Hi there,
Couldn’t find the slab building option in Avogadro2. I have installed the Avogadro using the instructions at http://wiki.openchemistry.org/Build.
Any help is appreciated.
The default 1.1.1 version on Ubuntu has the option but gives no atoms after building!
At the moment, Avogadro2 doesn’t have slab building - there’s a better solution coming soon.
If you’re having problems with 1.x versions, it would help to know the type of slab you’re trying to build (e.g., what crystal structure, what Miller plane, etc.)
At this moment I was trying to get the surface of ZnO (HCP) with the Miller indices (10-10). With older versions, after transformation, all the atoms are being deleted from the cell.
If yes, I have tried to follow it yesterday and when I was trying with 4 indices I got the below error (which I am not getting when using 3 indices). It is quite possible that I am doing something wrong (as I am using pymatgen for the first time) but I followed the tutorial to my best!
In [1]: from pymatgen.core.surface import SlabGenerator, generate_all_slabs, Structure, Lattice; import os
In [2]: lattice = Lattice.hexagonal(3.31700,5.31400); zno = Structure(lattice, [“Zn”, “O”],[[0.66667,0.33333,0.0],[0.66667,0.33333,0.345]])
In [3]: slabgen = SlabGenerator(zno,(1,0,-1,0), 10, 10)
However, I don’t think there is an explanation which will help you to code.
As far as I know, this paper can help you with coding (pyMatGen cited this paper and it seems to me that the authors of the paper have coded the procedure in pyMatGen). They claim that their procedure will always work.