Index

_

__call__() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) (asyncmd.trajectory.PyTrajectoryFunctionWrapper method) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper method) __hash__() (asyncmd.Trajectory method)

__len__() (asyncmd.Trajectory method) _get_id_str() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) _get_values_for_trajectory() (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper method) _parse_line() (asyncmd.mdconfig.LineBasedMDConfig method)

A

apply_constraints() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) apply_modification() (asyncmd.trajectory.convert.FrameExtractor method) (asyncmd.trajectory.InvertedVelocitiesFrameExtractor method) (asyncmd.trajectory.NoModificationFrameExtractor method) (asyncmd.trajectory.RandomVelocitiesFrameExtractor method) asyncmd module asyncmd.config module asyncmd.gromacs module asyncmd.gromacs.mdconfig module asyncmd.gromacs.mdengine module asyncmd.gromacs.utils module asyncmd.mdconfig module asyncmd.mdengine module asyncmd.slurm module asyncmd.slurm.cluster_mediator module asyncmd.slurm.config module

asyncmd.slurm.config.set_all_slurm_settings() built-in function asyncmd.slurm.config.set_slurm_settings() built-in function asyncmd.slurm.constants_and_errors module asyncmd.slurm.process module asyncmd.slurm.process.create_slurmprocess_submit() built-in function asyncmd.tools module asyncmd.trajectory module asyncmd.trajectory.convert module asyncmd.trajectory.functionwrapper module asyncmd.trajectory.propagate module asyncmd.trajectory.propagate.construct_tp_from_plus_and_minus_traj_segments() built-in function asyncmd.trajectory.trajectory module asyncmd.trajectory.trajectory_cache module asyncmd.utils module

B

built-in function asyncmd.slurm.config.set_all_slurm_settings() asyncmd.slurm.config.set_slurm_settings() asyncmd.slurm.process.create_slurmprocess_submit() asyncmd.trajectory.propagate.construct_tp_from_plus_and_minus_traj_segments()

C

call_kwargs (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper property) (asyncmd.trajectory.PyTrajectoryFunctionWrapper property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) changed (asyncmd.gromacs.MDP property) (asyncmd.mdconfig.LineBasedMDConfig property) clear_all_cache_values() (asyncmd.Trajectory method) communicate() (asyncmd.slurm.SlurmProcess method) concatenate() (asyncmd.trajectory.TrajectoryConcatenator method) concatenate_async() (asyncmd.trajectory.TrajectoryConcatenator method)

ConditionalTrajectoryPropagator (class in asyncmd.trajectory) conditions (asyncmd.trajectory.ConditionalTrajectoryPropagator property) construct_tp_from_plus_and_minus_traj_segments() (in module asyncmd.trajectory) create_slurmprocess_submit() (in module asyncmd.slurm) current_trajectory (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.mdengine.MDEngine property) cut_and_concatenate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method)

D

deffnm (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) del_sbatch_option() (asyncmd.slurm.SlurmProcess method) deregister_h5py_cache() (asyncmd.Trajectory method) (in module asyncmd.config)

dt (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.Trajectory property)

E

EngineCrashedError EngineError ensure_mdconfig_options() (in module asyncmd.utils) ensure_mdp_options() (in module asyncmd.gromacs.utils)

exclude_nodes (asyncmd.slurm.cluster_mediator.SlurmClusterMediator property) executable (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) extract() (asyncmd.trajectory.convert.FrameExtractor method) extract_async() (asyncmd.trajectory.convert.FrameExtractor method)

F

first_step (asyncmd.Trajectory property) first_time (asyncmd.Trajectory property) FrameExtractor (class in asyncmd.trajectory.convert)

frames_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) function (asyncmd.trajectory.PyTrajectoryFunctionWrapper property)

G

generate_velocities() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) get_all_file_parts() (in module asyncmd.gromacs.utils) (in module asyncmd.utils) get_all_traj_parts() (in module asyncmd.gromacs.utils) (in module asyncmd.utils) get_info_for_job() (asyncmd.slurm.cluster_mediator.SlurmClusterMediator method)

GmxEngine (class in asyncmd.gromacs) gro_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) grompp_executable (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) grompp_extra_args (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute)

I

id (asyncmd.trajectory.functionwrapper.TrajectoryFunctionWrapper property) (asyncmd.trajectory.PyTrajectoryFunctionWrapper property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property)

InPartsTrajectoryPropagator (class in asyncmd.trajectory) invert_v_for_negative_step (asyncmd.trajectory.TrajectoryConcatenator attribute) InvertedVelocitiesFrameExtractor (class in asyncmd.trajectory)

K

kill() (asyncmd.slurm.SlurmProcess method)

L

last_step (asyncmd.Trajectory property) last_time (asyncmd.Trajectory property)

LineBasedMDConfig (class in asyncmd.mdconfig) list_all_nodes() (asyncmd.slurm.cluster_mediator.SlurmClusterMediator method)

M

mdconfig (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) MDConfig (class in asyncmd.mdconfig) MDEngine (class in asyncmd.mdengine) mdp (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) MDP (class in asyncmd.gromacs) mdrun_executable (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) mdrun_extra_args (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) mdrun_time_conversion_factor (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) min_time_between_sacct_calls (asyncmd.slurm.cluster_mediator.SlurmClusterMediator attribute) module asyncmd asyncmd.config asyncmd.gromacs asyncmd.gromacs.mdconfig asyncmd.gromacs.mdengine asyncmd.gromacs.utils asyncmd.mdconfig asyncmd.mdengine asyncmd.slurm asyncmd.slurm.cluster_mediator asyncmd.slurm.config asyncmd.slurm.constants_and_errors asyncmd.slurm.process asyncmd.tools asyncmd.trajectory asyncmd.trajectory.convert asyncmd.trajectory.functionwrapper asyncmd.trajectory.propagate asyncmd.trajectory.trajectory asyncmd.trajectory.trajectory_cache asyncmd.utils

monitor_register_job() (asyncmd.slurm.cluster_mediator.SlurmClusterMediator method) monitor_remove_job() (asyncmd.slurm.cluster_mediator.SlurmClusterMediator method)

N

ndx_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) nodes (asyncmd.slurm.SlurmProcess property) NoModificationFrameExtractor (class in asyncmd.trajectory) nstout (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.Trajectory property)

nstout_from_mdconfig() (in module asyncmd.utils) nstout_from_mdp() (in module asyncmd.gromacs.utils) num_fails_for_broken_node (asyncmd.slurm.cluster_mediator.SlurmClusterMediator attribute)

O

original_file (asyncmd.gromacs.MDP property) (asyncmd.mdconfig.LineBasedMDConfig property)

output_traj_type (asyncmd.gromacs.GmxEngine attribute) (asyncmd.gromacs.SlurmGmxEngine attribute) (asyncmd.mdengine.MDEngine property)

P

parse() (asyncmd.gromacs.MDP method) (asyncmd.mdconfig.LineBasedMDConfig method) (asyncmd.mdconfig.MDConfig method) prepare() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) prepare_from_files() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method)

propagate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) propagate_and_concatenate() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) PyTrajectoryFunctionWrapper (class in asyncmd.trajectory)

R

RandomVelocitiesFrameExtractor (class in asyncmd.trajectory) register_h5py_cache() (in module asyncmd.config) remove_double_frames (asyncmd.trajectory.TrajectoryConcatenator attribute) remove_parts() (asyncmd.trajectory.ConditionalTrajectoryPropagator method) (asyncmd.trajectory.InPartsTrajectoryPropagator method) returncode (asyncmd.slurm.SlurmProcess property) run() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method)

run_steps() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method) run_walltime() (asyncmd.gromacs.GmxEngine method) (asyncmd.gromacs.SlurmGmxEngine method) (asyncmd.mdengine.MDEngine method)

S

sacct_executable (asyncmd.slurm.cluster_mediator.SlurmClusterMediator attribute) sbatch_executable (asyncmd.slurm.SlurmProcess attribute) sbatch_options (asyncmd.slurm.SlurmProcess property) (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) sbatch_script (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) scancel_executable (asyncmd.slurm.SlurmProcess attribute) send_signal() (asyncmd.slurm.SlurmProcess method) set_all_slurm_settings() (in module asyncmd.config) set_max_files_open() (in module asyncmd.config) set_max_process() (in module asyncmd.config) set_sbatch_option() (asyncmd.slurm.SlurmProcess method) set_slurm_max_jobs() (in module asyncmd.config) set_slurm_settings() (in module asyncmd.config) set_trajectory_cache_type() (in module asyncmd.config) show_config() (in module asyncmd.config) simulation_part (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) sinfo_executable (asyncmd.slurm.cluster_mediator.SlurmClusterMediator attribute)

sleep_time (asyncmd.slurm.SlurmProcess attribute) slurm_job_state (asyncmd.slurm.SlurmProcess property) slurm_jobid (asyncmd.slurm.SlurmProcess property) slurm_jobname (asyncmd.trajectory.SlurmTrajectoryFunctionWrapper property) SlurmCancellationError SlurmClusterMediator (class in asyncmd.slurm.cluster_mediator) SlurmError SlurmGmxEngine (class in asyncmd.gromacs) SlurmProcess (class in asyncmd.slurm) SlurmSubmissionError SlurmTrajectoryFunctionWrapper (class in asyncmd.trajectory) stdfiles_removal (asyncmd.slurm.SlurmProcess attribute) (asyncmd.slurm.SlurmProcess property) steps_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) (asyncmd.mdengine.MDEngine property) structure_file (asyncmd.Trajectory property) submit() (asyncmd.slurm.SlurmProcess method) success_to_fail_ratio (asyncmd.slurm.cluster_mediator.SlurmClusterMediator attribute)

T

T (asyncmd.trajectory.RandomVelocitiesFrameExtractor attribute) terminate() (asyncmd.slurm.SlurmProcess method) time (asyncmd.slurm.SlurmProcess property) time_done (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) top_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property)

tpr_file (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property) Trajectory (class in asyncmd) trajectory_files (asyncmd.Trajectory property) trajectory_hash (asyncmd.Trajectory property) TrajectoryConcatenator (class in asyncmd.trajectory) TrajectoryFunctionWrapper (class in asyncmd.trajectory.functionwrapper)

U

update_cache_type() (asyncmd.Trajectory method)

W

wait() (asyncmd.slurm.SlurmProcess method) workdir (asyncmd.gromacs.GmxEngine property) (asyncmd.gromacs.SlurmGmxEngine property)

write() (asyncmd.gromacs.MDP method) (asyncmd.mdconfig.LineBasedMDConfig method) (asyncmd.mdconfig.MDConfig method)