I apologize if I am dragging this into a lengthy exchange, but I just thought of a way to shape up surfaces and I would like to share it with the community.
While VMD scripting is ultimately how I want to do all the pre-processing, I’m finding it tricky when it comes to creating surface patterns for an amorphous cell (it worked fine for crystalline solids). Same goes for maintaining the shapes as the simulations run, as they may not stand still unless it’s a really careful equilibration. I was thinking of maybe “casting” the surface.
That is, I start with a crystalline strcuture (target) below a heavy, frozen and shaped surface. I heat the target surface and anneal it till it’s amorphous, then I push it into the cast (by displacing the box or such) and finally I quench. In the end, I delete the atoms of the cast and I have a well-shaped surface.
What do you guys think? Is it feasible?
HK