Index

A

active (DiagnosticEntry attribute) add_diagnostic_entry() (DiagDB method), [1] add_splitting_data() (AMSDB method) add_task() (AsIORunner method) add_trajectory() (CoreDB method), [1] advance() (ForwardModelBaseClass method), [1] (Trajectory method), [1] alive() (in module pyrevs.bin) (in module pyrevs.bin.bin) all_converged() (Database method), [1] AMS (class in pyrevs.strategies) (class in pyrevs.strategies.ams) (class in pyrevs.strategies.ams.ams) AMSConfig (class in pyrevs.strategies.ams) (class in pyrevs.strategies.ams.config) AMSDatabaseExtension (class in pyrevs.strategies.ams) (class in pyrevs.strategies.ams.extension)

AMSDB (class in pyrevs.strategies.ams.sql) ancestor_traj_ids (SplittingIterations attribute) append_archived_traj() (Database method), [1] append_splitting_iteration_data() (AMSDatabaseExtension method), [1] append_traj() (Database method), [1] append_trajectory_to_yaml() (in module pyrevs.utils.yamlutils) archive_discarded (DatabaseConfig attribute), [1] archive_trajectory() (CoreDB method), [1] (Database method), [1] archived_traj_list() (Database method), [1] archived_traj_list_len() (Database method), [1] ArchivedTrajectory (class in pyrevs.core.sqlcore) as_dict() (Config method), [1] AsIORunner (class in pyrevs.runner.taskrunner) attach_extension() (Database method), [1] available_strategies() (BaseSamplingStrategy class method), [1]

B

backend (DaskConfig attribute) BaseRunner (class in pyrevs.runner.taskrunner) BaseSamplingStrategy (class in pyrevs.strategies.base) (class in pyrevs.strategies.base.strategy) BaseSQLManager (class in pyrevs.core.sqlmanager)

bias (SplittingIterations attribute) branch_from_trajectory() (Trajectory class method), [1] build_database() (in module pyrevs.sampler.sampler) build_sampler() (in module pyrevs.sampler) (in module pyrevs.sampler.sampler) build_system_config() (in module pyrevs.sampler.sampler)

C

check_convergence() (ForwardModelBaseClass method), [1] check_exit_splitting_loop() (AMS method), [1], [2] check_new_min_of_maxes() (AMSDB method) check_termination() (ForwardModelBaseClass method), [1] check_trajectory_exist() (CoreDB method), [1] chkfile_dump_all (TrajectoryConfig attribute), [1] clean_signature() (in module pyrevs.utils.utils) clear() (ForwardModelBaseClass method), [1] clear_archived_trajectories() (CoreDB method), [1] clear_splitting_data() (AMSDB method) close() (BaseSQLManager method) (DiagDB method), [1] collect_sections() (in module pyrevs.core.config) compute_probability() (AMS method), [1], [2] (MonteCarlo method), [1], [2]

compute_weighted_stats() (DiagnosticAnalyst method), [1] Config (class in pyrevs.core) (class in pyrevs.core.config) CoreBase (class in pyrevs.core) (class in pyrevs.core.sqlcore) CoreDB (class in pyrevs.core) (class in pyrevs.core.sqlcore) count_computed_steps() (Database method), [1] count_converged_traj() (Database method), [1] count_terminated_traj() (Database method), [1] create() (BaseSamplingStrategy class method), [1] (Database class method), [1] current_step() (Trajectory method), [1] current_time() (Trajectory method), [1]

D

dask_config (RunnerConfig attribute), [1] DaskConfig (class in pyrevs.runner.config) DaskRunner (class in pyrevs.runner.taskrunner) Database (class in pyrevs.database) (class in pyrevs.database.database) database (RareEventSampler property), [1] (SystemConfig attribute) DatabaseConfig (class in pyrevs.database) (class in pyrevs.database.config) DatabaseCoreSpec (class in pyrevs.database) (class in pyrevs.database.database) db (DiagnosticAnalyst attribute), [1] default_name() (DiagDB class method), [1] delete() (Trajectory method), [1] deserialize() (AMSDatabaseExtension method), [1] (MCDatabaseExtension method), [1] (StrategyDatabaseExtension method), [1] deserialize_metadata() (Trajectory class method), [1] deterministic (DatabaseCoreSpec attribute), [1] (SamplerConfig attribute), [1]

diag_configs (DatabaseCoreSpec attribute), [1] DiagBase (class in pyrevs.diagnostics.diagdb) DiagDB (class in pyrevs.diagnostics) (class in pyrevs.diagnostics.diagdb) diaglabel (DiagnosticEntry attribute) diagnostic_hook() (ForwardModelBaseClass method), [1] DiagnosticAnalyst (class in pyrevs.diagnostics) (class in pyrevs.diagnostics.diagnostic) DiagnosticEntry (class in pyrevs.diagnostics.diagdb) diagnosticfactory() (in module pyrevs.diagnostics) (in module pyrevs.diagnostics.diagnostic) DiagnosticPlugin (class in pyrevs.diagnostics) (class in pyrevs.diagnostics.diagnostic) diagnostics (RuntimeConfig attribute), [1] dict_to_xml() (in module pyrevs.utils.xmlutils) discarded_traj_ids (SplittingIterations attribute) do_multilevel_splitting() (AMS method), [1], [2] dump_file_json() (AMSDB method) (CoreDB method), [1] dump_to_json() (DiagDB method), [1] duplicate_diagnostic_history() (DiagDB method), [1]

E

elapsed_time() (BaseSamplingStrategy method), [1] end_time (AMSConfig attribute), [1] (MCConfig attribute), [1] (TrajectoryConfig attribute), [1]

engine() (BaseSQLManager method) execute_promises() (AsIORunner method) (BaseRunner method) (DaskRunner method) extension() (Database method), [1]

F

fetch_archived_trajectory() (CoreDB method), [1] fetch_splitting_data() (AMSDB method) fetch_trajectory() (CoreDB method), [1] finish_ongoing_splitting() (AMS method), [1], [2]

FirstTimeCrossingDiagnostic (class in pyrevs.diagnostics.diagnostic) form_trajectory_id() (in module pyrevs.trajectory.trajectory) format (DatabaseConfig attribute), [1] ForwardModelBaseClass (class in pyrevs.core) (class in pyrevs.core.fmodel)

G

generate_subclass() (in module pyrevs.utils.utils) generate_trajectory_ensemble() (AMS method), [1], [2] (MonteCarlo method), [1], [2] get() (Config method), [1] get_archived_trajectory_count() (CoreDB method), [1] get_biases() (AMSDB method) get_checkfile() (Trajectory method), [1] get_computed_steps_count() (Trajectory method), [1] get_conditional_means() (DiagnosticAnalyst method), [1] get_converged_trajectory_count() (CoreDB method), [1] get_crossed_levels() (DiagnosticPlugin method), [1] (FirstTimeCrossingDiagnostic method) get_current_state() (ForwardModelBaseClass method), [1] get_diagnostic_data() (DiagDB method), [1] (DiagnosticAnalyst method), [1] get_event_probability() (AMSDatabaseExtension method), [1] (Database method), [1] (MCDatabaseExtension method), [1] (StrategyDatabaseExtension method), [1] get_highest_recorded_level() (DiagDB method), [1] get_index_from_id() (in module pyrevs.trajectory.trajectory) get_iteration_count() (AMSDB method) get_k_split() (AMSDB method)

get_last_state() (Trajectory method), [1] get_last_state_id() (Trajectory method), [1] get_length() (Trajectory method), [1] get_metadata() (Trajectory method), [1] get_min_scored() (in module pyrevs.utils.utils) get_minmax() (AMSDB method) get_module_local_import() (in module pyrevs.utils.utils) get_nbranching() (Trajectory method), [1] get_noise_array() (Trajectory method), [1] get_ongoing() (AMSDatabaseExtension method), [1] (AMSDB method) get_pool_db() (Database method), [1] get_restart_at_random() (AMS method), [1], [2] get_score_array() (Trajectory method), [1] get_state_list() (Trajectory method), [1] get_terminated_trajectory_count() (CoreDB method), [1] get_time_array() (Trajectory method), [1] get_total_computed_steps() (CoreDB method), [1] get_traj() (Database method), [1] get_trajectory_active_at_k() (AMSDatabaseExtension method), [1] get_trajectory_count() (CoreDB method), [1] get_val_type() (in module pyrevs.utils.xmlutils) get_weights() (AMSDB method) get_workdir() (Trajectory method), [1]

H

has_started() (Trajectory method), [1]

has_state (Snapshot property), [1] header_file() (Database method), [1]

I

id (ArchivedTrajectory attribute) (DiagnosticEntry attribute) (SplittingIterations attribute) (Trajectory attribute) id() (Trajectory method), [1] idstr() (Trajectory method), [1] IMMUTABLE (MergePolicy attribute), [1] import_forward_model() (in module pyrevs.utils.utils) info() (Database method), [1] init_active_ensemble() (Database method), [1] init_ensemble_done() (AMSDatabaseExtension method), [1] init_ensemble_only (AMSConfig attribute), [1] init_from_metadata() (Trajectory class method), [1] init_traj_pool() (Database method), [1]

initialize() (AMSDatabaseExtension method), [1] (MCDatabaseExtension method), [1] initialize_core_state() (Database method), [1] initialize_database_schema() (AMS method), [1], [2] (BaseSamplingStrategy method), [1] (MonteCarlo method), [1], [2] initialize_from_database() (AMSDatabaseExtension method), [1] (MCDatabaseExtension method), [1] input_help() (in module pyrevs.bin) (in module pyrevs.bin.bin) is_converged() (Trajectory method), [1] is_empty() (Database method), [1] is_mac_os() (in module pyrevs.utils.utils) is_terminated() (Trajectory method), [1] is_windows_os() (in module pyrevs.utils.utils)

J

job_prologue (DaskConfig attribute)

just_delay() (DaskRunner method)

K

k_split() (AMSDatabaseExtension method), [1]

L

l_j (AMSConfig attribute), [1] level_crossed (DiagnosticEntry attribute) load() (Config method), [1] (Database class method), [1] load_archived_trajectories() (Database method), [1] load_config() (in module pyrevs.sampler.sampler) load_data() (Database method), [1] load_database() (in module pyrevs.database) (in module pyrevs.database.bootstrap)

load_database_extension() (in module pyrevs.strategies.ams) (in module pyrevs.strategies.montecarlo) load_trajectories_from_yaml() (in module pyrevs.utils.yamlutils) lock_trajectory() (CoreDB method), [1] (Database method), [1] logfile (RuntimeConfig attribute), [1] loglevel (RuntimeConfig attribute), [1] LowScoreTerminationCriterion (class in pyrevs.strategies.base) (class in pyrevs.strategies.base.termination)

M

make_noise() (ForwardModelBaseClass method), [1] make_promise() (AsIORunner method) (BaseRunner method) (DaskRunner method) make_runner() (in module pyrevs.runner) (in module pyrevs.runner.taskrunner) make_xml_snapshot() (in module pyrevs.utils.xmlutils) manual_cast() (in module pyrevs.utils.xmlutils) manual_cast_snapshot() (in module pyrevs.utils.xmlutils) manual_cast_snapshot_noise() (in module pyrevs.utils.xmlutils) manual_cast_str() (in module pyrevs.utils.xmlutils) mark_last_iteration_as_completed() (AMSDB method) mark_last_splitting_iteration_as_done() (AMSDatabaseExtension method), [1] mark_trajectory_as_completed() (CoreDB method), [1] max_nbranch (Trajectory attribute), [1] max_ntraj (Trajectory attribute), [1] MCConfig (class in pyrevs.strategies.montecarlo) (class in pyrevs.strategies.montecarlo.config) MCDatabaseExtension (class in pyrevs.strategies.montecarlo) (class in pyrevs.strategies.montecarlo.extension) merge() (SystemConfig class method) merge_config() (in module pyrevs.core.config) MergePolicy (class in pyrevs.core) (class in pyrevs.core.config) min_max (SplittingIterations attribute) min_score (AMSConfig attribute), [1] min_vals (SplittingIterations attribute) model_data (DiagnosticEntry attribute) ModelTerminationCriterion (class in pyrevs.strategies.base.termination) module pyrevs pyrevs.bin pyrevs.bin.bin pyrevs.core pyrevs.core.config pyrevs.core.fmodel pyrevs.core.runtime_cfg pyrevs.core.snapshot pyrevs.core.sqlcore pyrevs.core.sqlmanager pyrevs.database pyrevs.database.bootstrap pyrevs.database.config pyrevs.database.database pyrevs.database.extension pyrevs.diagnostics pyrevs.diagnostics.diagdb pyrevs.diagnostics.diagnostic pyrevs.runner pyrevs.runner.config pyrevs.runner.taskrunner pyrevs.runner.worker pyrevs.sampler pyrevs.sampler.config pyrevs.sampler.sampler pyrevs.sampler.system_config pyrevs.strategies pyrevs.strategies.ams pyrevs.strategies.ams.ams pyrevs.strategies.ams.config pyrevs.strategies.ams.extension pyrevs.strategies.ams.sql pyrevs.strategies.base pyrevs.strategies.base.strategy pyrevs.strategies.base.termination pyrevs.strategies.montecarlo pyrevs.strategies.montecarlo.config pyrevs.strategies.montecarlo.extension pyrevs.strategies.montecarlo.montecarlo pyrevs.trajectory pyrevs.trajectory.config pyrevs.trajectory.trajectory pyrevs.utils pyrevs.utils.dbutils pyrevs.utils.utils pyrevs.utils.xmlutils pyrevs.utils.yamlutils

MonteCarlo (class in pyrevs.strategies) (class in pyrevs.strategies.montecarlo) (class in pyrevs.strategies.montecarlo.montecarlo) moving_avg() (in module pyrevs.utils.utils) ms_worker() (in module pyrevs.runner) (in module pyrevs.runner.worker)

N

n_traj() (Database method), [1] n_workers() (AsIORunner method) (BaseRunner method) (DaskRunner method) name() (BaseSQLManager method) (Database method), [1] (ForwardModelBaseClass class method), [1] ncores_per_worker (DaskConfig attribute) ndarray_representer() (in module pyrevs.utils.yamlutils) new_element() (in module pyrevs.utils.xmlutils)

noise (ForwardModelBaseClass property), [1] (Snapshot attribute), [1] noise_backlog (Trajectory attribute), [1] nsplititer (AMSConfig attribute), [1] ntasks_per_job (DaskConfig attribute) ntasks_per_node (DaskConfig attribute) ntraj (DatabaseCoreSpec attribute), [1] ntrajectories (AMSConfig attribute), [1] (MCConfig attribute), [1] nworkers (RunnerConfig attribute), [1]

O

oneliner_ndarray() (in module pyrevs.utils.xmlutils)

out_of_time() (BaseSamplingStrategy method), [1] overwrite_traj() (Database method), [1]

P

parse_cl_args() (in module pyrevs.bin.bin) (in module pyrevs.sampler.sampler) path (DatabaseConfig attribute), [1] path() (Database method), [1] ping_diag_database() (Database method), [1] plot_diagnostics (RuntimeConfig attribute), [1] plot_min_max_span() (AMSDatabaseExtension method), [1] plot_score_functions() (Database method), [1] POD_cast_dict (in module pyrevs.utils.xmlutils) pool_file() (Database method), [1] pool_worker() (in module pyrevs.runner) (in module pyrevs.runner.worker) post_trajectory_branching_hook() (ForwardModelBaseClass method), [1] post_trajectory_restore_hook() (ForwardModelBaseClass method), [1] prepare_database_path() (in module pyrevs.utils.dbutils) print_config_help() (in module pyrevs.core.config) (SystemConfig class method) print_info() (Database method), [1] PTDumper (class in pyrevs.utils.yamlutils) pyrevs module pyrevs.bin module pyrevs.bin.bin module pyrevs.core module pyrevs.core.config module pyrevs.core.fmodel module pyrevs.core.runtime_cfg module pyrevs.core.snapshot module pyrevs.core.sqlcore module pyrevs.core.sqlmanager module pyrevs.database module pyrevs.database.bootstrap module pyrevs.database.config module pyrevs.database.database module pyrevs.database.extension module pyrevs.diagnostics module pyrevs.diagnostics.diagdb module pyrevs.diagnostics.diagnostic module pyrevs.runner module

pyrevs.runner.config module pyrevs.runner.taskrunner module pyrevs.runner.worker module pyrevs.sampler module pyrevs.sampler.config module pyrevs.sampler.sampler module pyrevs.sampler.system_config module pyrevs.strategies module pyrevs.strategies.ams module pyrevs.strategies.ams.ams module pyrevs.strategies.ams.config module pyrevs.strategies.ams.extension module pyrevs.strategies.ams.sql module pyrevs.strategies.base module pyrevs.strategies.base.strategy module pyrevs.strategies.base.termination module pyrevs.strategies.montecarlo module pyrevs.strategies.montecarlo.config module pyrevs.strategies.montecarlo.extension module pyrevs.strategies.montecarlo.montecarlo module pyrevs.trajectory module pyrevs.trajectory.config module pyrevs.trajectory.trajectory module pyrevs.utils module pyrevs.utils.dbutils module pyrevs.utils.utils module pyrevs.utils.xmlutils module pyrevs.utils.yamlutils module

Q

queue (DaskConfig attribute)

R

RareEventSampler (class in pyrevs.sampler) (class in pyrevs.sampler.sampler) read_xml_snapshot() (in module pyrevs.utils.xmlutils) register() (BaseSamplingStrategy class method), [1] release_all_trajectories() (CoreDB method), [1] release_trajectory() (CoreDB method), [1] remaining_time() (BaseSamplingStrategy method), [1] REPLACE (MergePolicy attribute), [1] require() (Config method), [1] restart (DatabaseConfig attribute), [1]

restore_from_checkfile() (Trajectory class method), [1] run() (RareEventSampler method), [1] run_tasks() (AsIORunner method) runner (SystemConfig attribute) RunnerConfig (class in pyrevs.runner) (class in pyrevs.runner.config) RunnerError runtime (SystemConfig attribute) RuntimeConfig (class in pyrevs.core) (class in pyrevs.core.runtime_cfg)

S

sample() (BaseSamplingStrategy method), [1] sampler (SystemConfig attribute) SamplerConfig (class in pyrevs.sampler) (class in pyrevs.sampler.config) sampling_run() (in module pyrevs.bin) (in module pyrevs.bin.bin) save_trajectory() (Database method), [1] score (Snapshot attribute), [1] score() (ForwardModelBaseClass method), [1] score_max() (Trajectory method), [1] section() (Config method), [1] section_dict() (Config method), [1] serialize() (AMSDatabaseExtension method), [1] (MCDatabaseExtension method), [1] (StrategyDatabaseExtension method), [1] serialize_metadata_json() (Trajectory method), [1] session_scope() (AMSDB method) (BaseSQLManager method) set_checkfile() (Trajectory method), [1] set_current_state() (ForwardModelBaseClass method), [1] set_current_time_and_step() (Trajectory method), [1] set_init_ensemble_flag() (AMSDatabaseExtension method), [1] set_weight() (Trajectory method), [1] set_workdir() (ForwardModelBaseClass method), [1] (Trajectory method), [1] setup() (WorkerLoggerPlugin method) setup_logger() (in module pyrevs.utils) (in module pyrevs.utils.utils)

setup_noise() (Trajectory method), [1] should_terminate() (LowScoreTerminationCriterion method), [1] (ModelTerminationCriterion method) (TerminationCriterion method), [1] (TimeTerminationCriterion method), [1] slurm_config_file (DaskConfig attribute) Snapshot (class in pyrevs.core) (class in pyrevs.core.snapshot) sparse_freq (TrajectoryConfig attribute), [1] sparse_start (TrajectoryConfig attribute), [1] split_id (SplittingIterations attribute) SplittingIterations (class in pyrevs.strategies.ams.sql) STALL_TOL (in module pyrevs.strategies.ams.ams) state (Snapshot attribute), [1] status (SplittingIterations attribute) (Trajectory attribute) step_size (TrajectoryConfig attribute), [1] step_size() (Trajectory method), [1] store() (Trajectory method), [1] strategy (DatabaseCoreSpec attribute), [1] (SamplerConfig attribute), [1] (SystemConfig attribute) strategy() (Database method), [1] StrategyDatabaseExtension (class in pyrevs.database) (class in pyrevs.database.extension) SystemConfig (class in pyrevs.sampler.system_config)

T

T (in module pyrevs.core.config) (in module pyrevs.strategies.base.strategy) t_metadata (ArchivedTrajectory attribute) (Trajectory attribute) T_Noise (in module pyrevs.core.fmodel) (in module pyrevs.core.snapshot) (in module pyrevs.database.database) (in module pyrevs.strategies.ams.extension) (in module pyrevs.strategies.base.termination) (in module pyrevs.strategies.montecarlo.extension) (in module pyrevs.trajectory.trajectory) T_State (in module pyrevs.core.fmodel) (in module pyrevs.core.snapshot) (in module pyrevs.database.database) (in module pyrevs.strategies.ams.extension) (in module pyrevs.strategies.base.termination) (in module pyrevs.strategies.montecarlo.extension) (in module pyrevs.trajectory.trajectory) targetscore (TrajectoryConfig attribute), [1] template_model() (in module pyrevs.bin) (in module pyrevs.bin.bin)

TerminationCriterion (class in pyrevs.strategies.base) (class in pyrevs.strategies.base.termination) time (DiagnosticEntry attribute) (Snapshot attribute), [1] TimeTerminationCriterion (class in pyrevs.strategies.base) (class in pyrevs.strategies.base.termination) to_disk() (Database method), [1] traj_advance_with_exception() (in module pyrevs.runner.worker) traj_file (ArchivedTrajectory attribute) (Trajectory attribute) traj_id (DiagnosticEntry attribute) traj_list() (Database method), [1] traj_list_len() (Database method), [1] Trajectory (class in pyrevs.core.sqlcore) (class in pyrevs.trajectory) (class in pyrevs.trajectory.trajectory) trajectory (SystemConfig attribute) TrajectoryConfig (class in pyrevs.trajectory) (class in pyrevs.trajectory.config) tuple_representer() (in module pyrevs.utils.yamlutils) type (RunnerConfig attribute), [1]

U

unique_id() (Trajectory method), [1] unlock_trajectory() (Database method), [1] update() (DiagnosticPlugin method), [1] update_all_active_weights() (DiagDB method), [1] update_diagnostic_weights() (Database method), [1] update_metadata() (Trajectory method), [1] update_splitting_data() (AMSDB method)

update_splitting_iteration_data() (AMSDatabaseExtension method), [1] update_traj_list() (Database method), [1] update_trajectories_weights() (AMSDatabaseExtension method), [1] update_trajectory() (CoreDB method), [1] (Database method), [1] update_trajectory_in_sql() (in module pyrevs.runner.worker) update_trajectory_weight() (CoreDB method), [1]

V

valid_statuses (in module pyrevs.core.sqlcore) validate() (AMSConfig method), [1] (MCConfig method), [1] (TrajectoryConfig method), [1]

variant (AMSConfig attribute), [1]

W

walltime (RuntimeConfig attribute), [1] WallTimeLimitError weight (DiagnosticEntry attribute) (SplittingIterations attribute)

weights() (AMSDatabaseExtension method), [1] worker_async() (in module pyrevs.runner.worker) worker_walltime (DaskConfig attribute) WorkerLoggerPlugin (class in pyrevs.runner.taskrunner) write_toml() (SystemConfig method)

X

xml_to_dict() (in module pyrevs.utils.xmlutils)

XMLUtilsError