How to build the [111] slab model of NiSe2 with different terminations with ASE tool?

Question

The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database.

Now I want to study the properties of its [111] plane. In detail, I cut the slab with atomic simulation environment (ASE) as follows:

from ase.io import read, write
from ase.build import surface

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structA=read('NiSe2.vasp', format='vasp')
structB=surface(structA, (1,1,1), 3, vacuum=10)
write('111.vasp', structB, format='vasp')

The cutted slab is:

In particular, I find the Se5 atom is strange. In addition, the cutted slab is different from this paper:

Here different terminations are considered. Therefore, how can I use ASE cut these (111) slabs with different terminations?

Thanks in advance.

Answer 1

There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for example, Se atoms with only 1 neighbor). This will give you a more reasonable termination, but may not give you the desired Ni-Se ratio. With a complex unit cell like this, you may not find a solution that is automated unfortunately.

What you can do though if studying a common class of materials is to use ASE as a first pass, clean up the terminations in ase-gui, then save that template. Then start from this template rather than the bulk material if you study similar materials. You may find this easier if you color the atoms by coordination number.

You may find pymatgen or catkit more capable than ASE at generating surfaces, I have heard they tend to do a slightly better job but this is a complex issue.