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
directions.
I'd appreciate any ideas on what I need to change in my input file (below).
Thanks,
Vanessa
Input file: