Tutorials

Literature

• YouTube Overview (14 mins): doped: Python package for charged defect supercell calculations

  • B站 (Bilibili), 有中文字幕: 建模缺陷超胞与计算的Python软件包：doped

• Code Paper: S. R. Kavanagh et al. doped: Python toolkit for robust and repeatable charged defect supercell calculations. Journal of Open Source Software 9 (96), 6433, 2024

• General Defect Modelling Tutorial Video: Modelling Point Defects in Semiconductors with VASP

  • B站 (Bilibili), 有中文字幕: 使用VASP理解与计算半导体中的缺陷

• ShakeNBreak Documentation: ShakeNBreak documentation

• Guidelines for Defect Simulations: A. G. Squires et al. Guidelines for robust and reproducible point defect simulations in crystals Nature Reviews Materials 2026

See the Literature section on the main page for further recommended literature on defect simulations.

Code Tutorials

The typical defect calculation, parsing and analysis workflow using doped is exemplified through the tutorials:

• Generating defects with doped
  • Defect Generation
  • Determining the ground-state defect structures
  • Prepare VASP calculation files with doped
  • Chemical Potentials
• Defect Calculation Parsing
  • Example: CdTe Defect Calculations
  • Defect Formation Energy / Transition Level Diagrams
  • Analysing Finite-Size Charge Corrections
  • Further Defect Analysis
  • Open Science and Reproducibility
• Defect Thermodynamics & Doping
  • Dopability Limits
  • Doping Calculations
  • Carrier / Defect concentrations vs (μ, T)
  • CdTe: Defect Concentrations vs μ
  • Notes
• Competing Phases
  • Generating input files
  • Parsing Competing Phases
  • Summarising & Saving Results for Publication
  • Save to JSON
• Advanced Defect Analysis
  • Defect-Induced Site Displacements (Strain)
  • Eigenvalue / Electronic Structure Analysis
  • Custom Supercell Generation
  • Point Symmetry Analysis
  • Further Local Structure Analysis
• Advanced Defect/Carrier Concentration Analysis
  • CdTe: Defect Concentrations
  • Effective dopant concentrations
  • Custom Concentration/Equilibration Constraints
  • Cu₂SiSe₃: 2D Chemical Potential Scans
  • Complex Quinary: Na₂FePO₄F
• Plot Customisation with doped
  • Defect Formation Energy Plotting
  • Chemical Potential Heatmaps
  • Finite-Size Charge Correction Plots
  • Site Displacement / Strain Plots
  • Eigenvalue Plots
• Full Defect Workflow Example (w/GGA)
  • 1. Parse host structure
  • 2. Relax bulk structure
  • 3. Generate defects
  • 4. Determining the ground-state defect structures
  • 5. Prepare VASP calculation files with doped
  • 6. Chemical Potentials
  • 7. Dielectric constant
  • 8. Defect analysis
• NEB / CC Diagram Path Generation
  • CCD for Point Defects
  • NEB Between Crystal Polymorphs