Summary
Synthesis target construction explicitly supports mol_index that covers only a subset of the system, but multi-round connectivity handling crashes when an unselected spectator is close enough to a selected atom.
Reproduction
A three-hydrogen system with mol_index=((0,), (1,)), atom 2 as a nearby spectator, and Para(max_step=0) fails during initial connectivity construction:
detect_intermolecular_bonds() iterates over all atoms and can create a bond containing the spectator. _build_connectivity() creates its union-find parent map only from atoms listed in mol_index, then attempts to union the spectator index.
Relevant code is in rtipmd/jax/src/rtip_jax/workflows/md.py around lines 591-630.
Impact
A supported synthesis subset with environment or spectator atoms can crash before the first MD round.
Expected behavior
Either limit inter-molecular bond detection to selected atoms or explicitly model spectators in the connectivity graph. Add a regression test with a non-selected nearby atom.
Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh
Summary
Synthesis target construction explicitly supports
mol_indexthat covers only a subset of the system, but multi-round connectivity handling crashes when an unselected spectator is close enough to a selected atom.Reproduction
A three-hydrogen system with
mol_index=((0,), (1,)), atom 2 as a nearby spectator, andPara(max_step=0)fails during initial connectivity construction:detect_intermolecular_bonds()iterates over all atoms and can create a bond containing the spectator._build_connectivity()creates its union-find parent map only from atoms listed inmol_index, then attempts to union the spectator index.Relevant code is in
rtipmd/jax/src/rtip_jax/workflows/md.pyaround lines 591-630.Impact
A supported synthesis subset with environment or spectator atoms can crash before the first MD round.
Expected behavior
Either limit inter-molecular bond detection to selected atoms or explicitly model spectators in the connectivity graph. Add a regression test with a non-selected nearby atom.
Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh