chem-ts-optimization
OfficialOptimize molecular TS and verify saddle.
Education & Research#chemistry#mlip#transition state#saddle point#vibrational analysis#molecular optimization#sella
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill optimizes a molecular transition-state (TS) geometry from an initial guess and validates that it is a first-order saddle point using vibrational analysis.
Core Features & Use Cases
- TS optimization for non-periodic molecules: Runs Sella-based TS optimization followed by a finite-difference vibrational frequency check.
- First-order saddle validation: Classifies the optimized structure by counting imaginary modes below a configurable cm^-1 cutoff.
- Backend-ready execution: Supports MLIP backends for scoring/optimization (MACE or FAIRChem/UMA) and writes a complete results bundle.
Quick Start
Use the chem-ts-optimization Skill to optimize a TS guess for a non-periodic molecule and confirm first-order saddle character by generating ts_optimized.xyz and ts_optimization_results.json from a provided ts_guess.xyz file.
Dependency Matrix
Required Modules
None requiredComponents
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: chem-ts-optimization Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#chem-ts-optimization Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.