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chem-vibration

Calculate vibrational frequencies and zero-point energy for molecules using MLIP force models.

144|21|Updated Jan 8, 2026
Search Tags:#ase#mlip#vibrational analysis#molecular vibrations#zero-point energy#normal modes#finite-difference hessian
One-click install
npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-vibration
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: chem-vibration
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-vibration
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-vibration

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ase, numpy, json, logging, argparse, and includes scripts (resource) components.

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.

Frequently Asked Questions about chem-vibration

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I calculate molecular vibrational frequencies using a machine learning potential?▼

Molecular vibrational frequencies are calculated by evaluating a finite-difference Hessian with an ASE-compatible MLIP wrapper. This approach computes mass-weighted normal modes and zero-point energy for finite clusters in the harmonic approximation without manual analysis.

What is the best way to compute zero-point energy for non-periodic molecular systems?▼

Zero-point energy for non-periodic molecular systems is computed from the vibrational spectrum derived via finite-difference Hessian evaluation. The analysis outputs ZPE directly in eV and meV after optionally relaxing the structure with LBFGS.

Why does my vibrational analysis show spurious imaginary modes for a small molecule?▼

Spurious imaginary modes in vibrational analysis often result from incomplete structural relaxation. This Skill identifies and flags near-imaginary modes and separates them from real vibrational modes and translation or rotation-like modes in finite systems.

Can I use an ASE MLIP wrapper to run vibrational analysis on molecular clusters?▼

Yes, you can use an ASE-compatible MLIP wrapper, such as MACE or FairChem wrappers, to run vibrational analysis. The Skill targets non-periodic molecular and cluster structures, evaluating forces and writing per-mode trajectory files for visualization.

How do I identify translation and rotation modes when computing normal modes of a molecule?▼

When computing normal modes of a molecule, translation and rotation modes are identified and separated from real vibrational modes during the harmonic analysis. The Skill classifies these modes automatically and flags any spurious low-frequency or imaginary outputs.

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