Hi all,
My name is Marcos and I am a new user to Avogadro. I have just created a
simple graphene structure (unit cell, 2 atoms) in order to start using the
code. Took me a bit of trial and error, but now I think I got the hang of
it. The main reason I started using Avogadro is because I had read in the
LAMMPS website that it could create input files for it.
I’ve been searching the mailing list for posts on the creation of input
files for LAMMPS, and I saw a post from 2014 by Prof. Hutchison saying that
feedback from users would be useful in improving the LAMMPS input file
generator. Here are my 10 cents on the subject 
I am also a new user of LAMMPS, and I have to say: LAMMPS is a pretty
cryptical code to work with. I’m continuously biting the dust with it,
mostly because of one crucial part: coordinate and cell generation. It’s
really hard to create coordinates and cell specifications in LAMMPS for
non-cubical cells.
Graphene is my workhorse, and the primitive cell has two vectors at 120
degrees with each other. While the cell vectors are not difficult to
specify in LAMMPS, my difficulty lies in creating the atoms in the cell. I
am especially confused as to how to do what I really need, which is to
place two hydrogen atoms on top of the carbons (generating graphane).
So, for me, as a new user, a great thing to be implemented in Avogadro
would be inclusion of cell and atomic coordinate specifications in the
generated input file - something I was quite disappointed to find out
doesn’t exist in Avogadro (at least in version 1.1.1 installed as a debian
package in the latest Xubuntu distro). As far as I could tell, Abinit file
generation does generate the coordinates.
Best regards,
Marcos
Prof. Dr. Marcos Verissimo Alves
Prof. Adjunto II, Curso de Física Computacional
Instituto de Ciências Exatas, Polo Universitário de Volta Redonda
Universidade Federal Fluminense
Volta Redonda - RJ, Brasil