Clarification on special_pair.LJ interaction overlap with non-bonded potentials and energy assignment

[Boran-Zhao]

Hello HOOMD community,
I am setting up a simulation involving both standard non-bonded interactions and specific interactions between certain pairs within molecules using hoomd.md.special_pair.LJ. I have a couple of questions regarding how these interactions are handled, and I would appreciate some clarification.

Simulation Setup Context:
I am defining a standard non-bonded potential (e.g., using hoomd.md.pair.OPP) between particles of type 'A'. Let's say this is opp.params[('A', 'A')].
Within the same molecule, I also want to define a specific interaction between, for example, bead 1 (type A) and bead 10 (type A) using hoomd.md.special_pair.LJ.
For my specific research needs, I have modified the EvaluatorSpecialPairLJ.h source code to implement a 12-10 LJ potential instead of the standard 12-6 LJ for these special pairs (Compiled successfully).

My Questions:

Interaction Overlap and Exclusions:
When both a non-bonded A-A potential and a specific special_pair.LJ potential are defined for the pair (bead 1, bead 10), does the non-bonded potential still act between this specific pair? Or does the definition of a special pair interaction automatically exclude the non-bonded interaction between them? In other words, do I need to manually configure neighbor list exclusions (e.g., using hoomd.md.nlist.Cell's exclusions parameter based on molecule topology or type pairs) to prevent the non-bonded A-A potential from acting on pairs that also have a special_pair.LJ interaction?
Potential Energy Assignment:
I noticed the documentation for special pair forces mentions: "Special pair force classes assign 1/2 of the potential energy to each of the particles in the bond group."
When I looked at the source code , I didn't immediately see an explicit factor of 0.5 being applied in the potential energy calculation itself. Could you clarify the term "bond group" in this context? Does it refer only to pairs defined via hoomd.md.bond, or does it broadly include pairs defined using hoomd.md.special_pair as well?

Thank you very much for your time and any insights you can provide!

[Boran-Zhao]

I may have found the answer to part of the question. This command can be used to remove the non-bonded potential between special pairs:
hoomd.md.nlist.Cell(buffer, exclusions=(''special_pair''))

[joaander]

Yes, exclusions=("special_pair") is the correct solution.

The comment

Special pair force classes assign 1/2 of the potential energy to each of the particles in the bond group

answers a different question. The special pair energy is only physically defined as the sum over all pairwise terms. However, HOOMD-blue stores the sum decomposed into per-particle elements. The comment you quote is stating the specific decomposition chosen. It would be equally valid to assign the total pair energy to a single particle, in the particle with the lower tag of the pair, or many other possibilities.