reactive-md

Reactive Molecular Dynamics

Description

This skill covers reactive molecular dynamics (reactive MD) using LAMMPS with the ReaxFF and COMB force fields: force-field selection and parameter provenance, charge equilibration (QEq) setup and diagnostics, timestep and thermostat selection for reactive systems, thermal protocols for reaction sampling, reaction event detection and postprocessing, validation of reactive trajectories against DFT, and coupling reactive MD to active-learning ML potential workflows. Invoke this skill when bond-breaking or bond-forming chemistry must be modeled explicitly — combustion, oxidation, pyrolysis, stress corrosion cracking, catalyst surface chemistry, or shock-induced reactions — and a fixed-topology force field is physically inappropriate.

Domain Context

Reactive MD differs from classical fixed-topology MD in one fundamental respect: the connectivity of the bonding network is not fixed at the start of the simulation but emerges from the interatomic potential as atoms approach or recede. This requires a potential energy function that varies continuously from a bonded to a non-bonded description as a function of local geometry.

ReaxFF (reactive force field) achieves this through a bond-order formalism. The key physical approximations are:

• Bond order: Each pair interaction carries a continuous bond order that depends on the interatomic distance and the local coordination environment. The bond order BO_ij decays smoothly from 1 (full bond) to 0 (no bond) as the interatomic distance increases. Bond order is not a quantum-mechanical quantity — it is a scalar empirical function parameterized to reproduce DFT bond-dissociation curves and reaction barriers.
• Charge equilibration (QEq): At each timestep, atomic partial charges are self-consistently minimized by the electronegativity equalization principle (Rappé & Goddard, 1991). Every atom's charge responds to its instantaneous bonding environment. QEq adds a per-timestep iterative solver that dominates the computational cost of ReaxFF and can fail to converge for systems with large charge separation.
• Coupled energy terms: Bond energy, overcoordination penalty, undercoordination energy, valence angle energy, torsion energy, and van der Waals and Coulomb interactions are all functions of bond order. These terms are globally coupled through a single parameter file (ffield.reax). Partial substitution of parameters from different publications into one parameter file is physically invalid — all ReaxFF parameters for all elements in the system must come from the same source and fitting procedure.
• Transferability limits: A ReaxFF parameterization is fitted to a specific set of elements and a specific set of reference reactions, geometries, and bond energies. The parameterization domain is not universal. Using ReaxFF outside the element set or chemistry it was fitted for — even for elements present in the parameter file — is extrapolation with unbounded errors.