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

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
• 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
• Plot Customisation with doped
  • Defect Formation Energy Plotting
  • 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