chem-irc-verification

What problem does it solve?

This Skill verifies whether a saddle-point-optimized transition state (TS) correctly connects the intended reactant and product along the intrinsic reaction coordinate (IRC), avoiding false assumptions when endpoint geometries are misassigned or non-matching.

Core Features & Use Cases

• Forward/Reverse IRC from a TS: Runs IRC in both directions (forward and reverse) starting from the optimized TS for non-periodic molecules.
• Endpoint Connectivity + RMSD Matching: Checks endpoint-to-target assignment using both chemical connectivity graph equality and Kabsch-aligned RMSD against reactant/product targets.
• Optional Endpoint Relaxation: Optionally relaxes IRC endpoints before comparing them, improving robustness for borderline matches.

Use case: After optimizing a reactant, product, and TS geometry for an isomerization or rearrangement, use this Skill to confirm the TS truly connects the correct species rather than converging to the wrong basin.

Quick Start

Run the IRC verification on your optimized reactant, product, and TS by providing the files and selecting your MLIP backend and model, for example: use the script to compute forward and reverse IRC trajectories from ts_optimized.xyz and report whether the endpoints match reactant_optimized.xyz and product_optimized.xyz within the chosen RMSD threshold.