AtomVoxelizer

AtomVoxelizer builds periodic voxel grids around atomistic structures.

Start with Installation and Quickstart Tutorial if you are new to the package. Use Concepts for the grid model, masks, backends, and field grids. Use Analysis for connected volumes, surface areas, and probe-accessible pore volume.

Contents

• Installation
  • Install From PyPI
  • Install From Source
  • Optional Feature Map
• Quickstart Tutorial
  • Install Tutorial Dependencies
  • Build A Cube-Like WulffPack Nanoparticle
  • Build The Voxel Surface Mask
  • Sample Trial Sites
  • Minimal MCMD Loop
  • Run The Example
• Usage
  • Grid Dtype
  • Sphere Masks
  • Coordination-Surface Masks
  • Examples
• Concepts
  • How Sphere Painting Works
  • Sphere Operations And Masks
  • Grid Values And Dtypes
  • Backends
  • Field Voxel Grids
  • Periodic Surfaces
  • Dtype Benchmark Note
• Analysis
  • Connected Volumes
  • Scalar Distance Surfaces
  • Zeolite Pore Volume And Surface Area
  • Probe-Center Accessibility
  • BEA Probe Comparison To PoreBlazer
• Examples
  • Zeolite Voxelization
  • Zeolite Geometric Pore Analysis
  • Probe Pore Volume
  • Finite Wulff Distance Surface
  • Periodic Pt(211) Distance Surface
  • Voxel-Guided CO MCMD
  • Benchmarks
• Contributing
  • Project Links
  • Reporting Issues
  • Development Setup
  • Contribution Guidelines
  • Merge Requests
  • Contributors
  • Release Checklist
• Citation
  • Related Work
• API Reference
  • VoxelGrid
  • VoxelGridNumPy
  • Experimental Field Grids
  • Optional Backends
  • Analysis