deepest layers comes on top of surface after vacuum space

[venkatramana]

Dear sir,

I am new to VASP simulation community. I have created Ni surface with 3x2x2 dimensions using lattice constant of 3.524 angstroms.
My system has 6 layers and each layer has 12 Ni atoms with a total of 72 Ni atoms. I kept 12 angstroms vacuum space along z-direction for calculating surface energy.
I optimized this system using quasi-Newton algorithm. Herein, I got problem, i.e, the deepest two layers come to top position, and the system becomes 4-layers+12 angstroms vacuum space+2-layers. Similar problem is happened when keeping methane molecule on top of surface. Can anyone tell me how to resolve this problem.

Moreover, I continued calculations for finding minimum energy path using NEB after optimizing reactant (methane on top of Ni-surface) and product (chemisorbed methyl and chemisorbed hydrogen on top of Ni-surface). In this case, left side atoms coming to right side or right side atoms coming to left side and, unable to find out solution to this problem. Can you give suggestions regarding this. Many thanks in advance.

[admin]

Looks like displaying matter. Atoms which are close to the cell surface
can easily go out of the cell. Then they disappear at one side
and appear at the other side of the cell. To avoid this effect start
relaxation with atoms placed at larger distance from the cell surface.

[venkatramana]

Dear sir
Thank you for reply.
According to you, I took large atom coordinates, those are in 2-layer after surface vacuum and,
I did relaxation calculations with same vacuum space, then there is no change in my results.
It become 4-layers+12 angstroms vacuum space+2-layers.
I am unable to tackle this thing. I tried several days, but no solution at all.
Similarly when doing interpolation between reactant and product for NEB calculations, right side atoms goes to left side and, vice versa.
Because of this convergence problems are arising. Can you give reason behind this.
Is it because of code or something else. Please tell me.

[tfrankcombe]

You are working under periodic boundary conditions. What you describe is exactly what you should expect. When an atom crosses a cell edge, it re-enters on the opposite face. What would you expect it to do?

To make you slab stay together as you seem to want for visualisation/easier NEB setup, shift it to the centre of the cell. (Note that some claim there are subtleties here w.r.t. k-point sampling.)