SCGO Documentation

SCGO: Simple Cluster Global Optimization

Global optimization of atomic clusters with ASE: Basin Hopping, Genetic Algorithms, NEB transition-state search, and MLIPs (MACE, UMA, UPET).

See Quick Start to get started.

Contents

Getting Started

• Installation
  • Prerequisites
  • PyPI
  • From source
  • Parallel jobs and HPC
  • 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
• Database access
  • get_global_cache()
  • close_data_connection()
  • get_connection()
  • DatabaseSetupError
  • DatabaseMigrationError
  • setup_database()
  • extract_minima_from_database_file()
  • extract_transition_states_from_database_file()
  • load_previous_run_results()
  • load_reference_structures()
  • list_discovered_db_paths_with_run()
  • mark_final_minima_in_db()
  • persist_provenance()
  • SCGODatabaseManager
  • database_transaction()
  • stamp_scgo_database()
  • add_metadata()
  • get_metadata()
  • update_metadata()
  • filter_by_metadata()
  • RetryConfig
  • database_retry()
  • retry_transaction()
  • retry_with_backoff()
  • get_registry()
  • clear_registry_cache()
• Exceptions
  • SCGOError
  • SCGOValidationError
  • SCGOConfigurationError
  • SCGORuntimeError
  • SCGODatabaseError
  • SCGONotImplementedError
  • SCGOFileError
• 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
  • Preset Functions
  • Preset effects (vs defaults)
  • Parameter reference
  • Available Models
  • Usage Examples
  • Module Reference
• System Types
  • AdsorbateDefinition
  • CalculatorKwargs
  • OptimizerSlotParams
  • GLOptimizerParams
  • TSParams
  • SystemConfig
  • SystemPolicy
  • get_system_policy()
  • resolve_structure_mic()
  • resolve_neb_mic()
  • resolve_connectivity_factor()
  • validate_system_type_settings()
  • uses_surface()
  • validate_mobile_symbols_match_adsorbate_definition()
  • validate_structure_for_system_type()
  • resolve_mobile_composition()
  • extract_adsorbate_definition_from_params()
  • resolve_adsorbate_run_composition()
  • 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
• Utilities
  • Parameter resolution
  • Config aliases
  • Combine atoms
  • Logging
  • Phase logging
  • Run directories and metadata
  • Timing JSON
  • Output path helpers

Indices and tables

• Index

• Module Index

• Search Page