Export a problem of grpahene structure

[jeong9090]

Hi,

I tried to export a graphene structure to LAMMPS format.

First, I made graphene unit cell from a database and made its supercell with 10x10.

When I tried to export this structure to LAMMPS format but there was an error like "LAMMPS Exporter can only handle cells with zero yx,zx,zy components.

I attached a file also.

How can I figure it out?

Thanks,

Jaeyoung Jeong

[Petr Khomyakov]

LAMMPS assumes a certain convention for lattice vectors that is different from that in ATK. You have to set the unit cell type to Unit Cell in Lattice Parameters in the Builder, and change the A lattice vector to (a,0,0), where a is the lattice vector of graphene, and a=2.4612 Angs is  ATK default. Then you repeat the unit cell to get the 10x10 supercell structure and save this structure in the LAMMPS format.   

[jeong9090]

Hi,
Thanks, Peter Khomyakov.

I have one more question.

When I set A lattice vector to (a,0,0), do I need to change in A row? or need to change B and C  also?

I changed in A lattice vector as a below-attached file. is this right?

Thanks,

Jaeyoujng

[Petr Khomyakov]

You did it right. But you may see it by looking at the structure in the Builder after the lattice vector transformation. For this simple system, it would also be instructive to do it on a piece of paper with a pencil, as it would give you a clear idea on how this type of lattice vector transformations/choice actually works. :-) 

[jeong9090]

Thanks Petr Khomyakov