Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A ABFIX (autoplex.settings.BuildcellOptions attribute) add_dft_phonons() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow static method) add_dft_rattled() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow static method) add_species (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) ADDGRID (autoplex.settings.CustomIncar attribute) adjust_forces() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_momenta() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_positions() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_potential_energy() (autoplex.data.rss.utils.HookeanRepulsion method) ALGO (autoplex.settings.CustomIncar attribute) allow_missing_labels (autoplex.settings.M3GNETSettings attribute) allow_tf32 (autoplex.settings.NEQUIPSettings attribute) AMIX (autoplex.settings.CustomIncar attribute) amsgrad (autoplex.settings.MACESettings attribute) append (autoplex.settings.NEQUIPSettings attribute) as_dict() (autoplex.settings.AutoplexBaseModel method) ase_args (autoplex.settings.NEQUIPSettings attribute) at_file (autoplex.settings.GAPGeneralSettings attribute) atom_sigma (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) atomic_numbers (in module autoplex.data.rss.jobs) (in module autoplex.data.rss.utils) auto_delta (autoplex.settings.RssConfig attribute) autoplex.auto module autoplex.auto.phonons module autoplex.auto.phonons.flows module autoplex.auto.phonons.jobs module autoplex.auto.rss module autoplex.auto.rss.flows module autoplex.auto.rss.jobs module autoplex.benchmark module autoplex.benchmark.phonons module autoplex.benchmark.phonons.flows module autoplex.benchmark.phonons.jobs module autoplex.benchmark.phonons.utils module autoplex.benchmark.rss module autoplex.data module autoplex.data.common module autoplex.data.common.flows module autoplex.data.common.jobs module autoplex.data.common.utils module autoplex.data.phonons module autoplex.data.phonons.flows module autoplex.data.phonons.jobs module autoplex.data.phonons.utils module autoplex.data.rss module autoplex.data.rss.flows module autoplex.data.rss.jobs module autoplex.data.rss.utils module autoplex.fitting module autoplex.fitting.common module autoplex.fitting.common.flows module autoplex.fitting.common.jobs module autoplex.fitting.common.regularization module autoplex.fitting.common.utils module autoplex.fitting.phonons module autoplex.fitting.rss module autoplex.misc module autoplex.misc.castep module autoplex.misc.castep.flows module autoplex.misc.castep.jobs module autoplex.misc.castep.run module autoplex.misc.castep.schema module autoplex.misc.castep.utils module autoplex.misc.utils module autoplex.misc.utils.mock_castep module autoplex.settings module AutoplexPyACECalculator() (in module autoplex.fitting.common.utils) average (autoplex.settings.SoapParas attribute) avg_num_neighbors (autoplex.settings.NEQUIPSettings attribute) B backend (autoplex.settings.PacemakerSettings attribute) BaseCastepMaker (class in autoplex.misc.castep.jobs) basis_size (autoplex.settings.NEPSettings attribute) batch (autoplex.settings.NEPSettings attribute) batch_size (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) bcur_params (autoplex.settings.RssConfig attribute) besselbasis_trainable (autoplex.settings.NEQUIPSettings attribute) bolt_max_num (autoplex.settings.BcurParams attribute) boltzhist_cur_dual_iter() (in module autoplex.data.common.utils) boltzhist_cur_one_shot() (in module autoplex.data.common.utils) buildcell_options (autoplex.settings.RssConfig attribute) BuildMultiRandomizedStructure (class in autoplex.data.rss.flows) C calculate() (autoplex.fitting.common.utils.CustomPotential method) calculate_delta_2b() (in module autoplex.fitting.common.utils) calculate_hull_nd() (in module autoplex.fitting.common.regularization) CASTEP_CMD (autoplex.settings.AutoplexSettings attribute) CASTEP_INPUT_FILES (in module autoplex.misc.castep.jobs) (in module autoplex.misc.castep.utils) castep_job() (in module autoplex.misc.castep.jobs) CASTEP_KEYWORDS (autoplex.settings.AutoplexSettings attribute) CASTEP_OUTPUT_FILES (in module autoplex.misc.castep.jobs) (in module autoplex.misc.castep.utils) CastepInputGenerator (class in autoplex.misc.castep.utils) CastepStaticMaker (class in autoplex.misc.castep.jobs) CastepStaticSetGenerator (class in autoplex.misc.castep.utils) cell_seed_paths (autoplex.settings.RssConfig attribute) cell_updates (autoplex.misc.castep.utils.CastepInputGenerator property) (autoplex.misc.castep.utils.CastepStaticSetGenerator property) central_weight (autoplex.settings.SoapSettings attribute) check_convergence() (in module autoplex.fitting.common.utils) check_convergence_aims() (in module autoplex.data.common.jobs) check_convergence_castep() (in module autoplex.data.common.jobs) check_convergence_vasp() (in module autoplex.data.common.jobs) check_distances() (in module autoplex.data.common.utils) check_energy_force_stress_reading() (in module autoplex.fitting.common.utils) check_supercells() (in module autoplex.data.phonons.utils) chemical_symbols (autoplex.settings.NEQUIPSettings attribute) (in module autoplex.data.rss.utils) (in module autoplex.fitting.common.utils) clear_castep_inputs() (in module autoplex.misc.utils.mock_castep) collect_dft_data() (in module autoplex.data.common.jobs) compact_clusters (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) compare_plot() (in module autoplex.benchmark.phonons.utils) complete_benchmark() (in module autoplex.auto.phonons.jobs) CompleteDFTvsMLBenchmarkWorkflow (class in autoplex.auto.phonons.flows) CompleteDFTvsMLBenchmarkWorkflowMPSettings (class in autoplex.auto.phonons.flows) compute_avg_num_neighbors (autoplex.settings.MACESettings attribute) compute_bandstructure_benchmark_metrics() (in module autoplex.benchmark.phonons.utils) compute_forces (autoplex.settings.MACESettings attribute) compute_num_of_descriptor() (in module autoplex.fitting.common.utils) compute_statistics (autoplex.settings.MACESettings attribute) compute_stress (autoplex.settings.MACESettings attribute) CONFIG_FILE (autoplex.settings.AutoplexSettings attribute) config_type_weights (autoplex.settings.MACESettings attribute) config_types (autoplex.settings.RssConfig attribute) convert_to_extxyz() (in module autoplex.data.common.jobs) convert_to_pacemaker_pickle() (in module autoplex.fitting.common.utils) convert_xyz_to_structure() (in module autoplex.fitting.common.utils) convexhull_cur() (in module autoplex.data.common.utils) copy_castep_outputs() (in module autoplex.misc.utils.mock_castep) correlation (autoplex.settings.MACESettings attribute) covalent_radii (in module autoplex.data.rss.jobs) covariance_type (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) create_soap_descriptor() (in module autoplex.data.common.utils) cur_select() (in module autoplex.data.common.utils) current_iter_index (autoplex.settings.RssConfig attribute) custom_incar (autoplex.settings.RssConfig attribute) custom_potcar (autoplex.settings.RssConfig attribute) CustomPotential (class in autoplex.fitting.common.utils) cutoff (autoplex.settings.JACESettings attribute) (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.NEPSettings attribute) (autoplex.settings.PacemakerSettings attribute) (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) cutoff_transition_width (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) D data (autoplex.settings.PacemakerSettings attribute) data_distillation() (in module autoplex.data.common.utils) data_mean (autoplex.settings.M3GNETSettings attribute) data_std (autoplex.settings.M3GNETSettings attribute) DataPreprocessing (class in autoplex.fitting.common.flows) dataset (autoplex.settings.NEQUIPSettings attribute) dataset_file_name (autoplex.settings.NEQUIPSettings attribute) dataset_key_mapping (autoplex.settings.NEQUIPSettings attribute) dataset_seed (autoplex.settings.NEQUIPSettings attribute) decay_alpha (autoplex.settings.M3GNETSettings attribute) decay_steps (autoplex.settings.M3GNETSettings attribute) default_dtype (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) default_sigma (autoplex.settings.GAPGeneralSettings attribute) delta (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) device_for_fitting (autoplex.settings.RssConfig attribute) device_for_rss (autoplex.settings.RssConfig attribute) dft_phonopy_gen_data() (in module autoplex.auto.phonons.jobs) dft_random_gen_data() (in module autoplex.auto.phonons.jobs) dft_ref_file (autoplex.settings.RssConfig attribute) DFTPhononMaker (class in autoplex.data.phonons.flows) DFTStaticLabelling (class in autoplex.data.common.flows) DFTSupercellSettingsMaker (class in autoplex.auto.phonons.flows) dim_edge_embedding (autoplex.settings.M3GNETSettings attribute) dim_node_embedding (autoplex.settings.M3GNETSettings attribute) dim_state_embedding (autoplex.settings.M3GNETSettings attribute) dimer_box (autoplex.settings.RssConfig attribute) dimer_num (autoplex.settings.RssConfig attribute) dimer_range (autoplex.settings.RssConfig attribute) dir_name (autoplex.misc.castep.schema.TaskDoc attribute) disable_testing (autoplex.settings.RssConfig attribute) distance_Nb_order (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) distillation (autoplex.settings.RssConfig attribute) distributed (autoplex.settings.MACESettings attribute) do_copy_at_file (autoplex.settings.GAPGeneralSettings attribute) do_iterative_rattled_structures() (in module autoplex.auto.phonons.jobs) do_rss_iterations() (in module autoplex.auto.rss.jobs) do_rss_multi_node() (in module autoplex.data.rss.jobs) do_rss_single_node() (in module autoplex.data.rss.jobs) E e (autoplex.settings.Nonlinearity attribute) e0_offset (autoplex.settings.GAPGeneralSettings attribute) e0_spin (autoplex.settings.RssConfig attribute) E0s (autoplex.settings.MACESettings attribute) early_stopping_lower_bounds (autoplex.settings.NEQUIPSettings attribute) early_stopping_patiences (autoplex.settings.NEQUIPSettings attribute) EDIFF (autoplex.settings.CustomIncar attribute) element_refs (autoplex.settings.M3GNETSettings attribute) ElementCollection (class in autoplex.data.common.utils) ema (autoplex.settings.MACESettings attribute) ema_decay (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) ema_use_num_updates (autoplex.settings.NEQUIPSettings attribute) ENCUT (autoplex.settings.CustomIncar attribute) energy (autoplex.misc.castep.schema.OutputDoc attribute) energy_parameter_name (autoplex.settings.GAPGeneralSettings attribute) energy_per_atom (autoplex.misc.castep.schema.OutputDoc attribute) energy_plot() (in module autoplex.data.common.utils) energy_remain() (in module autoplex.fitting.common.utils) energy_weight (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) exp_name (autoplex.settings.M3GNETSettings attribute) extract_gap_label() (in module autoplex.fitting.common.utils) extract_pairstyle() (in module autoplex.data.rss.utils) F f0 (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) fake_run_castep() (in module autoplex.misc.utils.mock_castep) filter_outlier_energy() (in module autoplex.data.common.utils) filter_outlier_forces() (in module autoplex.data.common.utils) find_element_pairs() (autoplex.data.common.utils.ElementCollection method) fit (autoplex.settings.PacemakerSettings attribute) flatten() (in module autoplex.data.common.utils) (in module autoplex.fitting.common.utils) flatten_list() (in module autoplex.data.common.utils) force_delta (autoplex.settings.NEPSettings attribute) force_label (autoplex.settings.RssConfig attribute) force_max (autoplex.settings.RssConfig attribute) force_parameter_name (autoplex.settings.GAPGeneralSettings attribute) force_plot() (in module autoplex.data.common.utils) force_tol (autoplex.settings.RssConfig attribute) force_weight (autoplex.settings.M3GNETSettings attribute) forces (autoplex.misc.castep.schema.OutputDoc attribute) (autoplex.settings.LossCoeff attribute) forces_weight (autoplex.settings.MACESettings attribute) foundation_filter_elements (autoplex.settings.MACESettings attribute) foundation_model (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) foundation_model_readout (autoplex.settings.MACESettings attribute) frac_of_bcur (autoplex.settings.BcurParams attribute) fragment_file (autoplex.settings.RssConfig attribute) fragment_numbers (autoplex.settings.RssConfig attribute) from_dict() (autoplex.settings.AutoplexBaseModel class method) from_file() (autoplex.settings.AutoplexBaseModel class method) (autoplex.settings.RssConfig class method) G GAP (autoplex.settings.MLIPHypers attribute) gap_fitting() (in module autoplex.fitting.common.utils) gap_hyperparameter_constructor() (in module autoplex.fitting.common.utils) gcm3_to_Vm() (in module autoplex.fitting.common.utils) general (autoplex.settings.GAPSettings attribute) generate_randomized_structures() (in module autoplex.data.common.jobs) generate_supercells() (in module autoplex.auto.phonons.jobs) generated_struct_numbers (autoplex.settings.RssConfig attribute) GenerateTrainingDataForTesting (class in autoplex.data.common.flows) generation (autoplex.settings.NEPSettings attribute) generic type get_atomic_numbers() (in module autoplex.fitting.common.utils) get_convex_hull() (in module autoplex.fitting.common.regularization) get_e_distance_to_hull() (in module autoplex.fitting.common.regularization) get_e_distance_to_hull_nd() (in module autoplex.fitting.common.regularization) get_indices() (autoplex.data.rss.utils.HookeanRepulsion method) get_input_set() (autoplex.misc.castep.utils.CastepInputGenerator method) get_intersect() (in module autoplex.fitting.common.regularization) get_iso_atom() (in module autoplex.auto.phonons.jobs) get_list_of_vasp_calc_dirs() (in module autoplex.fitting.common.utils) get_mole_frac() (in module autoplex.fitting.common.regularization) get_number_of_species() (autoplex.data.common.utils.ElementCollection method) get_phonon_output() (in module autoplex.auto.phonons.jobs) get_removed_dof() (autoplex.data.rss.utils.HookeanRepulsion method) get_rmse() (in module autoplex.benchmark.phonons.utils) get_species() (autoplex.data.common.utils.ElementCollection method) get_species_Z() (autoplex.data.common.utils.ElementCollection method) get_supercell_job() (in module autoplex.data.common.jobs) GGA (autoplex.settings.CustomIncar attribute) gp_file (autoplex.settings.GAPGeneralSettings attribute) GPa (in module autoplex.data.common.utils) (in module autoplex.data.rss.utils) (in module autoplex.misc.castep.jobs) H handle_rss_trajectory() (in module autoplex.data.common.utils) has_ypace (in module autoplex.fitting.common.utils) hidden_irreps (autoplex.settings.MACESettings attribute) hookean_paras (autoplex.settings.RssConfig attribute) hookean_repul (autoplex.settings.RssConfig attribute) HookeanRepulsion (class in autoplex.data.rss.utils) I include_dimer (autoplex.settings.RssConfig attribute) include_isolated_atom (autoplex.settings.RssConfig attribute) include_line_graph (autoplex.settings.M3GNETSettings attribute) include_stresses (autoplex.settings.M3GNETSettings attribute) index_shuffle() (autoplex.data.rss.utils.HookeanRepulsion method) initial_kt (autoplex.settings.RssConfig attribute) initial_rss() (in module autoplex.auto.rss.jobs) initial_selection_enabled (autoplex.settings.RssConfig attribute) input (autoplex.misc.castep.schema.TaskDoc attribute) input_set (autoplex.misc.castep.schema.InputDoc attribute) invariant_layers (autoplex.settings.NEQUIPSettings attribute) invariant_neurons (autoplex.settings.NEQUIPSettings attribute) is_intensive (autoplex.settings.M3GNETSettings attribute) ISMEAR (autoplex.settings.CustomIncar attribute) IsoAtomMaker (class in autoplex.data.phonons.flows) IsoAtomStaticMaker (class in autoplex.data.phonons.flows) isolated_atom_energies (autoplex.settings.ResumeFromPreviousState attribute) isolatedatom_box (autoplex.settings.RssConfig attribute) ISYM (autoplex.settings.CustomIncar attribute) IterativeCompleteDFTvsMLBenchmarkWorkflow (class in autoplex.auto.phonons.flows) J J_ACE (autoplex.settings.MLIPHypers attribute) jace_fitting() (in module autoplex.fitting.common.utils) K keep_checkpoint (autoplex.settings.MACESettings attribute) keep_isolated_atoms (autoplex.settings.MACESettings attribute) keep_symmetry (autoplex.settings.RssConfig attribute) KPAR (autoplex.settings.CustomIncar attribute) KSPACING (autoplex.settings.CustomIncar attribute) L l_max (autoplex.settings.NEPSettings attribute) (autoplex.settings.NEQUIPSettings attribute) (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) label_stoichiometry_volume() (in module autoplex.fitting.common.regularization) lambda_1 (autoplex.settings.NEPSettings attribute) lambda_e (autoplex.settings.NEPSettings attribute) lambda_f (autoplex.settings.NEPSettings attribute) lambda_v (autoplex.settings.NEPSettings attribute) LCHARG (autoplex.settings.CustomIncar attribute) learning_rate (autoplex.settings.NEQUIPSettings attribute) log_batch_freq (autoplex.settings.NEQUIPSettings attribute) log_epoch_freq (autoplex.settings.NEQUIPSettings attribute) loss (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) loss_coeffs (autoplex.settings.NEQUIPSettings attribute) loss_params (autoplex.settings.M3GNETSettings attribute) LPLANE (autoplex.settings.CustomIncar attribute) lr (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) lr_scheduler_factor (autoplex.settings.NEQUIPSettings attribute) lr_scheduler_name (autoplex.settings.NEQUIPSettings attribute) lr_scheduler_patience (autoplex.settings.NEQUIPSettings attribute) LREAL (autoplex.settings.CustomIncar attribute) LSCALAPACK (autoplex.settings.CustomIncar attribute) LWAVE (autoplex.settings.CustomIncar attribute) M M3GNET (autoplex.settings.MLIPHypers attribute) m3gnet_fitting() (in module autoplex.fitting.common.utils) MACE (autoplex.settings.MLIPHypers attribute) mace_convert_virial_to_stress() (in module autoplex.fitting.common.utils) mace_fitting() (in module autoplex.fitting.common.utils) machine_learning_fit() (in module autoplex.fitting.common.jobs) magmom_target (autoplex.settings.M3GNETSettings attribute) magmom_weight (autoplex.settings.M3GNETSettings attribute) make() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow method) (autoplex.auto.phonons.flows.DFTSupercellSettingsMaker method) (autoplex.auto.phonons.flows.IterativeCompleteDFTvsMLBenchmarkWorkflow method) (autoplex.auto.rss.flows.RssMaker method) (autoplex.benchmark.phonons.flows.PhononBenchmarkMaker method) (autoplex.data.common.flows.DFTStaticLabelling method) (autoplex.data.common.flows.GenerateTrainingDataForTesting method) (autoplex.data.phonons.flows.IsoAtomMaker method) (autoplex.data.phonons.flows.RandomStructuresDataGenerator method) (autoplex.data.rss.flows.BuildMultiRandomizedStructure method) (autoplex.data.rss.jobs.RandomizedStructure method) (autoplex.fitting.common.flows.DataPreprocessing method) (autoplex.fitting.common.flows.MLIPFitMaker method) (autoplex.misc.castep.jobs.BaseCastepMaker method) make_from_ml_model() (autoplex.data.phonons.flows.MLPhononMaker method) max_epochs (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.NEQUIPSettings attribute) max_iteration_number (autoplex.settings.RssConfig attribute) max_l (autoplex.settings.M3GNETSettings attribute) max_n (autoplex.settings.M3GNETSettings attribute) max_num_epochs (autoplex.settings.MACESettings attribute) max_steps (autoplex.settings.RssConfig attribute) mc_rattle() (in module autoplex.data.common.utils) metadata (autoplex.settings.PacemakerSettings attribute) metrics_components (autoplex.settings.NEQUIPSettings attribute) metrics_key (autoplex.settings.NEQUIPSettings attribute) minimize_structures() (in module autoplex.data.rss.utils) MINSEP (autoplex.settings.BuildcellOptions attribute) ml_phonon_maker_preparation() (in module autoplex.data.phonons.utils) mlip_hypers (autoplex.settings.RssConfig attribute) mlip_path (autoplex.settings.ResumeFromPreviousState attribute) mlip_type (autoplex.settings.RssConfig attribute) MLIPFitMaker (class in autoplex.fitting.common.flows) MLPhononMaker (class in autoplex.data.phonons.flows) model (autoplex.settings.MACESettings attribute) model_dtype (autoplex.settings.NEQUIPSettings attribute) model_type (autoplex.settings.NEPSettings attribute) module autoplex.auto autoplex.auto.phonons autoplex.auto.phonons.flows autoplex.auto.phonons.jobs autoplex.auto.rss autoplex.auto.rss.flows autoplex.auto.rss.jobs autoplex.benchmark autoplex.benchmark.phonons autoplex.benchmark.phonons.flows autoplex.benchmark.phonons.jobs autoplex.benchmark.phonons.utils autoplex.benchmark.rss autoplex.data autoplex.data.common autoplex.data.common.flows autoplex.data.common.jobs autoplex.data.common.utils autoplex.data.phonons autoplex.data.phonons.flows autoplex.data.phonons.jobs autoplex.data.phonons.utils autoplex.data.rss autoplex.data.rss.flows autoplex.data.rss.jobs autoplex.data.rss.utils autoplex.fitting autoplex.fitting.common autoplex.fitting.common.flows autoplex.fitting.common.jobs autoplex.fitting.common.regularization autoplex.fitting.common.utils autoplex.fitting.phonons autoplex.fitting.rss autoplex.misc autoplex.misc.castep autoplex.misc.castep.flows autoplex.misc.castep.jobs autoplex.misc.castep.run autoplex.misc.castep.schema autoplex.misc.castep.utils autoplex.misc.utils autoplex.misc.utils.mock_castep autoplex.settings monkeypatch_castep() (in module autoplex.misc.utils.mock_castep) multiheads_finetuning (autoplex.settings.MACESettings attribute) N n_max (autoplex.settings.NEPSettings attribute) (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) n_sparse (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) n_train (autoplex.settings.NEQUIPSettings attribute) n_val (autoplex.settings.NEQUIPSettings attribute) name (autoplex.settings.MACESettings attribute) nblocks (autoplex.settings.M3GNETSettings attribute) NCORE (autoplex.settings.CustomIncar attribute) NELM (autoplex.settings.CustomIncar attribute) NEP (autoplex.settings.MLIPHypers attribute) nep_fitting() (in module autoplex.fitting.common.utils) NEQUIP (autoplex.settings.MLIPHypers attribute) nequip_fitting() (in module autoplex.fitting.common.utils) neuron (autoplex.settings.NEPSettings attribute) NFORM (autoplex.settings.BuildcellOptions attribute) nonlinearity_gates (autoplex.settings.NEQUIPSettings attribute) nonlinearity_scalars (autoplex.settings.NEQUIPSettings attribute) nonlinearity_type (autoplex.settings.NEQUIPSettings attribute) num_basis (autoplex.settings.NEQUIPSettings attribute) num_features (autoplex.settings.NEQUIPSettings attribute) num_groups (autoplex.settings.RssConfig attribute) num_layers (autoplex.settings.NEQUIPSettings attribute) num_of_initial_selected_structs (autoplex.settings.RssConfig attribute) num_of_rss_selected_structs (autoplex.settings.RssConfig attribute) num_processes_buildcell (autoplex.settings.RssConfig attribute) num_processes_fit (autoplex.settings.RssConfig attribute) num_processes_rss (autoplex.settings.RssConfig attribute) O o (autoplex.settings.Nonlinearity attribute) OCTET (autoplex.settings.BuildcellOptions attribute) openmp_chunk_size (autoplex.settings.GAPGeneralSettings attribute) optimizer (autoplex.settings.M3GNETSettings attribute) optimizer_amsgrad (autoplex.settings.NEQUIPSettings attribute) optimizer_name (autoplex.settings.NEQUIPSettings attribute) order (autoplex.settings.JACESettings attribute) output (autoplex.misc.castep.schema.TaskDoc attribute) OVERLAP (autoplex.settings.BuildcellOptions attribute) P P_ACE (autoplex.settings.MLIPHypers attribute) pace_fitting() (in module autoplex.fitting.common.utils) pair_repulsion (autoplex.settings.MACESettings attribute) parallel_calc_descriptor_vec() (in module autoplex.data.common.utils) param_updates (autoplex.misc.castep.utils.CastepInputGenerator property) (autoplex.misc.castep.utils.CastepStaticSetGenerator property) parity (autoplex.settings.NEQUIPSettings attribute) patience (autoplex.settings.MACESettings attribute) per_species_rescale_scales (autoplex.settings.NEQUIPSettings attribute) per_species_rescale_scales_trainable (autoplex.settings.NEQUIPSettings attribute) per_species_rescale_shifts (autoplex.settings.NEQUIPSettings attribute) per_species_rescale_shifts_trainable (autoplex.settings.NEQUIPSettings attribute) PhononBenchmarkMaker (class in autoplex.benchmark.phonons.flows) piecewise_linear() (in module autoplex.fitting.common.regularization) plot_convex_hull() (in module autoplex.fitting.common.utils) plot_energy_forces() (in module autoplex.data.common.utils) plot_force_distribution() (in module autoplex.data.common.jobs) point_in_simplex_nd() (in module autoplex.fitting.common.regularization) point_in_triangle_2D() (in module autoplex.fitting.common.regularization) polynomialcutoff_p (autoplex.settings.NEQUIPSettings attribute) population (autoplex.settings.NEPSettings attribute) potential (autoplex.settings.PacemakerSettings attribute) pre_database_dir (autoplex.settings.ResumeFromPreviousState attribute) (autoplex.settings.RssConfig attribute) PREC (autoplex.settings.CustomIncar attribute) prediction (autoplex.settings.NEPSettings attribute) prepare_fit_environment() (in module autoplex.fitting.common.utils) preprocess_data() (in module autoplex.data.common.jobs) process_rss() (in module autoplex.data.rss.utils) R r_max (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) random_seed (autoplex.settings.RssConfig attribute) random_vary_angle() (in module autoplex.data.common.utils) RandomizedStructure (class in autoplex.data.rss.jobs) RandomStructuresDataGenerator (class in autoplex.data.phonons.flows) rbf_type (autoplex.settings.M3GNETSettings attribute) reduce_supercell_size() (in module autoplex.data.phonons.utils) reduce_supercell_size_job() (in module autoplex.data.phonons.jobs) ref_energy_name (autoplex.settings.RssConfig attribute) ref_force_name (autoplex.settings.RssConfig attribute) ref_virial_name (autoplex.settings.RssConfig attribute) reg_minmax (autoplex.settings.RssConfig attribute) regularization (autoplex.settings.RssConfig attribute) remove_traj_files (autoplex.settings.RssConfig attribute) report_init_validation (autoplex.settings.NEQUIPSettings attribute) restart_latest (autoplex.settings.MACESettings attribute) results_dir (autoplex.settings.M3GNETSettings attribute) resume_from_previous_state (autoplex.settings.RssConfig attribute) retain_existing_sigma (autoplex.settings.RssConfig attribute) rms_dict() (in module autoplex.data.common.utils) rmse_qdep_plot() (in module autoplex.benchmark.phonons.utils) root (autoplex.settings.NEQUIPSettings attribute) rss_group (autoplex.settings.RssConfig attribute) rss_selection_method (autoplex.settings.RssConfig attribute) RssMaker (class in autoplex.auto.rss.flows) run_ace() (in module autoplex.fitting.common.utils) run_ase_gap() (in module autoplex.fitting.common.utils) run_castep() (in module autoplex.misc.castep.run) run_gap() (in module autoplex.fitting.common.utils) run_mace() (in module autoplex.fitting.common.utils) run_name (autoplex.settings.NEQUIPSettings attribute) run_nep() (in module autoplex.fitting.common.utils) run_nequip() (in module autoplex.fitting.common.utils) run_pacemaker() (in module autoplex.fitting.common.utils) run_supercells() (in module autoplex.auto.phonons.jobs) S safe_strip_hostname() (in module autoplex.data.common.jobs) sample_data() (in module autoplex.data.common.jobs) save_all_checkpoints (autoplex.settings.MACESettings attribute) save_checkpoint_freq (autoplex.settings.NEQUIPSettings attribute) save_cpu (autoplex.settings.MACESettings attribute) save_ema_checkpoint_freq (autoplex.settings.NEQUIPSettings attribute) scalar_exp_pressure (autoplex.settings.RssConfig attribute) scalar_pressure_exponential_width (autoplex.settings.RssConfig attribute) scalar_pressure_high (autoplex.settings.RssConfig attribute) scalar_pressure_low (autoplex.settings.RssConfig attribute) scalar_pressure_method (autoplex.settings.RssConfig attribute) scale_cell() (in module autoplex.data.common.utils) scaling (autoplex.settings.MACESettings attribute) scheduler (autoplex.settings.M3GNETSettings attribute) scheme (autoplex.settings.RssConfig attribute) seed (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) (autoplex.settings.PacemakerSettings attribute) set_custom_sigma() (in module autoplex.fitting.common.regularization) SETTINGS (in module autoplex.settings) shuffle (autoplex.settings.NEQUIPSettings attribute) SIGMA (autoplex.settings.CustomIncar attribute) SLACK (autoplex.settings.BuildcellOptions attribute) soap (autoplex.settings.GAPGeneralSettings attribute) (autoplex.settings.GAPSettings attribute) soap_paras (autoplex.settings.BcurParams attribute) solver (autoplex.settings.JACESettings attribute) sparse_jitter (autoplex.settings.GAPGeneralSettings attribute) sparse_method (autoplex.settings.SoapSettings attribute) (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) species (autoplex.settings.SoapParas attribute) split_structure_into_groups() (in module autoplex.data.rss.utils) start_swa (autoplex.settings.MACESettings attribute) static_run_and_convert() (autoplex.data.common.flows.GenerateTrainingDataForTesting method) std_rattle() (in module autoplex.data.common.utils) stop_criterion (autoplex.settings.RssConfig attribute) stratified_dataset_split() (in module autoplex.data.common.utils) stress (autoplex.misc.castep.schema.OutputDoc attribute) stress_tol (autoplex.settings.RssConfig attribute) stress_weight (autoplex.settings.M3GNETSettings attribute) (autoplex.settings.MACESettings attribute) structure (autoplex.misc.castep.schema.OutputDoc attribute) (autoplex.misc.castep.schema.TaskDoc attribute) swa (autoplex.settings.MACESettings attribute) SYMMOPS (autoplex.settings.BuildcellOptions attribute) sync_dist (autoplex.settings.M3GNETSettings attribute) SYSTEM (autoplex.settings.BuildcellOptions attribute) T tag (autoplex.settings.RssConfig attribute) task_label (autoplex.misc.castep.schema.TaskDoc attribute) test_error (autoplex.settings.ResumeFromPreviousState attribute) test_ratio (autoplex.settings.RssConfig attribute) theta_uniform (autoplex.settings.ThreebSettings attribute) (autoplex.settings.TwobSettings attribute) three_body (autoplex.settings.GAPGeneralSettings attribute) threeb (autoplex.settings.GAPSettings attribute) threebody_cutoff (autoplex.settings.M3GNETSettings attribute) TightDFTStaticMaker (class in autoplex.data.phonons.flows) to_ase_trajectory() (in module autoplex.data.common.utils) todict() (autoplex.data.rss.utils.HookeanRepulsion method) total_energy (autoplex.settings.LossCoeff attribute) totaldegree (autoplex.settings.JACESettings attribute) train_from_scratch (autoplex.settings.RssConfig attribute) two_body (autoplex.settings.GAPGeneralSettings attribute) twob (autoplex.settings.GAPSettings attribute) type (autoplex.settings.NEPSettings attribute) TYPE_CHECKING (in module autoplex.data.common.jobs) (in module autoplex.fitting.common.utils) (in module autoplex.misc.castep.jobs) (in module autoplex.misc.utils.mock_castep) type_weight (autoplex.settings.NEPSettings attribute) U units (autoplex.settings.M3GNETSettings attribute) update_parameters() (autoplex.settings.AutoplexBaseModel method) update_phonon_displacement_maker() (in module autoplex.data.phonons.utils) use_ema (autoplex.settings.NEQUIPSettings attribute) use_foundation_model_element_refs (autoplex.settings.M3GNETSettings attribute) use_sc (autoplex.settings.NEQUIPSettings attribute) V valid_batch_size (autoplex.settings.MACESettings attribute) validation_batch_size (autoplex.settings.NEQUIPSettings attribute) validation_dataset (autoplex.settings.NEQUIPSettings attribute) validation_dataset_file_name (autoplex.settings.NEQUIPSettings attribute) validation_dataset_key_mapping (autoplex.settings.NEQUIPSettings attribute) vaspoutput_2_extended_xyz() (in module autoplex.fitting.common.utils) verbose (autoplex.settings.NEQUIPSettings attribute) version (autoplex.settings.NEPSettings attribute) virial_parameter_name (autoplex.settings.GAPGeneralSettings attribute) virials_weight (autoplex.settings.MACESettings attribute) W wandb (autoplex.settings.MACESettings attribute) (autoplex.settings.NEQUIPSettings attribute) write_after_distillation_data_split() (in module autoplex.fitting.common.utils) write_benchmark_metrics() (in module autoplex.benchmark.phonons.jobs) Z zbl (autoplex.settings.NEPSettings attribute) zeta (autoplex.settings.SoapParas attribute) (autoplex.settings.SoapSettings attribute) zpath() (in module autoplex.misc.utils.mock_castep)
