I am performing calculations using Quantum Espresso to view the charge density differences in the gas-surface adsorption structures. I could see no missing atoms after optimizing in BURAI. But when I view the cube files for the same structures in VESTA, I see some missing atoms despite charge differences being shown in places of the missing atoms. May I know why this might be happening? Or if it is a major issue? I have attached the images for reference.
I don’t know if you find the answer for this, but I believe it is quite trivial, although probably not expected.
vesta does apply periodicity to the cube file but not to the unit cell: so an atom at the boundary should be cut into two pieces which should be appearing at the two sides of the unit cell. This would be confusing, so the choice is to assign the atom to only one of the two equivalent positions. This is not done for the density that is instead cut.
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