Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z A accuracy (eon.schema.XTBPot attribute) active_region (eon.schema.RecyclingConfig attribute) add_edge() (eon.movie.Graph method) add_node() (eon.movie.Graph method) add_process() (eon.akmcstate.AKMCState method) (eon.prstate.PRState method) (eon.state.State method) add_row() (eon.fileio.Table method) add_state() (eon.basinhopping.BHStates method) adjust_displacement (eon.schema.BasinHoppingConfig attribute) adjust_fraction (eon.schema.BasinHoppingConfig attribute) adjust_period (eon.schema.BasinHoppingConfig attribute) akmc() (in module eon.akmc) AKMCState (class in eon.akmcstate) AKMCStateList (class in eon.akmcstatelist) all_free_atoms (eon.schema.PrefactorConfig attribute) alphanum_key() (in module eon.communicator) amsbin (eon.schema.AMSEnvConfig attribute) amshome (eon.schema.AMSEnvConfig attribute) amsresources (eon.schema.AMSEnvConfig attribute) andersen_alpha (eon.schema.DynamicsConfig attribute) andersen_collision_period (eon.schema.DynamicsConfig attribute) append() (eon.atoms.Atoms method) (eon.fileio.Dynamics method) append_modified_process_table() (eon.askmc.ASKMC method) append_process_table() (eon.akmcstate.AKMCState method) (eon.prstate.PRState method) append_sb() (eon.fileio.Dynamics method) append_search_result() (eon.akmcstate.AKMCState method) append_state_table() (eon.statelist.StateList method) aquirelock() (eon.locking.LockFile method) ASKMC (class in eon.askmc) askmc_barrier_raise_param (eon.schema.CoarseGrainingConfig attribute) askmc_barrier_test_on (eon.schema.CoarseGrainingConfig attribute) askmc_confidence (eon.schema.CoarseGrainingConfig attribute) askmc_connections_test_on (eon.schema.CoarseGrainingConfig attribute) askmc_high_barrier_def (eon.schema.CoarseGrainingConfig attribute) atom_list (eon.schema.HessianConfig attribute) Atoms (class in eon.atoms) B basinhopping() (in module eon.basinhopping) basis (eon.schema.AMSConfig attribute) bb_boost_atom_list (eon.schema.HyperdynamicsConfig attribute) bb_ds_curvature (eon.schema.HyperdynamicsConfig attribute) bb_dvmax (eon.schema.HyperdynamicsConfig attribute) bb_rcut (eon.schema.HyperdynamicsConfig attribute) bb_rmd_time (eon.schema.HyperdynamicsConfig attribute) bb_stretch_threshold (eon.schema.HyperdynamicsConfig attribute) bh_minima (eon.schema.PathsConfig attribute) BHStates (class in eon.basinhopping) bias_potential (eon.schema.HyperdynamicsConfig attribute) bowl_active_atoms (eon.schema.SaddleSearchConfig attribute) bowl_breakout (eon.schema.SaddleSearchConfig attribute) box_to_length_angle() (in module eon.fileio) brute_neighbor_list() (in module eon.atoms) brute_neighbors (eon.schema.StructureComparisonConfig attribute) build_result() (eon.explorer.ProcessSearch method) C c_mcamc() (in module eon.mcamc.mcamc) cancel_job (eon.schema.CommunicatorConfig attribute) cancel_state() (eon.communicator.Communicator method) (eon.communicator.Local method) (eon.communicator.MPI method) (eon.communicator.Script method) cg_knock_out_max_move (eon.schema.CGConfig attribute) cg_line_converged (eon.schema.CGConfig attribute) cg_line_search (eon.schema.CGConfig attribute) cg_max_iter_before_reset (eon.schema.CGConfig attribute) cg_max_iter_line_search (eon.schema.CGConfig attribute) cg_no_overshooting (eon.schema.CGConfig attribute) charge (eon.schema.XTBPot attribute) check_command() (eon.communicator.Script method) check_consistency (eon.schema.Metatomic attribute) check_job() (eon.communicator.Local method) check_rotation (eon.schema.StructureComparisonConfig attribute) checkpoint (eon.schema.MainConfig attribute) ci_after (eon.schema.NudgedElasticBandConfig attribute) ci_mmf (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_after (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_angle (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_ci_stability_count (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_nsteps (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_penalty_base (eon.schema.NudgedElasticBandConfig attribute) ci_mmf_penalty_strength (eon.schema.NudgedElasticBandConfig attribute) cleanup() (eon.communicator.Local method) client_displace_type (eon.schema.SaddleSearchConfig attribute) client_path (eon.schema.CommunicatorConfig attribute) ClientMinModeExplorer (class in eon.explorer) climbing_image_method (eon.schema.NudgedElasticBandConfig attribute) cna() (in module eon.atoms) cnar() (in module eon.atoms) cnat() (in module eon.atoms) Communicator (class in eon.communicator) CommunicatorError compile_process_table() (eon.askmc.ASKMC method) confidence (eon.schema.AKMCConfig attribute) confidence_correction (eon.schema.AKMCConfig attribute) confidence_scheme (eon.schema.AKMCConfig attribute) config (in module eon.config) ConfigClass (class in eon.config) ConfigKey (class in eon.config) ConfigSection (class in eon.config) configuration (eon.schema.PrefactorConfig attribute) confine_positive (eon.schema.SaddleSearchConfig attribute) confine_positive_boost (eon.schema.SaddleSearchConfig attribute) confine_positive_min_active (eon.schema.SaddleSearchConfig attribute) confine_positive_min_force (eon.schema.SaddleSearchConfig attribute) confine_positive_scale_ratio (eon.schema.SaddleSearchConfig attribute) connect_state_sets() (eon.akmcstatelist.AKMCStateList method) connect_states() (eon.akmcstatelist.AKMCStateList method) contains_state() (eon.superbasin.Superbasin method) converged_angle (eon.schema.DimerConfig attribute) converged_force (eon.schema.NudgedElasticBandConfig attribute) (eon.schema.OptimizerConfig attribute) (eon.schema.SaddleSearchConfig attribute) convergence_metric (eon.schema.OptimizerConfig attribute) coordination_numbers() (in module eon.atoms) copy() (eon.atoms.Atoms method) covalent_scale (eon.schema.StructureComparisonConfig attribute) cut_global (eon.schema.ZBLPot attribute) cut_inner (eon.schema.ZBLPot attribute) D default_value (eon.schema.PrefactorConfig attribute) delete() (eon.superbasin.Superbasin method) delete_row() (eon.fileio.Table method) delete_row_func() (eon.fileio.Table method) dephase_loop_max (eon.schema.ParallelReplicaConfig attribute) dephase_loop_stop (eon.schema.ParallelReplicaConfig attribute) dephase_time (eon.schema.ParallelReplicaConfig attribute) device (eon.schema.Metatomic attribute) dijkstra() (eon.movie.Graph method) dimer_improved (eon.schema.DimerConfig attribute) dimer_max_iterations (eon.schema.DimerConfig attribute) dimer_remove_rotation (eon.schema.DimerConfig attribute) dimer_rotations_min (eon.schema.DimerConfig attribute) dimer_torque_max (eon.schema.DimerConfig attribute) dimer_torque_min (eon.schema.DimerConfig attribute) Displace (class in eon.displace) displace_all_listed (eon.schema.SaddleSearchConfig attribute) displace_atom_list (eon.schema.SaddleSearchConfig attribute) displace_least_coordinated_weight (eon.schema.SaddleSearchConfig attribute) displace_listed_atom_weight (eon.schema.SaddleSearchConfig attribute) displace_listed_type_weight (eon.schema.SaddleSearchConfig attribute) displace_magnitude (eon.schema.SaddleSearchConfig attribute) displace_max_coordination (eon.schema.SaddleSearchConfig attribute) displace_moved_only (eon.schema.RecyclingConfig attribute) displace_not_FCC_HCP_weight (eon.schema.SaddleSearchConfig attribute) displace_radius (eon.schema.SaddleSearchConfig attribute) displace_random_weight (eon.schema.SaddleSearchConfig attribute) displace_type_list (eon.schema.SaddleSearchConfig attribute) displace_under_coordinated_weight (eon.schema.SaddleSearchConfig attribute) DisplaceError displacement (eon.schema.BasinHoppingConfig attribute) displacement_distribution (eon.schema.BasinHoppingConfig attribute) DisplacementManager (class in eon.displace) distance_difference (eon.schema.StructureComparisonConfig attribute) dot() (eon.movie.Graph method) (in module eon.movie) Dynamics (class in eon.fileio) dynamics() (in module eon.movie) dynamics_linear_interpolation (eon.schema.SaddleSearchConfig attribute) dynamics_max_init_curvature (eon.schema.SaddleSearchConfig attribute) dynamics_record_interval (eon.schema.SaddleSearchConfig attribute) dynamics_state_check_interval (eon.schema.SaddleSearchConfig attribute) dynamics_temperature (eon.schema.SaddleSearchConfig attribute) E edgelist_to_statelist() (eon.askmc.ASKMC method) electronic_temperature (eon.schema.XTBPot attribute) elements (in module eon.atoms) energy_difference (eon.schema.StructureComparisonConfig attribute) energy_increment (eon.schema.CoarseGrainingConfig attribute) energy_weighted (eon.schema.NudgedElasticBandConfig attribute) EnergyLevel (class in eon.superbasinscheme) engine (eon.schema.AMSConfig attribute) (eon.schema.AMSIOConfig attribute) eon module eon.akmc module eon.akmcstate module eon.akmcstatelist module eon.askmc module eon.atoms module eon.basinhopping module eon.communicator module eon.config module eon.displace module eon.eon_kdb module eon.escaperate module eon.explorer module eon.fileio module eon.locking module eon.mcamc module eon.mcamc.mcamc module eon.mcamc.test module eon.movie module eon.mpiwait module eon.parallelreplica module eon.prstate module eon.prstatelist module eon.recycling module eon.server module eon.state module eon.statelist module eon.superbasin module eon.superbasinscheme module EONClientError eq_rate (eon.schema.AKMCConfig attribute) estimate_condition() (in module eon.mcamc.mcamc) estimate_neb_eigenvalues (eon.schema.DebugConfig attribute) ew_ksp_max (eon.schema.NudgedElasticBandConfig attribute) ew_ksp_min (eon.schema.NudgedElasticBandConfig attribute) ew_trigger (eon.schema.NudgedElasticBandConfig attribute) explore() (eon.explorer.MinModeExplorer method) (eon.explorer.ServerMinModeExplorer method) Explorer (class in eon.explorer) ext_pot_path (eon.schema.PotentialConfig attribute) extensions_directory (eon.schema.Metatomic attribute) F fastest_path() (in module eon.movie) filter_epicenters() (eon.displace.Displace method) filter_fraction (eon.schema.PrefactorConfig attribute) filter_scheme (eon.schema.PrefactorConfig attribute) find_repeat() (eon.akmcstate.AKMCState method) find_row() (eon.fileio.Table method) find_value() (eon.fileio.Table method) finish_minimization() (eon.explorer.ProcessSearch method) finish_search() (eon.explorer.ProcessSearch method) finite_angle (eon.schema.DimerConfig attribute) finite_difference (eon.schema.MainConfig attribute) forcefield (eon.schema.AMSConfig attribute) (eon.schema.AMSIOConfig attribute) free_r() (eon.atoms.Atoms method) G generate_corresponding_states() (eon.recycling.SB_Recycling method) generate_displacement() (eon.explorer.MinModeExplorer method) get() (eon.fileio.Dynamics method) (eon.fileio.ini method) get_akmc_metadata() (in module eon.akmc) get_askmc_metadata() (eon.askmc.ASKMC method) get_bad_saddle_count() (eon.akmcstate.AKMCState method) get_bundle_size() (eon.communicator.Communicator method) get_column() (eon.fileio.Table method) get_communicator() (in module eon.communicator) get_confidence() (eon.akmcstate.AKMCState method) (eon.superbasin.Superbasin method) get_containing_superbasin() (eon.superbasinscheme.SuperbasinScheme method) get_count() (eon.superbasinscheme.TransitionCounting method) get_displacement() (eon.displace.Displace method) (eon.displace.Water method) get_energy() (eon.state.State method) get_energy_increment() (eon.superbasinscheme.EnergyLevel method) get_fastest_process_id() (in module eon.movie) get_fastest_process_rate() (in module eon.movie) get_good_saddle_count() (eon.akmcstate.AKMCState method) get_job() (eon.explorer.ProcessSearch method) get_lowest_barrier() (eon.akmcstate.AKMCState method) get_lowest_confidence_state() (eon.superbasin.Superbasin method) get_mappings() (in module eon.atoms) get_minmodexplorer() (in module eon.explorer) get_modified_process_table() (eon.askmc.ASKMC method) get_moved_indices() (eon.recycling.Recycling method) get_num_procs() (eon.state.State method) get_num_states() (eon.statelist.StateList method) get_number_in_progress() (eon.communicator.Local method) (eon.communicator.MPI method) (eon.communicator.Script method) get_number_of_searches() (eon.akmcstate.AKMCState method) get_pr_metadata() (in module eon.escaperate) (in module eon.parallelreplica) get_previous_state() (eon.state.State method) get_prng_state() (in module eon.fileio) get_proc_random_count() (eon.akmcstate.AKMCState method) get_process() (eon.state.State method) get_process_atoms() (in module eon.atoms) get_process_id() (eon.askmc.ASKMC method) (eon.recycling.SB_Recycling method) get_process_ids() (eon.state.State method) get_process_mode() (eon.akmcstate.AKMCState method) get_process_product() (eon.akmcstate.AKMCState method) (eon.state.State method) get_process_reactant() (eon.akmcstate.AKMCState method) (eon.state.State method) get_process_saddle() (eon.akmcstate.AKMCState method) get_process_table() (eon.akmcstate.AKMCState method) (eon.state.State method) get_product_state() (eon.statelist.StateList method) get_queue_size() (eon.communicator.Communicator method) (eon.communicator.Local method) (eon.communicator.MPI method) (eon.communicator.Script method) get_queued_jobs() (eon.communicator.Script method) get_random_minimum() (eon.basinhopping.BHStates method) get_ratetable() (eon.akmcstate.AKMCState method) (eon.askmc.ASKMC method) get_reactant() (eon.state.State method) get_ready_ranks() (eon.communicator.MPI method) get_real_process_table() (eon.askmc.ASKMC method) get_relevant_procids() (eon.akmcstate.AKMCState method) get_repeats() (eon.akmcstate.AKMCState method) get_results() (eon.communicator.Communicator method) (eon.communicator.Local method) (eon.communicator.MPI method) (eon.communicator.Script method) get_rotation_matrix() (in module eon.atoms) get_row() (eon.fileio.Table method) get_rows() (eon.fileio.Table method) get_saddle() (eon.explorer.ProcessSearch method) get_saddle_file() (eon.explorer.ProcessSearch method) get_state() (eon.statelist.StateList method) get_statelist() (eon.superbasinscheme.EnergyLevel method) (in module eon.akmc) (in module eon.escaperate) (in module eon.parallelreplica) get_superbasin_scheme() (in module eon.akmc) get_time() (eon.akmcstate.AKMCState method) (eon.prstate.PRState method) get_time_by_temp() (eon.akmcstate.AKMCState method) get_total_saddle_count() (eon.akmcstate.AKMCState method) get_trajectory() (in module eon.movie) get_unique_saddle_count() (eon.akmcstate.AKMCState method) getboolean() (eon.fileio.ini method) getfloat() (eon.fileio.ini method) getint() (eon.fileio.ini method) Graph (class in eon.movie) guess_precision() (in module eon.mcamc.mcamc) H host (eon.schema.SocketNWChemPot attribute) I identical() (in module eon.atoms) images (eon.schema.NudgedElasticBandConfig attribute) in_array() (eon.askmc.ASKMC method) inc_proc_random_count() (eon.akmcstate.AKMCState method) inc_repeats() (eon.akmcstate.AKMCState method) inc_time() (eon.prstate.PRState method) incomplete (eon.schema.PathsConfig attribute) increment_time() (eon.akmcstate.AKMCState method) indistinguishable_atoms (eon.schema.StructureComparisonConfig attribute) ini (class in eon.fileio) init() (eon.config.ConfigClass method) (eon.displace.Undercoordinated method) (eon.fileio.Table method) init_force_threshold (eon.schema.NudgedElasticBandConfig attribute) init_max_iterations (eon.schema.NudgedElasticBandConfig attribute) init_max_move (eon.schema.NudgedElasticBandConfig attribute) initial_path_in (eon.schema.NudgedElasticBandConfig attribute) initial_random_structure_probability (eon.schema.BasinHoppingConfig attribute) initial_state_pool_size (eon.schema.BasinHoppingConfig attribute) initializer (eon.schema.NudgedElasticBandConfig attribute) insert() (in module eon.eon_kdb) interactive_shell (eon.schema.DebugConfig attribute) internal_motion() (in module eon.atoms) is_equal() (eon.askmc.ASKMC method) islocked() (eon.locking.LockFile method) J job (eon.schema.MainConfig attribute) jobs_in (eon.schema.PathsConfig attribute) jobs_out (eon.schema.PathsConfig attribute) jobs_per_bundle (eon.schema.CommunicatorConfig attribute) jump_max (eon.schema.BasinHoppingConfig attribute) jump_steps (eon.schema.BasinHoppingConfig attribute) K kdb (eon.schema.PathsConfig attribute) kdb_dc (eon.schema.KDBConfig attribute) kdb_mac (eon.schema.KDBConfig attribute) kdb_name (eon.schema.KDBConfig attribute) kdb_nf (eon.schema.KDBConfig attribute) kdb_only (eon.schema.KDBConfig attribute) kdb_scratch (eon.schema.PathsConfig attribute) keep_all_result_files (eon.schema.DebugConfig attribute) keep_bad_saddles (eon.schema.DebugConfig attribute) kmc_step() (in module eon.akmc) L lambertw() (in module eon.akmcstate) lammps_logging (eon.schema.PotentialConfig attribute) lammps_threads (eon.schema.PotentialConfig attribute) langevin_friction (eon.schema.DynamicsConfig attribute) lbfgs_angle_reset (eon.schema.LBFGSConfig attribute) lbfgs_auto_scale (eon.schema.LBFGSConfig attribute) lbfgs_distance_reset (eon.schema.LBFGSConfig attribute) lbfgs_inverse_curvature (eon.schema.LBFGSConfig attribute) lbfgs_max_inverse_curvature (eon.schema.LBFGSConfig attribute) lbfgs_memory (eon.schema.LBFGSConfig attribute) least_coordinated() (in module eon.atoms) Leastcoordinated (class in eon.displace) length_angle_to_box() (in module eon.fileio) length_unit (eon.schema.Metatomic attribute) libpath (in module eon.mcamc.mcamc) ListedAtoms (class in eon.displace) ListedTypes (class in eon.displace) load_mode() (in module eon.fileio) load_potfiles() (in module eon.fileio) load_process_table() (eon.akmcstate.AKMCState method) (eon.prstate.PRState method) load_result() (eon.explorer.ProcessSearch method) load_state_table() (eon.statelist.StateList method) load_wuid() (eon.explorer.Explorer method) loadcon() (in module eon.fileio) loadcons() (in module eon.fileio) loadposcar() (in module eon.fileio) loadposcars() (in module eon.fileio) Local (class in eon.communicator) LockFile (class in eon.locking) locsearch() (eon.askmc.ASKMC method) log_potential (eon.schema.PotentialConfig attribute) logger (in module eon.akmc) (in module eon.akmcstate) (in module eon.akmcstatelist) (in module eon.askmc) (in module eon.atoms) (in module eon.basinhopping) (in module eon.communicator) (in module eon.displace) (in module eon.eon_kdb) (in module eon.escaperate) (in module eon.explorer) (in module eon.fileio) (in module eon.mcamc.mcamc) (in module eon.mpiwait) (in module eon.parallelreplica) (in module eon.prstate) (in module eon.prstatelist) (in module eon.state) (in module eon.statelist) (in module eon.superbasin) (in module eon.superbasinscheme) M main() (in module eon.akmc) (in module eon.basinhopping) (in module eon.escaperate) (in module eon.mcamc.test) (in module eon.parallelreplica) main_directory (eon.schema.PathsConfig attribute) make_basin() (eon.superbasinscheme.SuperbasinScheme method) make_basin_from_sets() (eon.superbasinscheme.SuperbasinScheme method) make_bundles() (eon.communicator.Communicator method) make_displacement() (eon.displace.Displace method) (eon.displace.DisplacementManager method) (eon.displace.Leastcoordinated method) (eon.displace.ListedAtoms method) (eon.displace.ListedTypes method) (eon.displace.NotFCCorHCP method) (eon.displace.NotTCP method) (eon.displace.NotTCPorBCC method) (eon.displace.Random method) (eon.displace.Undercoordinated method) (eon.displace.Water method) make_graph() (in module eon.movie) make_jobs() (eon.explorer.ClientMinModeExplorer method) (eon.explorer.ServerMinModeExplorer method) make_movie() (in module eon.movie) make_searches() (in module eon.basinhopping) (in module eon.escaperate) (in module eon.parallelreplica) make_suggestion() (eon.recycling.Recycling method) (eon.recycling.SB_Recycling method) (in module eon.eon_kdb) make_template_input (eon.schema.SocketNWChemPot attribute) mass_weight_factor (eon.schema.RecyclingConfig attribute) match() (in module eon.atoms) max_displacement_algorithm (eon.schema.BasinHoppingConfig attribute) max_energy (eon.schema.SaddleSearchConfig attribute) max_force_calls (eon.schema.MainConfig attribute) max_iterations (eon.schema.LanczosConfig attribute) (eon.schema.OptimizerConfig attribute) (eon.schema.SaddleSearchConfig attribute) (eon.schema.XTBPot attribute) max_jobs (eon.schema.CommunicatorConfig attribute) max_kmc_steps (eon.schema.AKMCConfig attribute) max_move (eon.schema.OptimizerConfig attribute) max_rate (eon.schema.AKMCConfig attribute) max_row() (eon.fileio.Table method) max_single_displace (eon.schema.SaddleSearchConfig attribute) max_size (eon.schema.CoarseGrainingConfig attribute) max_value (eon.schema.PrefactorConfig attribute) max_value() (eon.fileio.Table method) mem_in_gb (eon.schema.SocketNWChemPot attribute) method (eon.schema.SaddleSearchConfig attribute) min_displacement (eon.schema.PrefactorConfig attribute) min_mode_method (eon.schema.SaddleSearchConfig attribute) min_row() (eon.fileio.Table method) min_value (eon.schema.PrefactorConfig attribute) min_value() (eon.fileio.Table method) minimization_offset (eon.schema.ProcessSearchConfig attribute) minimize_endpoints (eon.schema.NudgedElasticBandConfig attribute) minimize_endpoints_for_ipath (eon.schema.NudgedElasticBandConfig attribute) minimize_first (eon.schema.ProcessSearchConfig attribute) MinModeExplorer (class in eon.explorer) missed_connections() (eon.askmc.ASKMC method) missed_low_barriers() (eon.askmc.ASKMC method) mmf_peak_tolerance (eon.schema.NudgedElasticBandConfig attribute) mod_processtable_head_fmt (in module eon.askmc) mod_processtable_header (in module eon.askmc) model (eon.schema.AMSConfig attribute) (eon.schema.AMSIOConfig attribute) model_path (eon.schema.Metatomic attribute) modify_config() (in module eon.fileio) module eon eon.akmc eon.akmcstate eon.akmcstatelist eon.askmc eon.atoms eon.basinhopping eon.communicator eon.config eon.displace eon.eon_kdb eon.escaperate eon.explorer eon.fileio eon.locking eon.mcamc eon.mcamc.mcamc eon.mcamc.test eon.movie eon.mpiwait eon.parallelreplica eon.prstate eon.prstatelist eon.recycling eon.server eon.state eon.statelist eon.superbasin eon.superbasinscheme move_distance (eon.schema.RecyclingConfig attribute) MPI (class in eon.communicator) mpi_poll_period (eon.schema.PotentialConfig attribute) mpiwait() (in module eon.mpiwait) multiplicity (eon.schema.ASE_NWCHEM attribute) N name_prefix (eon.schema.CommunicatorConfig attribute) neb_climbing_image_converged_only (eon.schema.NudgedElasticBandConfig attribute) neb_doubly_nudged (eon.schema.NudgedElasticBandConfig attribute) neb_doubly_nudged_switching (eon.schema.NudgedElasticBandConfig attribute) neb_elastic_band (eon.schema.NudgedElasticBandConfig attribute) neb_max_iterations (eon.schema.NudgedElasticBandConfig attribute) neb_mmf_estimator (eon.schema.DebugConfig attribute) neighbor_cutoff (eon.schema.StructureComparisonConfig attribute) neighbor_list() (in module eon.atoms) neighbor_list_vectors() (in module eon.atoms) neighbors() (eon.movie.Graph method) nodes() (eon.movie.Graph method) nonlocal_count_abort (eon.schema.SaddleSearchConfig attribute) nonlocal_distance_abort (eon.schema.SaddleSearchConfig attribute) nonnegative_displacement_abort (eon.schema.SaddleSearchConfig attribute) nose_mass (eon.schema.DynamicsConfig attribute) not_HCP_or_FCC() (in module eon.atoms) not_TCP() (in module eon.atoms) not_TCP_or_BCC() (in module eon.atoms) NotFCCorHCP (class in eon.displace) NotImplementedError, [1] NotTCP (class in eon.displace) NotTCPorBCC (class in eon.displace) np_mcamc() (in module eon.mcamc.mcamc) nproc (eon.schema.ASE_NWCHEM attribute) (eon.schema.ASE_ORCA attribute) num_jobs (eon.schema.CommunicatorConfig attribute) number_of_CPUs (eon.schema.CommunicatorConfig attribute) number_of_transitions (eon.schema.CoarseGrainingConfig attribute) numElements (in module eon.atoms) nwchem_path (eon.schema.ASE_NWCHEM attribute) nwchem_settings (eon.schema.SocketNWChemPot attribute) O old_tangent (eon.schema.NudgedElasticBandConfig attribute) om_k_max (eon.schema.NudgedElasticBandConfig attribute) om_k_min (eon.schema.NudgedElasticBandConfig attribute) om_k_scale (eon.schema.NudgedElasticBandConfig attribute) om_optimize_k (eon.schema.NudgedElasticBandConfig attribute) onsager_machlup (eon.schema.NudgedElasticBandConfig attribute) opt_method (eon.schema.DimerConfig attribute) (eon.schema.OptimizerConfig attribute) orca_path (eon.schema.ASE_ORCA attribute) P parallelreplica() (in module eon.escaperate) (in module eon.parallelreplica) paramset (eon.schema.XTBPot attribute) parse_results() (in module eon.fileio) pbc() (in module eon.atoms) per_atom_norm() (in module eon.atoms) per_atom_norm_gen() (in module eon.atoms) perp_force_ratio (eon.schema.SaddleSearchConfig attribute) point_energy_match() (in module eon.atoms) points_energies_match() (in module eon.atoms) port (eon.schema.SocketNWChemPot attribute) post_transition_time (eon.schema.ParallelReplicaConfig attribute) potential (eon.schema.PotentialConfig attribute) potential_files (eon.schema.PathsConfig attribute) priorityDictionary (class in eon.movie) proc_mode_path() (eon.akmcstate.AKMCState method) proc_product_path() (eon.state.State method) proc_reactant_path() (eon.state.State method) proc_results_path() (eon.state.State method) proc_saddle_path() (eon.akmcstate.AKMCState method) proc_stdout_path() (eon.state.State method) process_result() (eon.explorer.ProcessSearch method) processes() (in module eon.movie) ProcessSearch (class in eon.explorer) processtable_head_fmt (eon.akmcstate.AKMCState attribute) (eon.prstate.PRState attribute) (in module eon.askmc) processtable_header (eon.akmcstate.AKMCState attribute) (eon.prstate.PRState attribute) (in module eon.askmc) processtable_line (eon.akmcstate.AKMCState attribute) (eon.prstate.PRState attribute) (in module eon.askmc) PRState (class in eon.prstate) PRStateList (class in eon.prstatelist) push_apart_distance (eon.schema.BasinHoppingConfig attribute) Q qm_steepest_descent (eon.schema.QuickMinConfig attribute) quenching_steps (eon.schema.BasinHoppingConfig attribute) query() (in module eon.eon_kdb) queued_jobs (eon.schema.CommunicatorConfig attribute) quiet (eon.schema.MainConfig attribute) QUIT (in module eon.mpiwait) quit_early (eon.schema.LanczosConfig attribute) R raiseup() (eon.askmc.ASKMC method) Random (class in eon.displace) random_chain() (in module eon.mcamc.test) random_seed (eon.schema.MainConfig attribute) rate_estimation (eon.schema.PrefactorConfig attribute) rate_threshold (eon.schema.CoarseGrainingConfig attribute) RateThreshold (class in eon.superbasinscheme) read() (eon.fileio.ini method) (eon.fileio.Table method) read_data() (eon.superbasin.Superbasin method) (eon.superbasinscheme.EnergyLevel method) (eon.superbasinscheme.RateThreshold method) (eon.superbasinscheme.SuperbasinScheme method) (eon.superbasinscheme.TransitionCounting method) read_metadata() (eon.recycling.SB_Recycling method) read_recycling_metadata() (eon.recycling.Recycling method) Recycling (class in eon.recycling) refine_opt_method (eon.schema.RefineConfig attribute) refine_threshold (eon.schema.RefineConfig attribute) refine_transition (eon.schema.ParallelReplicaConfig attribute) register_bad_saddle() (eon.akmcstate.AKMCState method) register_extra_results (eon.schema.DebugConfig attribute) register_process() (eon.akmcstatelist.AKMCStateList method) (eon.prstatelist.PRStateList method) register_results() (eon.explorer.ClientMinModeExplorer method) (eon.explorer.ServerMinModeExplorer method) (in module eon.basinhopping) (in module eon.escaperate) (in module eon.parallelreplica) register_transition() (eon.askmc.ASKMC method) (eon.superbasinscheme.EnergyLevel method) (eon.superbasinscheme.RateThreshold method) (eon.superbasinscheme.SuperbasinScheme method) (eon.superbasinscheme.TransitionCounting method) remove_duplicates (eon.schema.KDBConfig attribute) remove_net_force (eon.schema.MainConfig attribute) remove_rotation (eon.schema.SaddleSearchConfig attribute) remove_translation (eon.schema.StructureComparisonConfig attribute) removelock() (eon.locking.LockFile method) reset_repeats() (eon.akmcstate.AKMCState method) resources (eon.schema.AMSConfig attribute) result_files_path (eon.schema.DebugConfig attribute) results (eon.schema.PathsConfig attribute) rot_match() (in module eon.atoms) rotate() (in module eon.atoms) rotate_water() (eon.displace.Water static method) rotations_max (eon.schema.DimerConfig attribute) rotm() (in module eon.atoms) run_resume_jobs() (eon.communicator.MPI method) S save() (eon.explorer.ServerMinModeExplorer method) save_askmc_metadata() (eon.askmc.ASKMC method) save_jobids() (eon.communicator.Script method) save_mode() (in module eon.fileio) save_modified_process_table() (eon.askmc.ASKMC method) save_prng_state() (in module eon.fileio) save_process_table() (eon.akmcstate.AKMCState method) (eon.prstate.PRState method) save_result() (eon.explorer.ProcessSearch method) save_results_dat() (in module eon.fileio) save_state_table() (eon.statelist.StateList method) save_stdout (eon.schema.DebugConfig attribute) save_suggestions (eon.schema.RecyclingConfig attribute) save_wuid() (eon.explorer.Explorer method) savecon() (in module eon.fileio) saveposcar() (in module eon.fileio) SB_Recycling (class in eon.recycling) scf_maxiter (eon.schema.ASE_NWCHEM attribute) scf_thresh (eon.schema.ASE_NWCHEM attribute) scm_pythondir (eon.schema.AMSEnvConfig attribute) scm_tmpdir (eon.schema.AMSEnvConfig attribute) scmlicense (eon.schema.AMSEnvConfig attribute) scratch (eon.schema.PathsConfig attribute) Script (class in eon.communicator) script_path (eon.schema.CommunicatorConfig attribute) sd_alpha (eon.schema.SDConfig attribute) sd_twopoint (eon.schema.SDConfig attribute) search_result_header (eon.prstate.PRState attribute) server() (in module eon.server) server_side_process_search (eon.schema.AKMCConfig attribute) ServerMinModeExplorer (class in eon.explorer) set() (eon.fileio.ini method) set_bad_saddle_count() (eon.akmcstate.AKMCState method) set_converged_force() (eon.schema.SaddleSearchConfig class method) set_default_paths() (eon.schema.PathsConfig class method) set_energy() (eon.state.State method) set_good_saddle_count() (eon.akmcstate.AKMCState method) set_log_potential() (eon.schema.PotentialConfig class method) set_max_iterations() (eon.schema.SaddleSearchConfig class method) set_unique_saddle_count() (eon.akmcstate.AKMCState method) setdefault() (eon.movie.priorityDictionary method) setup_mmf_peaks (eon.schema.NudgedElasticBandConfig attribute) shortest_path() (eon.movie.Graph method) sidpp_growth_alpha (eon.schema.NudgedElasticBandConfig attribute) signal_handler() (in module eon.mpiwait) significant_structure (eon.schema.BasinHoppingConfig attribute) simpleinput (eon.schema.ASE_ORCA attribute) single_atom_displace (eon.schema.BasinHoppingConfig attribute) smallest() (eon.movie.priorityDictionary method) sort_nicely() (in module eon.communicator) spring (eon.schema.NudgedElasticBandConfig attribute) start_minimization() (eon.explorer.ProcessSearch method) start_search() (eon.explorer.ProcessSearch method) State (class in eon.state) state_check_interval (eon.schema.ParallelReplicaConfig attribute) state_file (eon.schema.CoarseGrainingConfig attribute) state_path() (eon.statelist.StateList method) state_save_interval (eon.schema.ParallelReplicaConfig attribute) StateList (class in eon.statelist) states (eon.schema.PathsConfig attribute) step() (eon.superbasin.Superbasin method) (in module eon.escaperate) (in module eon.parallelreplica) steps (eon.schema.BasinHoppingConfig attribute) stop_after_transition (eon.schema.ParallelReplicaConfig attribute) stop_criterion (eon.schema.DebugConfig attribute) submit_job (eon.schema.CommunicatorConfig attribute) submit_jobs() (eon.communicator.Communicator method) (eon.communicator.Local method) (eon.communicator.MPI method) (eon.communicator.Script method) Superbasin (class in eon.superbasin) superbasin_confidence (eon.schema.CoarseGrainingConfig attribute) superbasin_recycling (eon.schema.PathsConfig attribute) superbasin_scheme (eon.schema.CoarseGrainingConfig attribute) superbasins (eon.schema.PathsConfig attribute) SuperbasinScheme (class in eon.superbasinscheme) swap_probability (eon.schema.BasinHoppingConfig attribute) sweep_and_prune() (in module eon.atoms) T Table (class in eon.fileio) TableException tar_procdata() (eon.state.State method) target_ratio (eon.schema.BasinHoppingConfig attribute) target_trajectory (eon.schema.DebugConfig attribute) temperature (eon.schema.MainConfig attribute) thermally_accessible_buffer (eon.schema.AKMCConfig attribute) thermally_accessible_window (eon.schema.AKMCConfig attribute) thermostat (eon.schema.DynamicsConfig attribute) time (eon.schema.DynamicsConfig attribute) time_step (eon.schema.DynamicsConfig attribute) (eon.schema.FIREConfig attribute) (eon.schema.OptimizerConfig attribute) (eon.schema.QuickMinConfig attribute) time_step_max (eon.schema.FIREConfig attribute) tolerance (eon.schema.LanczosConfig attribute) TransitionCounting (class in eon.superbasinscheme) tryint() (in module eon.communicator) type (eon.schema.CommunicatorConfig attribute) U uhf (eon.schema.XTBPot attribute) unbundle() (eon.communicator.Communicator method) uncertainty_threshold (eon.schema.Metatomic attribute) Undercoordinated (class in eon.displace) unix_socket_mode (eon.schema.SocketNWChemPot attribute) unix_socket_path (eon.schema.SocketNWChemPot attribute) update_lowest_barrier() (eon.akmcstate.AKMCState method) use_askmc (eon.schema.CoarseGrainingConfig attribute) use_covalent (eon.schema.StructureComparisonConfig attribute) use_kdb (eon.schema.KDBConfig attribute) use_mcamc (eon.schema.CoarseGrainingConfig attribute) use_mean_time (eon.schema.DebugConfig attribute) use_recycling (eon.schema.RecyclingConfig attribute) use_sb_recycling (eon.schema.RecyclingConfig attribute) V variant_base (eon.schema.Metatomic attribute) variant_energy (eon.schema.Metatomic attribute) variant_energy_uncertainty (eon.schema.Metatomic attribute) W Water (class in eon.displace) within_radius (eon.schema.PrefactorConfig attribute) write() (eon.fileio.Table method) write_akmc_metadata() (in module eon.akmc) write_data() (eon.superbasin.Superbasin method) (eon.superbasinscheme.EnergyLevel method) (eon.superbasinscheme.RateThreshold method) (eon.superbasinscheme.SuperbasinScheme method) (eon.superbasinscheme.TransitionCounting method) write_log (eon.schema.MainConfig attribute) write_metadata() (eon.recycling.SB_Recycling method) write_movies (eon.schema.DebugConfig attribute) write_movies_interval (eon.schema.DebugConfig attribute) write_pr_metadata() (in module eon.escaperate) (in module eon.parallelreplica) write_recycling_metadata() (eon.recycling.Recycling method) write_unique (eon.schema.BasinHoppingConfig attribute) writefilehandle() (eon.fileio.Table method) X xc (eon.schema.AMSConfig attribute) (eon.schema.AMSIOConfig attribute) Z zero_freq_value (eon.schema.HessianConfig attribute) zero_mode_abort_curvature (eon.schema.SaddleSearchConfig attribute) zero_time() (eon.prstate.PRState method)
