Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | U | V A adsorbate_fragment_lengths (scgo.system_types.AdsorbateDefinition attribute) adsorbate_move_scale (scgo.system_types.SystemPolicy attribute) adsorbate_symbols (scgo.system_types.AdsorbateDefinition attribute) AdsorbateDefinition (class in scgo.system_types) adsorption_height_max (scgo.surface.config.SurfaceSystemConfig attribute) adsorption_height_min (scgo.surface.config.SurfaceSystemConfig attribute) allow_composition_permutations (scgo.system_types.SystemPolicy attribute) anchor (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) B 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_two_element_compositions() (in module scgo.runner_api) C cell_margin (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) clash_details (scgo.initialization.StructureDiagnostics attribute) closest_inter_component_distance (scgo.initialization.StructureDiagnostics 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_use_mic (scgo.surface.config.SurfaceSystemConfig attribute) CompositionInput (in module scgo.runner_api) compute_cell_side() (in module scgo.initialization) compute_surface_site_candidates() (in module scgo.cluster_adsorbate.sites) 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) create_initial_cluster() (in module scgo.initialization) create_initial_cluster_batch() (in module scgo.initialization) D describe_surface_config() (in module scgo.surface) E enforce_frozen_adsorbate_geometry() (in module scgo.cluster_adsorbate.rigid) estimate_fragment_footprint_radius() (in module scgo.cluster_adsorbate.feasibility) F fix_all_slab_atoms (scgo.surface.config.SurfaceSystemConfig attribute) flatten_adsorbate_symbols() (in module scgo.system_types) fragment_anchor_index (scgo.system_types.AdsorbateDefinition attribute) fragment_bond_axis (scgo.system_types.AdsorbateDefinition attribute) FragmentRepositionMutation (class in scgo.cluster_adsorbate.reposition) G 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_template_structure() (in module scgo.initialization) generate_tetrahedron() (in module scgo.initialization) generate_truncated_octahedron() (in module scgo.initialization) 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_diversity_params() (in module scgo.param_presets) get_high_energy_params() (in module scgo.param_presets) 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_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_vdw_radius() (in module scgo.initialization) 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) height_min (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) I init_mode (scgo.surface.config.SurfaceSystemConfig attribute) 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 log_go_ts_summary() (in module scgo.runner_api) M make_graphite_surface_config() (in module scgo.surface) make_surface_config() (in module scgo.surface) max_placement_attempts (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) (scgo.surface.config.SurfaceSystemConfig attribute) module scgo.initialization scgo.param_presets scgo.runner_api scgo.system_types mutate() (scgo.cluster_adsorbate.reposition.FragmentRepositionMutation method) N n_components (scgo.initialization.StructureDiagnostics attribute) n_fix_bottom_slab_layers (scgo.surface.config.SurfaceSystemConfig attribute) n_relax_top_slab_layers (scgo.surface.config.SurfaceSystemConfig attribute) neb_disable_alignment (scgo.system_types.SystemPolicy attribute) neb_force_mic (scgo.system_types.SystemPolicy attribute) neb_surface_cell_remap (scgo.system_types.SystemPolicy attribute) neb_surface_lattice_rotation (scgo.system_types.SystemPolicy attribute) needs_supported_deposit_validation (scgo.system_types.SystemPolicy attribute) normal (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) normalize_adsorbates_input() (in module scgo.system_types) P parse_composition_arg() (in module scgo.runner_api) place_fragment_on_cluster() (in module scgo.cluster_adsorbate.placement) R radii_derived_height_bounds() (in module scgo.cluster_adsorbate.placement) random_spherical() (in module scgo.initialization) random_spin_about_normal (scgo.cluster_adsorbate.config.ClusterAdsorbateConfig attribute) requires_slab_prefix_validation (scgo.system_types.SystemPolicy attribute) resolve_adsorbate_fragments() (in module scgo.system_types) resolve_connectivity_factor() (in module scgo.system_types) resolve_workflow_seed() (in module scgo.runner_api) restore_rigid_adsorbate_fragments() (in module scgo.cluster_adsorbate.rigid) 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_ts_campaign() (in module scgo.runner_api) run_ts_search() (in module scgo.runner_api) S scgo.initialization module scgo.param_presets module scgo.runner_api module scgo.system_types module site_type (scgo.cluster_adsorbate.sites.SurfaceSiteCandidate attribute) slab (scgo.surface.config.SurfaceSystemConfig attribute) 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) summary (scgo.initialization.StructureDiagnostics 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.SystemPolicy attribute) SystemPolicy (class in scgo.system_types) U uses_surface (scgo.system_types.SystemPolicy attribute) uses_surface() (in module scgo.system_types) V validate_adsorbate_definition() (in module scgo.system_types) validate_adsorbate_placement_feasibility() (in module scgo.cluster_adsorbate.feasibility) 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)