chem-neb-barrier

Calculate NEB activation energy barriers for atomic migration and reactions.

144|21|Updated Jan 8, 2026

Search Tags:#ase #neb #mlip #materials modeling #activation barrier #transition state #chemistry computation

Ready to run

npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-neb-barrier

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: chem-neb-barrier
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-neb-barrier
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-neb-barrier

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires matplotlib, ase, numpy, pymatgen, itertools, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps you calculate activation energy barriers for atomic migration or chemical reaction transition states without manually assembling and tuning an NEB workflow.

Core Features & Use Cases

NEB barrier calculation for endpoints: Builds an NEB path between a start and end structure and optimizes intermediate images.
Periodic and non-periodic support: Auto-detects periodic boundary conditions and outputs CIF for periodic systems or XYZ for non-periodic molecules.
MLIP-driven energetics: Uses an MLIP model (MACE, FairChem, or MatGL) to compute forces/energies along the reaction pathway.
Barrier visualization and export: Produces a barrier plot, trajectory, optimized path structures, and a JSON summary including barrier energy.
Practical use cases: Solid-state diffusion barriers in crystalline materials and molecular reaction transition-state barriers.

Quick Start

Ask the Skill to compute the NEB activation barrier between start.cif and end.cif using an MLIP model (for example MACE-OMAT-0-small) and save the results to output/.

Frequently Asked Questions about chem-neb-barrier

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

FAQPage Schema

How do I calculate activation energy barriers using NEB with an MLIP force field?▼

To calculate activation energy barriers, build a Nudged Elastic Band path between start and end structures, then optimize intermediate images using an MLIP calculator like MACE, FairChem, or MatGL to compute forces and energies.

Can I use the NEB method for both solid-state diffusion and molecular transition states?▼

Yes, the NEB method supports both periodic solid-state materials diffusion and non-periodic molecular transition-state barrier estimation by auto-detecting boundary conditions and exporting CIF or XYZ files accordingly.

What is the best way to automate transition state search without manually tuning NEB workflows?▼

Automate transition state search by providing initial and final structures to a script that automatically handles MLIP loading, periodicity detection, interpolation, and climbing-image optimization to output barrier plots and JSON summaries.

Does ASE NEBTools support interpolation methods like idpp for reaction pathway generation?▼

ASE NEBTools support configurable interpolation methods including linear and idpp to generate initial reaction pathways, alongside a climbing-image option to accurately locate the transition state saddle point.

What formats are needed for start and end structures to compute a chemical reaction barrier?▼

Start and end structures can be provided as files like CIF for periodic crystalline materials or XYZ for non-periodic molecules, which the system reads to build and optimize the intermediate migration pathway.

Why does my NEB barrier calculation require an MLIP model and what outputs should I expect?▼

An MLIP model is required to compute forces and energies along the Nudged Elastic Band path, producing outputs that include a barrier plot, trajectory, optimized path structures, and a JSON summary with the barrier energy.