boundary x y z
z= p or s
p is periodic s is non-periodic and shrink-wrapped
boundary p s s
This command sets the boundary conditions of the simulation cell along the x, y, and z directions. Along each axis, the same condition is applied to both the lower and upper faces of the cell.
p sets periodic boundary conditions (PBCs). The nodes/atoms interact across the boundary and can exit one end of the cell and re-enter the other end. For more information of the PBCs in the coarse-grained domain, read chapter 3 of Shuozhi Xu's Ph.D. dissertation.
s sets non-periodic boundary conditions, where nodes/atoms do not interact across the boundary and do not move from one side of the cell to the other. The positions of both faces are set so as to encompass the nodes/atoms in that dimension, no matter how far they move.
Under neither boundary condition will any nodes/atoms be lost during a CAC simulation.
When p is set along a certain direction, the corresponding zigzag is set to f. In other words, a boundary has to be flat to apply the PBCs.
boundary p p p