Index

_

__init__() (aimmd.engines.toy.ToyEngine method) (aimmd.network.rescalable.Rescalable method)

__task_name__ (aimmd.execute.processes.ProcessExecutor attribute) (aimmd.execute.threads.ThreadExecutor attribute)

A

accepted (aimmd.Path property) (aimmd.PathEnsemble property) accepts_system_id() (in module aimmd.core.utils) add() (aimmd.Launcher method) aimmd.analysis.utils module aimmd.cache.mda module aimmd.cache.npy module aimmd.core.utils module aimmd.engines.toy module aimmd.execute.processes module aimmd.execute.threads module aimmd.execute.utils module aimmd.network.fit module

aimmd.network.rescalable module aimmd.network.rescale_utils module aimmd.network.utils module aimmd.resources.binding module aimmd.resources.cpu module aimmd.resources.gpu module all() (aimmd.Path method) (aimmd.PathEnsemble method) always_select_inside_the_bins (aimmd.Params attribute) append() (aimmd.PathEnsemble method) are_complete() (aimmd.PathEnsemble method) are_excursions() (aimmd.PathEnsemble method) are_internal() (aimmd.PathEnsemble method) are_transitions() (aimmd.PathEnsemble method) at_least_one_transition_in_pool (aimmd.Params attribute) atom_types (aimmd.Params attribute)

B

backward() (aimmd.Path method) (aimmd.PathEnsemble method) bias_function (aimmd.Params attribute) bias_reactive_threshold (aimmd.Params attribute)

bias_reactive_threshold_of() (aimmd.Params method) bias_source (aimmd.Params attribute) bin_centers() (in module aimmd.analysis.utils) bind_resources() (in module aimmd.resources.binding) binomial_mean_and_confidence_interval() (in module aimmd.analysis.utils)

C

chain_type (aimmd.Params attribute) check_engine() (aimmd.Params method) check_if_initialized() (aimmd.Params method) check_stop() (aimmd.Path method) compute() (aimmd.Path method) (aimmd.PathEnsemble method) compute_bins() (in module aimmd.analysis.utils) compute_descriptors_args (aimmd.Params property) compute_states_args (aimmd.Params property)

compute_values_args (aimmd.Params property) concatenate() (in module aimmd.core.utils) copy() (aimmd.Params method) (aimmd.Path method) (aimmd.PathEnsemble method) count_safe_frames() (in module aimmd.cache.mda) create_job() (aimmd.Launcher method) cutoff_max (aimmd.Params attribute) cutoff_min (aimmd.Params attribute) cycle() (in module aimmd.core.utils)

D

default() (in module aimmd.network.fit) density_adjustment (aimmd.Params attribute) descriptor_transform (aimmd.Params attribute)

descriptors_function (aimmd.Params attribute) directories (aimmd.Launcher property) dt (aimmd.Path property)

E

engine (aimmd.Params attribute) exclude_from (aimmd.Path property) (aimmd.PathEnsemble property) execute_command() (in module aimmd.execute.utils) extend() (aimmd.Path method) (aimmd.PathEnsemble method) extend_array() (in module aimmd.core.utils)

extra_free_frames (aimmd.Params attribute) extract() (aimmd.PathEnsemble method) extract_bias_reweighted_rate_estimates_from_log_file() (in module aimmd.analysis.utils) extract_folder_and_name() (in module aimmd.core.utils) extract_indices_and_series() (in module aimmd.network.utils) extract_lsr_pairs() (in module aimmd.network.utils) extract_mar_sequences() (in module aimmd.network.utils) extract_rate_estimates_from_log_file() (in module aimmd.analysis.utils)

F

factors() (aimmd.PathEnsemble method) filenames (aimmd.Path property) final() (aimmd.Path method) (aimmd.PathEnsemble method) find_extremes_with_free_simulations() (in module aimmd.analysis.utils) find_extremes_with_transitions() (in module aimmd.analysis.utils) find_knots_and_values() (in module aimmd.network.rescale_utils) find_path_lineages() (in module aimmd.analysis.utils) find_shooting_index() (aimmd.Path method) first (aimmd.Path property) fit() (aimmd.Params static method) (in module aimmd.network.fit) fname (aimmd.Path property) (aimmd.PathEnsemble property)

fnames (aimmd.Path property) (aimmd.PathEnsemble property) forward() (aimmd.network.utils.PlaceholderNetwork method) (aimmd.Path method) (aimmd.PathEnsemble method) frame() (aimmd.PathEnsemble method) free() (aimmd.Worker method) free_overriding_attempts (aimmd.Params attribute) free_overriding_bins (aimmd.Params attribute) free_overriding_recovery_rate (aimmd.Params attribute) free_overriding_states (aimmd.Params attribute) free_trajectories() (aimmd.Params method) from_files() (aimmd.Path method) (aimmd.PathEnsemble method)

G

gen_temperature (aimmd.Params attribute) get() (aimmd.Path method) (aimmd.PathEnsemble method) get_available_cpus() (in module aimmd.resources.cpu) get_available_gpus() (in module aimmd.resources.gpu) get_local_index() (in module aimmd.core.utils)

get_num_cpus() (in module aimmd.resources.cpu) get_num_gpus() (in module aimmd.resources.gpu) gmx_eneconv (aimmd.Params attribute) gmx_grompp (aimmd.Params attribute) gmx_mdp (aimmd.Params attribute) gmx_mdrun (aimmd.Params attribute) guess_masses() (in module aimmd.core.utils)

I

in_memory() (aimmd.Path method) (aimmd.PathEnsemble method) index() (aimmd.PathEnsemble method) indices (aimmd.Path property) initial() (aimmd.Path method) (aimmd.PathEnsemble method) initial_paths (aimmd.Params attribute) (aimmd.Worker property)

initialize_simulation() (aimmd.Params method) internal() (aimmd.Path method) (aimmd.PathEnsemble method) is_complete() (aimmd.Path method) is_excursion() (aimmd.Path method) is_internal() (aimmd.Path method) is_transition() (aimmd.Path method)

J

join() (aimmd.PathEnsemble method)

K

kinetics_convergence() (aimmd.Worker method)

L

last (aimmd.Path property) Launcher (class in aimmd) lengths (aimmd.Path property) (aimmd.PathEnsemble property) load() (aimmd.Params class method) (aimmd.PathEnsemble class method)

load_bins_and_densities() (aimmd.Params method) load_npy() (in module aimmd.cache.npy) load_state_dict() (aimmd.network.utils.PlaceholderNetwork method) locs (aimmd.Path property) log_file (aimmd.Worker property) longest_true_segment() (in module aimmd.core.utils) lorentzian (aimmd.Params attribute)

M

masses (aimmd.Params property) masses_of() (aimmd.Params method) max() (aimmd.Path method) (aimmd.PathEnsemble method) max_backward() (aimmd.Path method) (aimmd.PathEnsemble method) max_forward() (aimmd.Path method) (aimmd.PathEnsemble method) max_length (aimmd.Params attribute) max_size (aimmd.cache.mda.MDAReaderCache attribute), [1] (aimmd.cache.npy.NpyReaderCache attribute), [1] MDAReaderCache (class in aimmd.cache.mda) memory_reader_from_timesteps() (in module aimmd.core.utils) merge() (aimmd.PathEnsemble method) merge_empty_bins() (in module aimmd.analysis.utils) merge_marginal_bins() (in module aimmd.analysis.utils) merge_ranges() (in module aimmd.core.utils) middle() (aimmd.Path method) (aimmd.PathEnsemble method) min() (aimmd.Path method) (aimmd.PathEnsemble method) min_backward() (aimmd.Path method) (aimmd.PathEnsemble method)

min_forward() (aimmd.Path method) (aimmd.PathEnsemble method) minimize_energy() (aimmd.Params method) module aimmd.analysis.utils aimmd.cache.mda aimmd.cache.npy aimmd.core.utils aimmd.engines.toy aimmd.execute.processes aimmd.execute.threads aimmd.execute.utils aimmd.network.fit aimmd.network.rescalable aimmd.network.rescale_utils aimmd.network.utils aimmd.resources.binding aimmd.resources.cpu aimmd.resources.gpu multi_system (aimmd.Params attribute) multi_system_share_network (aimmd.Params attribute) must_stop (aimmd.Worker property)

N

n_atoms (aimmd.Path property) n_files (aimmd.Path property) (aimmd.PathEnsemble property) n_frames (aimmd.Path property) (aimmd.PathEnsemble property) n_paths (aimmd.PathEnsemble property)

name (aimmd.Params attribute) nbins (aimmd.Params attribute) network (aimmd.Params attribute) network_batch_size (aimmd.Params attribute) network_save_interval (aimmd.Params attribute) now() (in module aimmd.core.utils) NpyReaderCache (class in aimmd.cache.npy)

O

offsets (aimmd.Path property) (aimmd.PathEnsemble property)

P

params (aimmd.Launcher property) Params (class in aimmd) parent (aimmd.Params property) partial() (aimmd.Path method) path (aimmd.Params attribute) (aimmd.PathEnsemble property) Path (class in aimmd) PathEnsemble (class in aimmd) pathensemble() (aimmd.Params method) paths (aimmd.Launcher property) (aimmd.PathEnsemble property)

pipeline (aimmd.Params property) PlaceholderNetwork (class in aimmd.network.utils) plot_path_lineages() (in module aimmd.analysis.utils) pop() (aimmd.Launcher method) (aimmd.PathEnsemble method) print_report() (aimmd.PathEnsemble method) process_state() (in module aimmd.core.utils) processes (aimmd.Launcher property) ProcessExecutor (class in aimmd.execute.processes) project() (aimmd.PathEnsemble method)

R

randomize_velocities() (in module aimmd.core.utils) Reader() (in module aimmd.cache.mda) record_bias (aimmd.Params attribute) remove() (aimmd.PathEnsemble method) (in module aimmd.core.utils) remove_offset_files() (in module aimmd.cache.mda) replace_in_cache() (in module aimmd.core.utils) report() (aimmd.PathEnsemble method) report_shooting_results() (aimmd.PathEnsemble method) Rescalable (class in aimmd.network.rescalable)

rescale() (in module aimmd.network.rescale_utils) rescale_committor (aimmd.Params attribute) reset_parameters() (aimmd.network.rescalable.Rescalable method) restart_free_simulations_with_transitions (aimmd.Params attribute) retry_with_state_definition_glitches (aimmd.Params attribute) reweight() (aimmd.PathEnsemble method) reweight_parameters (aimmd.Params attribute) run() (aimmd.Launcher method) (aimmd.Worker method) run_simulation() (aimmd.Params method)

S

sample() (aimmd.Path method) (aimmd.PathEnsemble method) save() (aimmd.Params method) (aimmd.PathEnsemble method) save_npy() (in module aimmd.cache.npy) selection_pool_size (aimmd.Params attribute) set_knots_and_values() (aimmd.network.rescalable.Rescalable method) shared_density_adjustment (aimmd.Params attribute) shoot() (aimmd.Worker method) shooting() (aimmd.Path method) (aimmd.PathEnsemble method) shooting_index (aimmd.Path property) shooting_indices (aimmd.PathEnsemble property) shooting_result() (aimmd.Path method)

shooting_results() (aimmd.PathEnsemble method) shot_chains() (aimmd.Params method) shot_paths() (aimmd.Params method) slurm_header (aimmd.Params attribute) solve_committor_by_relaxation() (in module aimmd.analysis.utils) sorted_states (aimmd.Params property) split() (aimmd.Path method) (aimmd.PathEnsemble method) state_dict() (aimmd.network.utils.PlaceholderNetwork method) states (aimmd.Params attribute) states_function (aimmd.Params attribute) subsample() (aimmd.PathEnsemble method) subsample_caps (aimmd.Params attribute) subsample_caps_of() (aimmd.Params method) system_ids (aimmd.Params attribute)

T

target_wrapper() (in module aimmd.execute.utils) terminal_bin_extension (aimmd.Params attribute) ThreadExecutor (class in aimmd.execute.threads) to_memory() (aimmd.Path method) (aimmd.PathEnsemble method) topology (aimmd.Params attribute) total_frames (aimmd.Worker property) total_steps (aimmd.Worker property) toy_mdrun (aimmd.Params attribute)

toy_slowdown (aimmd.Params attribute) ToyEngine (class in aimmd.engines.toy) train() (aimmd.Worker method) trainers_share_gpu (aimmd.Params attribute) trajectory_extension (aimmd.Params attribute) trajectory_update_batch_size (aimmd.Params attribute) true_states (aimmd.PathEnsemble property) type (aimmd.Path property) types() (aimmd.PathEnsemble method)

U

unique_path() (in module aimmd.core.utils) universe (aimmd.Params property) universe_of() (aimmd.Params method)

update() (aimmd.Params method) update_exclude_from() (aimmd.Path method) update_network() (aimmd.Params method) update_npy() (in module aimmd.cache.npy)

V

values_function (aimmd.Params attribute)

W

weight (aimmd.Path property) weights (aimmd.PathEnsemble property)

Worker (class in aimmd) write() (aimmd.Path method)