SCGO Documentation

SCGO: Simple Cluster Global Optimization

A compact toolkit for global optimization of atomic clusters using ASE, with Basin Hopping, Genetic Algorithms, NEB transition-state search, and MLIP support.

Key Features

• Basin Hopping and Genetic Algorithm global optimization with automatic algorithm selection by cluster size

• MLIP Support: MACE and UMA (fairchem) for GPU-accelerated optimization

• Surface Workflows: slab-supported clusters and adsorbates; hull-site fragment placement and tag-aware GA operators

• Transition State Search: NEB-based TS search with automated pair selection and PBC-aware endpoint alignment

• Flexible API: high-level runners and low-level control for custom workflows

• Reproducible initialization: composition-canonical atom ordering for multi-element GA runs

See Quick Start to get started.

Contents

Getting Started

• Installation
  • Prerequisites
  • PyPI (recommended)
  • Conda (development from source)
  • Editable install from source
  • Development Installation
  • Dependency Notes
  • Parallel jobs and output directories
  • HPC and shared filesystems
  • Publishing releases
• Quick Start
  • System Types
• All Parameters
  • Parameter resolution
  • GO Parameters
  • TS Parameters
  • Surface Config
  • Adsorbate Config
  • See Also
• Benchmarks
  • Dependencies
  • Output layout
  • Entry points
  • Pytest

API Reference

• API Reference
  • Main Functions
  • Output directories
  • Complete Examples
  • Utility Functions
  • Timing and Profiling
  • Module Reference
• Cluster initialization
  • Initialization modes
  • Atom ordering (multi-element GA)
  • Placement order and diversity
  • Reproducibility
  • Connectivity and steric checks
  • Module reference
• Surface workflows
  • Deposition and adsorbate initialization
• Cluster adsorbate placement
  • Configuration
  • Surface site discovery
  • Placement and hierarchical builds
  • Pre-GO feasibility checks
  • GA repositioning and rigid geometry
  • Radii and steric scoring
• Parameter Presets
  • Overview
• System Types
  • AdsorbateDefinition
  • SystemPolicy
  • get_system_policy()
  • resolve_connectivity_factor()
  • validate_system_type_settings()
  • uses_surface()
  • validate_mobile_symbols_match_adsorbate_definition()
  • validate_structure_for_system_type()
  • validate_composition_against_adsorbate()
  • validate_adsorbate_definition()
  • resolve_adsorbate_fragments()
  • normalize_adsorbates_input()
  • flatten_adsorbate_symbols()
  • combine_adsorbates_to_template()
  • build_adsorbate_definition_from_inputs()
  • Available System Types

Indices and tables

• Index

• Module Index

• Search Page