problem came.
By observing atoms structure of the bicrystal visualized by the 'ATOMEYE', i found the grain boundary and the two free surface gradully disappeared with the process of heating, and finally there was no boundry in the bicrystal system, but this kind of phenomenon does not happen if i set the bc of the bicrystal as 'p p p'. So i think it is the non-periodic boundary condition in Y-direction causing the problem, is that ture?

i would describe it differently. if your grain boundary vanishes upon
heating, that effectively means that your crystal is melting. now why
it doesn't happen with periodic boundary conditions, may be either due
to the open surface reducing the melting point,
or that the melting is delayed due to lack of nucleation. this is a
quite common phenomenon in molecular simulations.

If yes, then how can i heat the bicrystal with bc 'p s p' without appearance of boundaries?

you should rather ask, 'why does it melt?'. perhaps there are some
issues with your simulation or the choice of parameters or other
things, that we don't know about.

axel.

i would describe it differently. if your grain boundary vanishes upon
heating, that effectively means that your crystal is melting. now why
it doesn't happen with periodic boundary conditions, may be either due
to the open surface reducing the melting point,
or that the melting is delayed due to lack of nucleation. this is a
quite common phenomenon in molecular simulations.

Said another way, the periodicity constrains the defect (grain boundary
in this case) so it is not free to relax.

Steve

Dear Axel and Steve: