Dear Lammps-users,
I'm trying to create a set of "molecules" (actually patchy colloids) that each contain two atom types through the "molecule" command. I list these two atom types as type 1 and type 2 in the molecule definition file. However, when I try to create the molecule using the create_atoms mol command, I get the error message "Invalid atom type in create_atoms mol command", unless I define my simulation box with 3 (rather than 2) atom types. My two atom types will then be assigned type 2 and 3, while type 1 will be carried around as "ghost atoms", which are actually not present in the simulation but still requires to be fully defined with pair styles etc, so it's a bit annoying although not prohibitive. I've tried solving it using the "offset" keyword (by setting this to 0), but with no success.
I assume this is mostly me not understanding properly how atom/molecule types are sorted in LAMMPS, but could someone tell me quickly if there's a simple way around this? Thank you!
Kind regards,
Joakim Stenhammar