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.
1---2name: defects-reactions3description: This skill group covers calculations involving crystallographic defects and chemical reaction pathways in solid-state materials. Two main approaches are available:4---5
6---
7name: defects-reactions
8description: 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,
9---
10
11# Defects and Reactions
12
13## Overview
14
15This skill group covers calculations involving crystallographic defects and chemical reaction pathways in solid-state materials. Two main approaches are available:
16
171. **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.
182. **Quantum ESPRESSO (QE)** -- Full DFT. Required for publication-quality energetics, charged defect calculations, electronic structure at defect sites, and accurate chemical bonding at surfaces.
19
20Both 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.
21
22## Sub-Skills
23
24| Sub-Skill | Directory | Description |
25|---|---|---|
26| 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 |
27| Point Defects | `point-defect/` | Vacancy and interstitial creation, supercell convergence, formation energy with chemical potential references, finite-size corrections for charged defects |
28| NEB Transition States | `neb-transition-state/` | Nudged Elastic Band calculations for migration barriers and transition states using ASE+MACE or QE neb.x |
29| Surface Adsorption | `surface-adsorption/` | Slab generation, adsorption site identification, adsorption energy calculations, work function |
30| Configuration Coordinate Diagram | `configuration-coordinate/` | CCD for non-radiative transitions: DeltaQ, ZPL, Franck-Condon shifts, Huang-Rhys factor, classical barrier for carrier capture |
31
32## Method Decision Guide
33
34```
35What do you need?
36
37Defect formation energy (neutral)?
38 Quick screening --> ASE + MACE (point-defect/)
39 Publication quality --> QE DFT (point-defect/)
40
41Charged defect formation energy / transition levels?
42 --> QE DFT required (point-defect/, need electrostatic corrections)
43
44Migration barrier / reaction pathway?
45 Quick estimate --> ASE + MACE NEB (neb-transition-state/)
46 Accurate barrier --> QE NEB (neb-transition-state/)
47
48Explore unknown transitions / don't know the final state?
49 --> ART nouveau (activation-relaxation-technique/)
50 Build KMC event catalog --> ART with systematic sampling (activation-relaxation-technique/)
51
52Adsorption energy / surface chemistry?
53 Quick screening --> ASE + MACE (surface-adsorption/)
54 Publication quality --> QE DFT with slab model (surface-adsorption/)
55
56Non-radiative recombination / luminescence quenching / carrier capture?
57 Structural screening (DeltaQ) --> ASE + MACE (configuration-coordinate/)
58 Publication quality (ZPL, barrier, Huang-Rhys) --> QE DFT (configuration-coordinate/)
59```
60
61## Common Prerequisites
62
63- **Structure**: Start from a CIF, POSCAR, or Materials Project query. Use pymatgen for structure manipulation (supercells, defect creation, slab generation).
64- **Pseudopotentials**: QE calculations need pseudopotential files (SSSP library recommended).
65- **Python packages**: pymatgen, ASE, mace-torch, numpy, scipy, matplotlib are pre-installed. Install extras with `pip install pymatgen-analysis-defects pymatgen-diffusion` as needed.
66- **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.
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