I am having trouble describing partial occupancy in the input file. One of the site is occupied by two atoms with (50% occupancy). when I generate input file, the other atom is getting ignored. how to describe this in the input file?
For this just create a conventional cell. For example Conventional cell of Silicon contain 8 atoms. So for this now you are having 8 atomic positions.
and If you want to add some atom other than Silicon then just add that to the , respective Silicon atom.
For example if I want 50% mixing Of carbon in Si then it can be achieved even by just replacing half of the silicon atoms with carbon.
example: Here I am taking unit cell of silicon
Si 0 0 0
Si 0.25 0.25 0.25
now if I want to mix 50% carbon then I will replace one of silicon atom with carbon and it will look like
Si 0 0 0
C 0.25 0.25 0.25
A single atom having two different chemical species in the same location obviously makes no physical sense. Hence, you need to create a supercell consisting of 2 unit cells, one of which has the first atom-type in the specified position and the other unit cell has the second atom-type in the symmetrically equivalent position. However, this is still an approximation because in nature the crystal's occupancy is typically random (50% of the time atom-type 1 and 50% atom-type 2) but in the simulation case, due to periodic boundaries, it is switching between atom-type 1 and atom-type 2 in an alternating fashion (ABABAB... instead of random). Another artifact of this is that you get "sheets" of unit cells with only atom-type 1 followed by sheets of unit cells with only atom-type 2. This is because you doubled the unit cell in one crystalline direction but not in the other two directions.
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