help with lattice and region commands to create larger crystal lattice

Hello Mail List Denizens,

I seem to be having some trouble using the lattice and region commands properly.

Specifically, I'm trying to use the lattice command to help generate
an alpha quartz structure. Initially, I had verified that the lattice
input parameters were correct by visualizing the structure of a single
unit cell generated by LAMMPS. The single unit cell structure looked
exactly as it should- both atom types are located in their correct
positions within the unit cell. However, if I expand the number of
unit cells in the alpha quartz lattice (say to 10 unit cells), the
resulting structure does not look correct along the y direction but
looks fine in both the x and z directions. I initially assumed that I
needed to shift the unit cell in the y direction (for the region
command), but after having tried this (with many permutations), the
lattice in the y direction never looked correct. I've re-checked that
the lattice spacings in the input file are correct, which I also
assume is the case because the lattice looks good in both the x and z

I'd appreciate any ideas on what I need to change in my input file (below).


Input file:

I suggest you remove the spacing option from
the lattice command, and simply specify the
prism dimensions directly to start with. Once
you have that correct, you can simply infer
good spacings. I also don't see how a prism
xy value of -0.5 creates a volume that is
consistent with the shape of your unit cell.
This means that when you tile the prism with
atoms, you will likely not get consistency
across periodic boundaries.