Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W A add_metadata() (in module scgo.database) adsorbate_definition (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.SystemConfig attribute) adsorbate_fragment_lengths (scgo.system_types.AdsorbateDefinition attribute) adsorbate_fragment_template (scgo.system_types.GLOptimizerParams attribute) adsorbate_move_scale (scgo.system_types.SystemPolicy attribute) adsorbate_symbols (scgo.system_types.AdsorbateDefinition attribute) AdsorbateDefinition (class in scgo.system_types) adsorption_energy() (in module scgo.surface) adsorption_height_max (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig property) (scgo.surface.config.SurfaceSystemConfig attribute) adsorption_height_min (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig property) (scgo.surface.config.SurfaceSystemConfig attribute) aggressive_burst_multiplier (scgo.system_types.OptimizerSlotParams attribute) allow_adsorbate_surface_detachment (scgo.system_types.GLOptimizerParams attribute) allow_cluster_fragmentation (scgo.system_types.GLOptimizerParams attribute) allow_composition_permutations (scgo.system_types.SystemPolicy attribute) anchor (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) B backoff_factor (scgo.database.RetryConfig attribute) batch_size (scgo.system_types.OptimizerSlotParams attribute) blmin_ratio (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) build_adsorbate_definition_from_inputs() (in module scgo.system_types) build_adsorbate_only_cluster() (in module scgo.cluster_adsorbate.hierarchical) build_blmin() (in module scgo.initialization.atomic_radii) build_blmin_from_zs() (in module scgo.initialization.atomic_radii) build_hierarchical_core_fragment_cluster() (in module scgo.cluster_adsorbate.hierarchical) build_one_element_compositions() (in module scgo.runner_api) build_run_timing_document() (in module scgo.utils.timing_report) build_timing_payload() (in module scgo.utils.timing_report) build_two_element_compositions() (in module scgo.runner_api) C calculator (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.TSParams attribute) calculator_kwargs (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.TSParams attribute) CalculatorKwargs (class in scgo.system_types) cell_margin (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) check_hessian (scgo.system_types.GLOptimizerParams attribute) clash_details (scgo.initialization.StructureDiagnostics attribute) cleanup_torch_cuda() (in module scgo.utils.run_helpers) clear_cache() (scgo.database.SCGODatabaseManager method) clear_registry_cache() (in module scgo.database) close() (scgo.database.SCGODatabaseManager method) close_data_connection() (in module scgo.database) closest_inter_component_distance (scgo.initialization.StructureDiagnostics attribute) cluster_adsorbate_config (scgo.system_types.GLOptimizerParams attribute) cluster_init_vacuum (scgo.surface.config.SurfaceSystemConfig attribute) ClusterAdsorbateConfig (class in scgo.cluster_adsorbate.config) combine_adsorbates_to_template() (in module scgo.system_types) combine_and_grow() (in module scgo.initialization) combine_seeds() (in module scgo.initialization) comparator_n_top (scgo.system_types.OptimizerSlotParams attribute) comparator_pair_cor_max (scgo.system_types.OptimizerSlotParams attribute) comparator_tol (scgo.system_types.OptimizerSlotParams attribute) comparator_use_mic (scgo.surface.config.SurfaceSystemConfig attribute) composition (scgo.utils.run_tracking.RunMetadata attribute) CompositionInput (in module scgo.runner_api) compute_cell_side() (in module scgo.initialization) compute_surface_site_candidates() (in module scgo.cluster_adsorbate.sites) concatenate_inherit_cell_pbc() (in module scgo.utils.combine_atoms) configure_logging() (in module scgo.utils.logging) connectivity_factor (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.TSParams attribute) constrain_adsorbate_moves (scgo.system_types.SystemPolicy attribute) core_symbols (scgo.system_types.AdsorbateDefinition attribute) count_adsorption_site_candidates() (in module scgo.cluster_adsorbate.feasibility) cpu_non_relax_seconds_from_timings() (in module scgo.utils.timing_report) create_deposited_cluster() (in module scgo.surface) create_deposited_cluster_batch() (in module scgo.surface) create_initial_cluster() (in module scgo.initialization) create_initial_cluster_batch() (in module scgo.initialization) D database_retry() (in module scgo.database) database_transaction() (in module scgo.database) DatabaseMigrationError DatabaseSetupError dedupe_minima (scgo.system_types.TSParams attribute) deduplicate (scgo.system_types.OptimizerSlotParams attribute) default() (scgo.utils.run_tracking.RunMetadataJSONEncoder method) describe_surface_config() (in module scgo.surface) device (scgo.system_types.CalculatorKwargs attribute) diff_param_overrides() (in module scgo.utils.run_helpers) diversity_max_references (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.OptimizerSlotParams attribute) diversity_reference_db (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.OptimizerSlotParams attribute) diversity_update_interval (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.OptimizerSlotParams attribute) dr (scgo.system_types.OptimizerSlotParams attribute) dtype (scgo.system_types.CalculatorKwargs attribute) E early_stopping_niter (scgo.system_types.OptimizerSlotParams attribute) emit_summary() (scgo.utils.phase_logging.InitDiagnosticsCollector class method) energy_gap_threshold (scgo.system_types.TSParams attribute) energy_tolerance (scgo.system_types.OptimizerSlotParams attribute) enforce_adsorbate_subgraph_integrity (scgo.system_types.GLOptimizerParams attribute) enforce_frozen_adsorbate_geometry() (in module scgo.cluster_adsorbate.rigid) ensure_run_id() (in module scgo.utils.run_tracking) estimate_fragment_footprint_radius() (in module scgo.cluster_adsorbate.feasibility) extract_adsorbate_definition_from_params() (in module scgo.system_types) extract_minima_from_database_file() (in module scgo.database) extract_transition_states_from_database_file() (in module scgo.database) F filter_by_metadata() (in module scgo.database) fitness_strategy (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.OptimizerSlotParams attribute) fix_all_slab_atoms (scgo.surface.config.SurfaceSystemConfig attribute) flatten_adsorbate_symbols() (in module scgo.system_types) flatten_run_timing_payload() (in module scgo.utils.timing_report) fmax (scgo.system_types.OptimizerSlotParams attribute) fmax_threshold (scgo.system_types.GLOptimizerParams attribute) format_count_summary() (in module scgo.utils.phase_logging) format_offspring_outcome_line() (in module scgo.utils.phase_logging) formula (scgo.utils.run_tracking.RunMetadata attribute) formula_searches_dir() (in module scgo.utils.output_paths) formula_ts_results_dir() (in module scgo.utils.output_paths) fragment_anchor_index (scgo.system_types.AdsorbateDefinition attribute) fragment_bond_axis (scgo.system_types.AdsorbateDefinition attribute) FragmentRepositionMutation (class in scgo.cluster_adsorbate.reposition) freeze_adsorbate_internal_geometry (scgo.system_types.GLOptimizerParams attribute) from_dict() (scgo.utils.run_tracking.RunMetadata class method) G ga_relax_seconds_from_timings() (in module scgo.utils.timing_report) generate_cube() (in module scgo.initialization) generate_cuboctahedron() (in module scgo.initialization) generate_decahedron() (in module scgo.initialization) generate_icosahedron() (in module scgo.initialization) generate_octahedron() (in module scgo.initialization) generate_run_id() (in module scgo.utils.run_tracking) generate_template_structure() (in module scgo.initialization) generate_tetrahedron() (in module scgo.initialization) generate_truncated_octahedron() (in module scgo.initialization) get_calculator_class() (in module scgo.utils.run_helpers) get_connection() (in module scgo.database) get_covalent_radius() (in module scgo.initialization) get_default_params() (in module scgo.param_presets) get_default_uma_params() (in module scgo.param_presets) get_default_upet_params() (in module scgo.param_presets) get_delay() (scgo.database.RetryConfig method) get_diversity_params() (in module scgo.param_presets) get_global_cache() (in module scgo.database) get_high_energy_params() (in module scgo.param_presets) get_logger() (in module scgo.utils.logging) get_metadata() (in module scgo.database) get_minimal_ga_params() (in module scgo.param_presets) get_nearest_magic_number() (in module scgo.initialization) get_new_individual() (scgo.cluster_adsorbate.reposition.FragmentRepositionMutation method) get_registry() (in module scgo.database) get_run_directories() (in module scgo.utils.run_tracking) get_run_id_from_dir() (in module scgo.utils.run_tracking) get_structure_diagnostics() (in module scgo.initialization) get_system_policy() (in module scgo.system_types) get_testing_params() (in module scgo.param_presets) get_torchsim_ga_params() (in module scgo.param_presets) get_ts_defaults() (in module scgo.param_presets) get_ts_search_params() (in module scgo.param_presets) get_uma_ga_benchmark_params() (in module scgo.param_presets) get_upet_ga_benchmark_params() (in module scgo.param_presets) get_vdw_radius() (in module scgo.initialization) GLOptimizerParams (class in scgo.system_types) grow_from_seed() (in module scgo.initialization) H has_adsorbate (scgo.system_types.SystemPolicy attribute) has_clashes (scgo.initialization.StructureDiagnostics attribute) height_max (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) (scgo.surface.config.SurfaceSystemConfig property) height_min (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) (scgo.surface.config.SurfaceSystemConfig property) I imag_freq_threshold (scgo.system_types.GLOptimizerParams attribute) infer_verbosity() (in module scgo.utils.phase_logging) init_mode (scgo.surface.config.SurfaceSystemConfig attribute) InitDiagnosticsCollector (class in scgo.utils.phase_logging) initial_delay (scgo.database.RetryConfig attribute) initialize_params() (in module scgo.utils.run_helpers) initialize_ts_params() (in module scgo.utils.run_helpers) is_cluster_connected() (in module scgo.initialization) is_disconnected (scgo.initialization.StructureDiagnostics attribute) is_near_magic_number() (in module scgo.initialization) is_valid (scgo.initialization.StructureDiagnostics attribute) L list_discovered_db_paths_with_run() (in module scgo.database) load_previous_results() (scgo.database.SCGODatabaseManager method) load_previous_run_results() (in module scgo.database) load_reference_structures() (in module scgo.database) (scgo.database.SCGODatabaseManager method) load_run_metadata() (in module scgo.utils.run_tracking) load_run_timing_payload() (in module scgo.utils.timing_report) log_configuration() (in module scgo.utils.run_helpers) log_debug_v() (in module scgo.utils.logging) log_error_v() (in module scgo.utils.logging) log_exception_v() (in module scgo.utils.logging) log_generation_offspring_summaries() (in module scgo.utils.phase_logging) log_go_ts_summary() (in module scgo.runner_api) log_info_v() (in module scgo.utils.logging) log_params_resolution() (in module scgo.utils.run_helpers) log_phase_header() (in module scgo.utils.phase_logging) log_phase_subheader() (in module scgo.utils.phase_logging) log_timing_summary() (in module scgo.utils.timing_report) log_ts_configuration() (in module scgo.utils.run_helpers) log_warning_v() (in module scgo.utils.logging) M make_graphite_surface_config() (in module scgo.surface) make_surface_config() (in module scgo.surface) mark_final_minima_in_db() (in module scgo.database) max_delay (scgo.database.RetryConfig attribute) max_endpoint_mismatch (scgo.system_types.TSParams attribute) max_mutation_probability (scgo.system_types.OptimizerSlotParams attribute) max_pairs (scgo.system_types.TSParams attribute) max_placement_attempts (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) (scgo.surface.config.SurfaceSystemConfig attribute) max_retries (scgo.database.RetryConfig attribute) minima_energy_tolerance (scgo.system_types.TSParams attribute) model_name (scgo.system_types.CalculatorKwargs attribute) module scgo.database scgo.exceptions scgo.initialization scgo.param_presets scgo.runner_api scgo.system_types scgo.utils.combine_atoms scgo.utils.config_aliases scgo.utils.logging scgo.utils.output_paths scgo.utils.phase_logging scgo.utils.run_helpers scgo.utils.run_tracking scgo.utils.timing_report move_fraction (scgo.system_types.OptimizerSlotParams attribute) move_strategy (scgo.system_types.OptimizerSlotParams attribute) mutate() (scgo.cluster_adsorbate.reposition.FragmentRepositionMutation method) mutation_probability (scgo.system_types.OptimizerSlotParams attribute) N n_components (scgo.initialization.StructureDiagnostics attribute) n_fix_bottom_slab_layers (scgo.surface.config.SurfaceSystemConfig attribute) n_jobs_offspring (scgo.system_types.OptimizerSlotParams attribute) n_jobs_population_init (scgo.system_types.OptimizerSlotParams attribute) n_relax_top_slab_layers (scgo.surface.config.SurfaceSystemConfig attribute) neb_align_endpoints (scgo.system_types.TSParams attribute) neb_climb (scgo.system_types.TSParams attribute) neb_disable_alignment (scgo.system_types.SystemPolicy attribute) neb_fmax (scgo.system_types.TSParams attribute) neb_force_mic (scgo.system_types.SystemPolicy attribute) neb_interpolation_method (scgo.system_types.TSParams attribute) neb_interpolation_mic (scgo.system_types.TSParams attribute) neb_n_images (scgo.system_types.TSParams attribute) neb_perturb_sigma (scgo.system_types.TSParams attribute) neb_spring_constant (scgo.system_types.TSParams attribute) neb_steps (scgo.system_types.TSParams attribute) neb_surface_cell_remap (scgo.system_types.SystemPolicy attribute) (scgo.system_types.TSParams attribute) neb_surface_lattice_rotation (scgo.system_types.SystemPolicy attribute) (scgo.system_types.TSParams attribute) neb_surface_max_lattice_shift (scgo.system_types.TSParams attribute) neb_tangent_method (scgo.system_types.TSParams attribute) needs_supported_deposit_validation (scgo.system_types.SystemPolicy attribute) niter (scgo.system_types.OptimizerSlotParams attribute) niter_local_relaxation (scgo.system_types.OptimizerSlotParams attribute) normal (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) normalize_adsorbates_input() (in module scgo.system_types) O offspring_fraction (scgo.system_types.OptimizerSlotParams attribute) optimizer (scgo.system_types.OptimizerSlotParams attribute) optimizer_params (scgo.system_types.GLOptimizerParams attribute) OptimizerSlotParams (class in scgo.system_types) P parallel_neb_max_bands (scgo.system_types.TSParams attribute) params (scgo.utils.run_tracking.RunMetadata attribute) parse_composition_arg() (in module scgo.runner_api) persist_provenance() (in module scgo.database) place_fragment_on_cluster() (in module scgo.cluster_adsorbate.placement) population_size (scgo.system_types.OptimizerSlotParams attribute) prepare_algorithm_kwargs() (in module scgo.utils.run_helpers) R radii_derived_height_bounds() (in module scgo.cluster_adsorbate.placement) random_rotation_matrix() (in module scgo.utils.combine_atoms) random_spherical() (in module scgo.initialization) random_spin_about_normal (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) read_timing_file() (in module scgo.utils.timing_report) record_fallback() (scgo.utils.phase_logging.InitDiagnosticsCollector class method) record_placement_failure() (scgo.utils.phase_logging.InitDiagnosticsCollector class method) recovery_window (scgo.system_types.OptimizerSlotParams attribute) relax_seconds_from_timings() (in module scgo.utils.timing_report) relaxer (scgo.system_types.OptimizerSlotParams attribute) reorder_cluster_to_composition() (in module scgo.initialization.geometry_helpers) requires_slab_prefix_validation (scgo.system_types.SystemPolicy attribute) reset() (scgo.utils.phase_logging.InitDiagnosticsCollector class method) resolve_adsorbate_fragments() (in module scgo.system_types) resolve_adsorbate_run_composition() (in module scgo.system_types) resolve_aliased_float() (in module scgo.utils.config_aliases) resolve_auto_params() (in module scgo.utils.run_helpers) resolve_campaign_root() (in module scgo.utils.output_paths) resolve_connectivity_factor() (in module scgo.system_types) resolve_diversity_params() (in module scgo.utils.run_helpers) resolve_go_campaign_searches_dir() (in module scgo.utils.output_paths) resolve_go_searches_dir() (in module scgo.utils.output_paths) resolve_go_ts_pipeline_paths() (in module scgo.utils.output_paths) resolve_minima_dir() (in module scgo.utils.output_paths) resolve_mobile_composition() (in module scgo.system_types) resolve_neb_mic() (in module scgo.system_types) resolve_run_id_from_db_path() (in module scgo.utils.run_tracking) resolve_run_timing_path() (in module scgo.utils.timing_report) resolve_structure_mic() (in module scgo.system_types) resolve_ts_campaign_paths() (in module scgo.utils.output_paths) resolve_workflow_seed() (in module scgo.runner_api) restore_rigid_adsorbate_fragments() (in module scgo.cluster_adsorbate.rigid) retry_transaction() (in module scgo.database) retry_with_backoff() (in module scgo.database) RetryConfig (class in scgo.database) run_go() (in module scgo.runner_api) run_go_campaign() (in module scgo.runner_api) run_go_ts() (in module scgo.runner_api) run_go_ts_campaign() (in module scgo.runner_api) run_id (scgo.utils.run_tracking.RunMetadata attribute) run_ts_campaign() (in module scgo.runner_api) run_ts_search() (in module scgo.runner_api) RunMetadata (class in scgo.utils.run_tracking) RunMetadataJSONEncoder (class in scgo.utils.run_tracking) S save_run_metadata() (in module scgo.utils.run_tracking) scgo.database module scgo.exceptions module scgo.initialization module scgo.param_presets module scgo.runner_api module scgo.system_types module scgo.utils.combine_atoms module scgo.utils.config_aliases module scgo.utils.logging module scgo.utils.output_paths module scgo.utils.phase_logging module scgo.utils.run_helpers module scgo.utils.run_tracking module scgo.utils.timing_report module SCGOConfigurationError SCGODatabaseError SCGODatabaseManager (class in scgo.database) SCGOError SCGOFileError SCGONotImplementedError SCGORuntimeError SCGOValidationError seed (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.TSParams attribute) select_scgo_minima_algorithm() (in module scgo.runner_api) setup_database() (in module scgo.database) should_show_progress() (in module scgo.utils.logging) similarity_pair_cor_max (scgo.system_types.TSParams attribute) similarity_tolerance (scgo.system_types.TSParams attribute) site_type (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) slab (scgo.surface.config.SurfaceSystemConfig attribute) slab_surface_extreme() (in module scgo.utils.combine_atoms) stagnation_full_trigger (scgo.system_types.OptimizerSlotParams attribute) stagnation_trigger (scgo.system_types.OptimizerSlotParams attribute) stamp_scgo_database() (in module scgo.database) steric_deficit() (in module scgo.initialization.steric_scoring) steric_deficit_two_sets() (in module scgo.initialization.steric_scoring) structure_check_clashes (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) structure_check_connectivity (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) structure_connectivity_factor (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) (scgo.surface.config.SurfaceSystemConfig attribute) structure_min_distance_factor (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) StructureDiagnostics (class in scgo.initialization) suggested_connectivity_factor (scgo.initialization.StructureDiagnostics attribute) sum_neb_seconds_from_ts_results() (in module scgo.utils.timing_report) summary (scgo.initialization.StructureDiagnostics attribute) surface_config (scgo.system_types.GLOptimizerParams attribute) (scgo.system_types.OptimizerSlotParams attribute) (scgo.system_types.SystemConfig attribute) (scgo.system_types.TSParams attribute) surface_normal_axis (scgo.surface.config.SurfaceSystemConfig attribute) SurfaceSiteCandidate (class in scgo.cluster_adsorbate.sites) SurfaceSystemConfig (class in scgo.surface.config) system_type (scgo.system_types.OptimizerSlotParams attribute) (scgo.system_types.SystemConfig attribute) (scgo.system_types.SystemPolicy attribute) (scgo.system_types.TSParams attribute) SystemConfig (class in scgo.system_types) SystemPolicy (class in scgo.system_types) T tag_final_minima (scgo.system_types.GLOptimizerParams attribute) temperature (scgo.system_types.OptimizerSlotParams attribute) timestamp (scgo.utils.run_tracking.RunMetadata attribute) to_dict() (scgo.utils.run_tracking.RunMetadata method) top_layer_indices() (in module scgo.utils.combine_atoms) torchsim_fmax (scgo.system_types.TSParams attribute) torchsim_max_steps (scgo.system_types.TSParams attribute) TSParams (class in scgo.system_types) U update_metadata() (in module scgo.database) use_adaptive_mutations (scgo.system_types.OptimizerSlotParams attribute) use_parallel_neb (scgo.system_types.TSParams attribute) use_torchsim (scgo.system_types.TSParams attribute) uses_surface (scgo.system_types.SystemPolicy attribute) uses_surface() (in module scgo.system_types) V vacuum (scgo.system_types.OptimizerSlotParams attribute) validate_adsorbate_definition() (in module scgo.system_types) validate_adsorbate_placement_feasibility() (in module scgo.cluster_adsorbate.feasibility) validate_algorithm_params() (in module scgo.utils.run_helpers) validate_cluster() (in module scgo.initialization) validate_cluster_structure() (in module scgo.initialization) validate_combined_structure (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) validate_composition_against_adsorbate() (in module scgo.system_types) validate_mobile_symbols_match_adsorbate_definition() (in module scgo.system_types) validate_structure_for_system_type() (in module scgo.system_types) validate_system_type_settings() (in module scgo.system_types) validate_with_hessian (scgo.system_types.GLOptimizerParams attribute) W write_run_timing_file() (in module scgo.utils.timing_report) write_timing_file() (in module scgo.utils.timing_report) write_timing_json (scgo.system_types.TSParams attribute)