while developing a program involving rigid molecules and polymerization,
I noticed that
"neigh_modify exclude molecule/intra all"
prevents the formation of bonds (using "fix bond/create") between single atoms.
I am using lammps 11Aug17 as a library.
This is consistent with the documentation, as non bonded atoms share the same molecule id = 0. However, this is not consistent with the use of a molecule id = 0 as a flag to identify single atoms, not actual molecules, as in others lammps commands.
I am adding an example file; if "neigh_modify exclude molecule/intra all" is not
commented out, then no bonds are created.
I would suggest to change this behavior, or to add a note in the documentation.
Minor and unrelated:
In the documentation of create_bonds many, rmax is defined as the "minimum" distance, while it should be the "maximum" one.