chem-vibration
OfficialCompute molecular vibrations with MLIPs.
System Documentation
What problem does it solve?
This Skill computes vibrational frequencies, normal modes, zero-point energy, and IR-relevant outputs for non-periodic molecules and clusters using Machine Learning Interatomic Potentials (MLIPs), avoiding manual vibrational analysis.
Core Features & Use Cases
- Harmonic vibration analysis for finite systems: Calculates vibrational mode frequencies from the (mass-weighted) Hessian in the harmonic approximation.
- Zero-point energy (ZPE): Outputs ZPE in eV (and meV) derived from the vibrational spectrum.
- Mode classification + trajectories: Separates real vibrational modes from translation/rotation-like and (near) imaginary modes, and writes per-mode trajectory files for visualization.
- Practical MLIP workflows: Works with MLIP wrappers (e.g., MACE/MatGL/FairChem wrappers) and optionally relaxes structures before evaluating vibrations.
Typical use case: compute and compare the vibrational spectrum of a small molecule (e.g., H2O) against experimental reference values, including identifying spurious low-frequency/imaginary modes from incomplete relaxation.
Quick Start
Use the chem-vibration skill to analyze water by running the vibrations script for H2O with an OMAT-trained MACE model.
Dependency Matrix
Required Modules
Components
💻 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-vibration Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#chem-vibration 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.