name: defects-reactions
description: Defects and Reactions (13 sub-skills: activation-relaxation-technique, adsorption-energy, configuration-coordinate, defect-thermodynamics, interstitial-defect, migration-barrier, neb-transition-state, point-defect, reaction-pathway,
Defects and Reactions
Overview
This skill group covers calculations involving crystallographic defects and chemical reaction pathways in solid-state materials. Two main approaches are available:
- MACE (via ASE) -- Fast ML-potential-based calculations. Good for rapid screening of defect formation energies, NEB barriers, and adsorption energies. Seconds to minutes per calculation on typical supercells.
- Quantum ESPRESSO (QE) -- Full DFT. Required for publication-quality energetics, charged defect calculations, electronic structure at defect sites, and accurate chemical bonding at surfaces.
Both approaches follow workflows inspired by atomate2's defect, NEB, and adsorption flows: create the defect/surface structure, relax, compute relevant energies, and post-process thermodynamic quantities.
Sub-Skills
| Sub-Skill | Directory | Description |
|---|
| Activation Relaxation Technique | activation-relaxation-technique/ | ART nouveau saddle point searching: discover transition states and activation energies without knowing the final state, systematic event catalogs for KMC |
| Point Defects | point-defect/ | Vacancy and interstitial creation, supercell convergence, formation energy with chemical potential references, finite-size corrections for charged defects |
| NEB Transition States | neb-transition-state/ | Nudged Elastic Band calculations for migration barriers and transition states using ASE+MACE or QE neb.x |
| Surface Adsorption | surface-adsorption/ | Slab generation, adsorption site identification, adsorption energy calculations, work function |
| Configuration Coordinate Diagram | configuration-coordinate/ | CCD for non-radiative transitions: DeltaQ, ZPL, Franck-Condon shifts, Huang-Rhys factor, classical barrier for carrier capture |
Method Decision Guide
What do you need?
Defect formation energy (neutral)?
Quick screening --> ASE + MACE (point-defect/)
Publication quality --> QE DFT (point-defect/)
Charged defect formation energy / transition levels?
--> QE DFT required (point-defect/, need electrostatic corrections)
Migration barrier / reaction pathway?
Quick estimate --> ASE + MACE NEB (neb-transition-state/)
Accurate barrier --> QE NEB (neb-transition-state/)
Explore unknown transitions / don't know the final state?
--> ART nouveau (activation-relaxation-technique/)
Build KMC event catalog --> ART with systematic sampling (activation-relaxation-technique/)
Adsorption energy / surface chemistry?
Quick screening --> ASE + MACE (surface-adsorption/)
Publication quality --> QE DFT with slab model (surface-adsorption/)
Non-radiative recombination / luminescence quenching / carrier capture?
Structural screening (DeltaQ) --> ASE + MACE (configuration-coordinate/)
Publication quality (ZPL, barrier, Huang-Rhys) --> QE DFT (configuration-coordinate/)
Common Prerequisites
- Structure: Start from a CIF, POSCAR, or Materials Project query. Use pymatgen for structure manipulation (supercells, defect creation, slab generation).
- Pseudopotentials: QE calculations need pseudopotential files (SSSP library recommended).
- Python packages: pymatgen, ASE, mace-torch, numpy, scipy, matplotlib are pre-installed. Install extras with
pip install pymatgen-analysis-defects pymatgen-diffusion as needed.
- Supercell sizes: Defect and NEB calculations require supercells large enough to minimize periodic image interactions. Typical minimum: 3x3x3 for cubic, or at least 10 A between periodic images.
