I Am still confused about the periodic boundary conditions. I can add them
to the file? How can I do this? I put in:

write_once("Boundary") {
    0 13*2.4595121467478 xlo xhi
    14*2.13 ylo yhi

Unfortunately, this won't work. You have to actually do the
calculation yourself. (Neither moltemplate, nor LAMMPS' read_data
command attempts to understand what *,/,+,- means.) In this example,
you need:

write_once("Data Boundary") {
   0 31.973657907721396 xlo xhi
   0 29.82 ylo yhi

(Note: It's "Data Boundary", not "Boundary")

(I apologize for not choosing a more specific title for this post.)