Index

A

add_missing_backward_trials() (aimmd.distributed.CommittorSimulation method) aimmd module aimmd.analysis module aimmd.analysis.gradient_movie module aimmd.analysis.hipr module aimmd.base module aimmd.base.density_collection module aimmd.base.rcmodel module aimmd.base.rcmodel_train_decision module aimmd.base.storage module aimmd.base.trainset module aimmd.base.utils module aimmd.coords module aimmd.coords.internal module aimmd.coords.symmetry module

aimmd.coords.utils module aimmd.distributed module aimmd.distributed.committors module aimmd.distributed.config module aimmd.distributed.dataclasses module aimmd.distributed.dataclasses_internal module aimmd.distributed.pathmovers module aimmd.distributed.pathsampling module aimmd.distributed.spselectors module aimmd.distributed.utils module aimmd.ops module aimmd.ops.hooks module aimmd.ops.selector module aimmd.ops.utils module aimmd.tools module

B

biases() (aimmd.distributed.spselectors.RCModelSPSelector method) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ method) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj method) build_frame_extractors() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method)

build_propagators() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method)

C

CommittorConfiguration (class in aimmd.distributed)

CommittorSimulation (class in aimmd.distributed) configurations (aimmd.distributed.CommittorSimulation property)

D

delete_model() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.PathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method) DensityAdaptionParameters (class in aimmd.distributed.dataclasses)

directory_backward (aimmd.distributed.CommittorSimulation property) directory_configuration_prefix (aimmd.distributed.CommittorSimulation property) directory_forward (aimmd.distributed.CommittorSimulation property) directory_trial_prefix (aimmd.distributed.CommittorSimulation property) distribution (aimmd.distributed.spselectors.RCModelSPSelector property) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ property) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj property)

E

exclude_frames (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj property)

F

f_sel (aimmd.distributed.spselectors.RCModelSPSelector property) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ property) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj property) fileout_deffnm_engine (aimmd.distributed.CommittorSimulation property) fileout_initial_configuration (aimmd.distributed.CommittorSimulation property)

fileout_initial_configuration_backward (aimmd.distributed.CommittorSimulation property) fileout_trajectory_to_state (aimmd.distributed.CommittorSimulation property) fileout_trajectory_to_state_backward (aimmd.distributed.CommittorSimulation property) fileout_transition_trajectory (aimmd.distributed.CommittorSimulation property) FixedLengthTwoWayShootingPathMover (class in aimmd.distributed.pathmovers)

G

generate_move() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.PathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method) get_model() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.PathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method) get_or_generate_sp_bw() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method)

get_or_generate_sp_fw() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method) get_or_generate_sps() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method)

M

max_retries_on_crash (aimmd.distributed.CommittorSimulation property) max_retries_on_max_steps (aimmd.distributed.CommittorSimulation property) md_engine_spec (aimmd.distributed.CommittorSimulation property) MDEngineSpec (class in aimmd.distributed) module aimmd aimmd.analysis aimmd.analysis.gradient_movie aimmd.analysis.hipr aimmd.base aimmd.base.density_collection aimmd.base.rcmodel aimmd.base.rcmodel_train_decision aimmd.base.storage aimmd.base.trainset aimmd.base.utils aimmd.coords aimmd.coords.internal aimmd.coords.symmetry aimmd.coords.utils aimmd.distributed aimmd.distributed.committors aimmd.distributed.config aimmd.distributed.dataclasses aimmd.distributed.dataclasses_internal aimmd.distributed.pathmovers aimmd.distributed.pathsampling aimmd.distributed.spselectors aimmd.distributed.utils aimmd.ops aimmd.ops.hooks aimmd.ops.selector aimmd.ops.utils aimmd.tools

move() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.PathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method)

O

output_traj_type (aimmd.distributed.MDEngineSpec attribute)

P

PathMover (class in aimmd.distributed.pathmovers) pick() (aimmd.distributed.spselectors.RCModelSPSelector method) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ method) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj method) (aimmd.distributed.spselectors.SPSelector method) (aimmd.distributed.spselectors.UniformSPSelector method) pick_snapshot() (aimmd.distributed.spselectors.RCModelSPSelector method) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ method) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj method)

probability() (aimmd.distributed.spselectors.RCModelSPSelector method) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ method) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj method) (aimmd.distributed.spselectors.SPSelector method) (aimmd.distributed.spselectors.UniformSPSelector method)

R

RandomVelocitiesShootingPathMover (class in aimmd.distributed.pathmovers) RCModelSPSelector (class in aimmd.distributed.spselectors) RCModelSPSelectorFromEQ (class in aimmd.distributed.spselectors)

RCModelSPSelectorFromTraj (class in aimmd.distributed.spselectors) reinitialize_from_workdir() (aimmd.distributed.CommittorSimulation method) run() (aimmd.distributed.CommittorSimulation method)

S

scale (aimmd.distributed.spselectors.RCModelSPSelector property) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ property) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj property) ShootingPathMover (class in aimmd.distributed.pathmovers) SPSelector (class in aimmd.distributed.spselectors) states (aimmd.distributed.CommittorSimulation property) states_reached (aimmd.distributed.CommittorSimulation property) states_reached_backward (aimmd.distributed.CommittorSimulation property) states_reached_per_trial (aimmd.distributed.CommittorSimulation property)

states_reached_per_trial_backward (aimmd.distributed.CommittorSimulation property) store_model() (aimmd.distributed.pathmovers.FixedLengthTwoWayShootingPathMover method) (aimmd.distributed.pathmovers.PathMover method) (aimmd.distributed.pathmovers.RandomVelocitiesShootingPathMover method) (aimmd.distributed.pathmovers.ShootingPathMover method) (aimmd.distributed.pathmovers.TwoWayShootingPathMover method) sum_bias() (aimmd.distributed.spselectors.RCModelSPSelector method) (aimmd.distributed.spselectors.RCModelSPSelectorFromEQ method) (aimmd.distributed.spselectors.RCModelSPSelectorFromTraj method)

T

temperature (aimmd.distributed.CommittorSimulation property) trajectories_to_state (aimmd.distributed.CommittorSimulation property) trajectories_to_state_backward (aimmd.distributed.CommittorSimulation property)

transition_trajectories (aimmd.distributed.CommittorSimulation property) trial_counter (aimmd.distributed.CommittorSimulation property) two_way (aimmd.distributed.CommittorSimulation property) TwoWayShootingPathMover (class in aimmd.distributed.pathmovers)

U

UniformSPSelector (class in aimmd.distributed.spselectors)

W

workdir (aimmd.distributed.CommittorSimulation property)