How to mix the potential from reaxff and a bond_style

LAMMPS LAMMPS General Discussion
,
1

Dear LAMMPS users,
I would like to simulate the dynamics of a few organic molecules (methanol, CH3OH) on a periodic metal slab surface (e.g. Cu(111)). The interactions between all the pairs of atoms are described by the reaxff method (pair_style reaxff).

I don’t want to break the identity of organic molecules during the simulation ( I would like to see how the molecules assemble on the metal surface), hence I would like to add an extra harmonic interaction between pairs of the atoms in the adsorbed molecules.

It seems that the “pair_style hybrid/overlay” is very close to what I need, However, it is not clear for me how to set up the input properly. Can I set up the bond infomation only for the adsorbed molecules without metal slab and without angle informations? will lammps allow me to do that?

Is there any working example that I can learn or is there a simpler method to set up the input for what I need?
Thank you very much in advance.
Best,
Geng

2

This is not as simple as you think.

You could add a bond style and add bonds to the topology, but that requires atom style full instead of charge. Also adding bonds to your topology would also trigger that all pairs with a bond would become an excluded pair which will break ReaxFF unless you turn that off with the special_bonds command. In addition, there is no way to avoid double counting the interactions with bonds added, if you use the custom special_bonds command.