Index _ | A | B | C | D | E | F | G | H | I | L | M | O | P | R | S | T | U | V | X | Y | Z _ __init() (adsorpy.rsa_config.RsaConfig method) __init__() (adsorpy.randomsequentialadsorption.BoundaryParameters method) (adsorpy.randomsequentialadsorption.CandidateMolecule method) (adsorpy.randomsequentialadsorption.Config method) (adsorpy.randomsequentialadsorption.MoleculeData method) (adsorpy.randomsequentialadsorption.MoleculeGroup method) (adsorpy.randomsequentialadsorption.Simulator method) (adsorpy.randomsequentialadsorption.Surface method) (adsorpy.rsa_config.RsaConfig method) __max_rotation (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) __return_key_value() (adsorpy.rsa_config.RsaConfig method) __unclaimed (adsorpy.randomsequentialadsorption.Simulator attribute) _calculate_radii() (adsorpy.randomsequentialadsorption.Simulator method) _column_datatypes (adsorpy.randomsequentialadsorption.MoleculeData attribute) _error_checker() (in module adsorpy.run_simulation) _estimate_site_count() (adsorpy.randomsequentialadsorption.Surface method) _fill_vals (adsorpy.randomsequentialadsorption.MoleculeData attribute) _header_names (adsorpy.randomsequentialadsorption.MoleculeData attribute) _heads_dtypes (adsorpy.randomsequentialadsorption.MoleculeData attribute) _initialise_reader() (in module adsorpy.molecule_lib) _initialise_run_parameters() (in module adsorpy.run_simulation) _mirr_datatypes (adsorpy.randomsequentialadsorption.MoleculeData attribute) _mirr_fill_vals (adsorpy.randomsequentialadsorption.MoleculeData attribute) _mirr_heads_dtypes (adsorpy.randomsequentialadsorption.MoleculeData attribute) _mirr_names (adsorpy.randomsequentialadsorption.MoleculeData attribute) _otomir_fill_vals (adsorpy.randomsequentialadsorption.MoleculeData attribute) _otomir_heads_dtypes (adsorpy.randomsequentialadsorption.MoleculeData attribute) _otomir_names (adsorpy.randomsequentialadsorption.MoleculeData attribute) _otomir_types (adsorpy.randomsequentialadsorption.MoleculeData attribute) _postprocessing() (in module adsorpy.run_simulation) _repeater() (in module adsorpy.run_simulation) _run_cascade() (in module adsorpy.run_simulation) _run_codosing() (in module adsorpy.run_simulation) _run_flux() (in module adsorpy.run_simulation) _run_flux_fixedrotation() (in module adsorpy.run_simulation) _run_sequential() (in module adsorpy.run_simulation) _select_and_run() (in module adsorpy.run_simulation) _set_xy_max() (adsorpy.randomsequentialadsorption.Surface method) _turn_into_list() (in module adsorpy.run_simulation) _update() (in module adsorpy.molecule_lib) A add_entry() (adsorpy.randomsequentialadsorption.MoleculeData method) add_mirror() (adsorpy.randomsequentialadsorption.MoleculeData method) adsorpy module adsorpy.molecule_lib module adsorpy.randomsequentialadsorption module adsorpy.rsa_calculator module adsorpy.rsa_config module adsorpy.run_simulation module adsorpy.typing module all_site_count (adsorpy.randomsequentialadsorption.Surface attribute) allowed_bools (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) allowed_idx (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) allowed_rotations (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) analyse_gap_size() (adsorpy.randomsequentialadsorption.Simulator method) area (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) (adsorpy.randomsequentialadsorption.Surface attribute) attempt_cascading_placement() (adsorpy.randomsequentialadsorption.Simulator method) attempt_place_molecule() (adsorpy.randomsequentialadsorption.Simulator method) attempt_random_placement() (adsorpy.randomsequentialadsorption.Simulator method) B biggest_radius (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) BoolArray (in module adsorpy.typing) Bools2D (in module adsorpy.typing) boundary_type (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) (adsorpy.randomsequentialadsorption.Config attribute) BoundaryParameters (class in adsorpy.randomsequentialadsorption) bp (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) (adsorpy.randomsequentialadsorption.Simulator attribute) (adsorpy.randomsequentialadsorption.Surface attribute) BufferArray (in module adsorpy.typing) C calculate_square_distance() (in module adsorpy.rsa_calculator) CandidateMolecule (class in adsorpy.randomsequentialadsorption) check_hard_border() (in module adsorpy.rsa_calculator) check_hard_molecule() (in module adsorpy.rsa_calculator) check_outer_radius() (in module adsorpy.rsa_calculator) check_shape_overlap() (in module adsorpy.rsa_calculator) circulium() (in module adsorpy.molecule_lib) close_to_border (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) close_to_edge (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) config (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) (adsorpy.randomsequentialadsorption.Simulator attribute) (adsorpy.randomsequentialadsorption.Surface attribute) Config (class in adsorpy.randomsequentialadsorption) coordinates (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) CoordPair (in module adsorpy.typing) coords (adsorpy.randomsequentialadsorption.MoleculeData attribute) CoordsArray (in module adsorpy.typing) CoordsArray3D (in module adsorpy.typing) create_periodic_images() (in module adsorpy.rsa_calculator) current_mirror_num (adsorpy.randomsequentialadsorption.MoleculeData attribute) current_mol_id (adsorpy.randomsequentialadsorption.MoleculeData attribute) D discorectangle() (in module adsorpy.molecule_lib) DistArray (in module adsorpy.typing) dogbonium() (in module adsorpy.molecule_lib) E edge_flag (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) exists (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) extended_grid (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) extended_idx (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) extended_occupied_by (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) extended_vacant (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) F first_time_loader() (in module adsorpy.molecule_lib) FloatArray (in module adsorpy.typing) flux_flag (adsorpy.randomsequentialadsorption.Simulator attribute) G gap_dists (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) generate_boundary_conditions() (adsorpy.randomsequentialadsorption.BoundaryParameters method) generate_custom_surface() (adsorpy.randomsequentialadsorption.Surface method) generate_grid() (adsorpy.randomsequentialadsorption.Surface method) generate_rotated_molecules() (adsorpy.randomsequentialadsorption.MoleculeGroup method) GeoArray (in module adsorpy.typing) get_canddata() (adsorpy.randomsequentialadsorption.CandidateMolecule method) get_item() (adsorpy.rsa_config.RsaConfig method) get_value() (adsorpy.rsa_config.RsaConfig method) grid_coordinates (adsorpy.randomsequentialadsorption.Surface attribute) grid_index (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) (adsorpy.randomsequentialadsorption.Surface attribute) group_id (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) H hard_flag (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) hard_inner (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) I IdxArray (in module adsorpy.typing) InDict (in module adsorpy.typing) L last_accessed_idx (adsorpy.randomsequentialadsorption.MoleculeData attribute) lattice_a (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.Surface attribute) lattice_type (adsorpy.randomsequentialadsorption.Surface attribute) M main() (in module adsorpy.run_simulation) make_rectangular_filter() (in module adsorpy.rsa_calculator) make_rtree_filter() (in module adsorpy.rsa_calculator) make_struct_array() (adsorpy.randomsequentialadsorption.MoleculeData static method) max_array_length (adsorpy.randomsequentialadsorption.MoleculeData attribute) max_molecule_count (adsorpy.randomsequentialadsorption.Config attribute) max_radius (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) min_radius (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) minmax_gaps (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) minmax_rads (adsorpy.randomsequentialadsorption.Simulator attribute) mirr_counter (adsorpy.randomsequentialadsorption.MoleculeData attribute) mirr_tree (adsorpy.randomsequentialadsorption.MoleculeData attribute) mirror_coords (adsorpy.randomsequentialadsorption.MoleculeData attribute) mirror_counter (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) mirrors (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) module adsorpy adsorpy.molecule_lib adsorpy.randomsequentialadsorption adsorpy.rsa_calculator adsorpy.rsa_config adsorpy.run_simulation adsorpy.typing mol_counter (adsorpy.randomsequentialadsorption.MoleculeData attribute) mol_data (adsorpy.randomsequentialadsorption.Simulator attribute) mol_tree (adsorpy.randomsequentialadsorption.MoleculeData attribute) molecule (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) molecule_counter (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) molecule_group_idx (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) molecule_number (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) MoleculeData (class in adsorpy.randomsequentialadsorption) MoleculeGroup (class in adsorpy.randomsequentialadsorption) molecules_bounding_coords (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) molecules_flag (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) molgrcount (adsorpy.randomsequentialadsorption.Simulator attribute) molgroups (adsorpy.randomsequentialadsorption.Simulator attribute) O occupied_by (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) orig_to_mirrors (adsorpy.randomsequentialadsorption.MoleculeData attribute) outer_rads (adsorpy.randomsequentialadsorption.Simulator attribute) P periodic_flag (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) plot_covered_grid() (adsorpy.randomsequentialadsorption.Simulator method) plot_surface_sites() (adsorpy.randomsequentialadsorption.Surface method) polygonium() (in module adsorpy.molecule_lib) PrepGeoArray (in module adsorpy.typing) R reflection_symmetry (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) rng (adsorpy.randomsequentialadsorption.Simulator attribute) rot_idx (adsorpy.randomsequentialadsorption.CandidateMolecule attribute) rot_refl_count (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) rotated_buffer_molecules (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) rotated_molecules (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) rotation_count (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) rotation_symmetry (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) RotMatrix (in module adsorpy.typing) rsa_config (adsorpy.randomsequentialadsorption.Config attribute) RsaConfig (class in adsorpy.rsa_config) run_simulation() (in module adsorpy.run_simulation) S set_boundary_flags() (adsorpy.randomsequentialadsorption.BoundaryParameters static method) simple_shape_flag (adsorpy.randomsequentialadsorption.Surface attribute) Simulator (class in adsorpy.randomsequentialadsorption) sites (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.Surface attribute) soft_flag (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) squared_cdist() (in module adsorpy.rsa_calculator) sticking_probability (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) (adsorpy.randomsequentialadsorption.Surface attribute) stored_data (adsorpy.randomsequentialadsorption.MoleculeData attribute) stored_mirr_data (adsorpy.randomsequentialadsorption.MoleculeData attribute) surf (adsorpy.randomsequentialadsorption.Simulator attribute) Surface (class in adsorpy.randomsequentialadsorption) T to_dict() (adsorpy.rsa_config.RsaConfig method) total_molecule_counter (adsorpy.randomsequentialadsorption.Simulator attribute) tree (adsorpy.randomsequentialadsorption.BoundaryParameters attribute) (adsorpy.randomsequentialadsorption.Surface attribute) trim_buffer() (adsorpy.randomsequentialadsorption.Simulator method) U update_placement() (adsorpy.randomsequentialadsorption.Simulator method) V vacancy_count (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) vacant (adsorpy.randomsequentialadsorption.MoleculeGroup attribute) X x_max (adsorpy.randomsequentialadsorption.Surface attribute) xsize (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.Surface attribute) xyz_reader() (in module adsorpy.molecule_lib) Y y_max (adsorpy.randomsequentialadsorption.Surface attribute) ysize (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.Surface attribute) Z zsize (adsorpy.randomsequentialadsorption.Config attribute) (adsorpy.randomsequentialadsorption.Surface attribute)