I am working on a di-atomic periodic 2D glass system and I am encountering some issues with defining the boundary conditions. I am utilizing the Wang-Tiling approach to generate a large system composed of different tiles i.e. square shaped construct.
My aim is to able to replicate an initial ‘square’ system repeatedly to form a larger system.
My LAMMPS input is capable of assembling the required number of tiles but post the assembly of the the system, I have the following observations:
- The left to right end and the top to down boundaries do not match,
- The tiles contain overlapping of atoms and large gaps are being observed.
Since I need to keep the boundaries ‘unmodified’ during simulations, I freeze this region and proceed to minimize the interior of the tiles. This does not improve the performance of the edges and I end up with a patterned surface that has high energy zones and low energy zones. The high energy zones represent the boundaries that were not minimized because they would change and no longer mimics Wang Tilings.
It would be of great help to be able to modify ALL boundaries at the same time in the same manner (ending up with the same boundary scheme in the full model). Has anybody been able to displace separate groups of atoms at the same time? I can provide you with the LAMMPS input file on request.