QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: jeong9090 on January 25, 2018, 18:59

Title: Export a problem of grpahene structure
Post by: jeong9090 on January 25, 2018, 18:59

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

Title: Re: Export a problem of grpahene structure
Post by: Petr Khomyakov on January 26, 2018, 11:41

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.   

Title: Re: Export a problem of grpahene structure
Post by: jeong9090 on January 26, 2018, 17:01

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

Title: Re: Export a problem of grpahene structure
Post by: Petr Khomyakov on January 29, 2018, 14:57

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. :-) 

Title: Re: Export a problem of grpahene structure
Post by: jeong9090 on January 29, 2018, 21:30

Thanks Petr Khomyakov