PyExtal documentation

PyExtal is a Python package for simulating and refining convergent electron beam diffraction and large angle rocking beam eletron diffraction patterns. check out the GitHub repository.

Note

This is a work in progress. The documentation is not complete yet.

Contents:

• Introduction
  • Convergent Beam Electron Diffraction (CBED)
  • Large Angle Rocking Beam Electron Diffraction (LARBED)
  • Bloch Wave Simulation
  • Crystal Structure and Structure Factor Refinement
  • PyExtal-JAX Optimization Engine
  • Citations
• Getting started with PyExtal
  • What you need
  • Installation
  • FAQ
• Package Architecture
  • Bloch Wave Simulation Engine
  • Interface for Optimization and Analysis
  • Basic Workflow
  • detail explaination of the workflow
• Simulation
  • CBED simulation
  • LARBED simulation
  • Number of cores
  • Adjusting structure factors
  • Aperture modes
  • Sample tilt
  • Complete LARBED example
• Superspace: incommensurate crystallography in (3+d) dimensions
  • Modules
  • Rank: how many dimensions the structure actually needs
  • Satellite order is not sum |m|
  • The structure factor
  • Dynamical calculations: the commensurate approximant
  • The 1T-TaS2 model
  • Modulated structures inside the Bloch engine
  • The commensurate phase
  • Diffraction patterns as images
  • Limits
  • Reference
• PyExtal-JAX: Gradient-Based Refinement
  • Complete Workflow
  • Stage 1: Pre-refinement
  • Stage 2: JAX Refinement
  • HDF5 File Layout
  • OptConfig Parameter Reference
  • Batching strategies
  • Saving and loading OptConfig
• Simulation Engine
  • Number of cores
  • How the eigensolver works
  • Performance
• Examples
  • PyExtal example for CBED refinement
  • Structure Factor refinement of Si LARBED 111 systematic row
  • High voltage calibration example
  • Pre-refinement for PyExtal-JAX
  • In the repository
• Bloch Engine API
• API Reference
  • pyextal