Extra atom type when using molecule command?

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

Start your command with “create_atoms 0 …”.
It is explained here: http://lammps.sandia.gov/doc/create_atoms.html


Indeed, thanks a lot! And sorry for missing it in the manual…

Best wishes,