Index

_

__init__() (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

A

a3fe.analyse module a3fe.analyse.analyse_set module a3fe.analyse.compare module a3fe.analyse.detect_equil module a3fe.analyse.mbar module a3fe.analyse.plot module a3fe.analyse.rmsd module a3fe.analyse.waters module a3fe.configuration module a3fe.configuration.engine_config module a3fe.configuration.slurm_config module a3fe.configuration.system_prep_config module

a3fe.run module a3fe.run._simulation_runner module a3fe.run._utils module a3fe.run._virtual_queue module a3fe.run.system_prep module analyse() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) analyse_convergence() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

C

CalcSet (class in a3fe.run) Calculation (class in a3fe.run) check_equil_block_gradient() (in module a3fe.analyse.detect_equil) check_equil_multiwindow_modified_geweke() (in module a3fe.analyse.detect_equil) check_equil_multiwindow_paired_t() (in module a3fe.analyse.detect_equil) check_has_wat_and_box() (in module a3fe.run._utils) clean() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

compare_variances_brown_forsythe() (in module a3fe.analyse.compare) compute_statistic() (in module a3fe.analyse.analyse_set) compute_stats() (in module a3fe.analyse.analyse_set) copy() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method) create_stage_input_dirs() (a3fe.run.Leg method)

D

dummy_check_equil_multiwindow() (in module a3fe.analyse.detect_equil) dump() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method)

E

equil_time (a3fe.run._simulation_runner.SimulationRunner property) (a3fe.run.CalcSet property) (a3fe.run.Calculation property) (a3fe.run.LamWindow property) (a3fe.run.Leg property) (a3fe.run.Simulation property) (a3fe.run.Stage property)

equilibrated (a3fe.run.LamWindow property)

F

failed (a3fe.run.Simulation property) failed_simulations (a3fe.run._simulation_runner.SimulationRunner property) (a3fe.run.CalcSet property) (a3fe.run.Calculation property) (a3fe.run.LamWindow property) (a3fe.run.Leg property) (a3fe.run.Simulation property) (a3fe.run.Stage property)

G

general_plot() (in module a3fe.analyse.plot) get_av_waters_lambda_window() (in module a3fe.analyse.waters) get_av_waters_simulation() (in module a3fe.analyse.waters) get_av_waters_stage() (in module a3fe.analyse.waters) get_bootstrapped_results() (in module a3fe.analyse.analyse_set) get_comparitive_convergence_data() (in module a3fe.analyse.compare) get_default_partition() (a3fe.configuration.slurm_config.SlurmConfig class method) get_file_name() (a3fe.configuration.engine_config.SomdConfig static method) (a3fe.configuration.slurm_config.SlurmConfig static method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig static method) get_gelman_rubin_rhat() (in module a3fe.analyse.detect_equil) get_optimal_lam_vals() (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.Leg method) (a3fe.run.Stage method) get_results_df() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

get_rmsd() (in module a3fe.analyse.rmsd) get_run_cmd() (a3fe.configuration.engine_config.SomdConfig method) get_simtime() (in module a3fe.run._utils) get_single_mol() (in module a3fe.run._utils) get_slurm_output_file_base() (a3fe.configuration.slurm_config.SlurmConfig method) get_submission_cmds() (a3fe.configuration.slurm_config.SlurmConfig method) get_tot_gpu_time() (a3fe.run.LamWindow method) (a3fe.run.Simulation method) get_tot_simtime() (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method) (a3fe.run.LamWindow method) (a3fe.run.Simulation method)

H

has_failed() (a3fe.run._virtual_queue.Job method)

heat_and_preequil_input() (in module a3fe.run.system_prep)

I

input_dir (a3fe.run._simulation_runner.SimulationRunner property) (a3fe.run.CalcSet property) (a3fe.run.Calculation property) (a3fe.run.LamWindow property) (a3fe.run.Leg property) (a3fe.run.Simulation property) (a3fe.run.Stage property)

is_equilibrated() (a3fe.run.LamWindow method)

J

Job (class in a3fe.run._virtual_queue)

K

kill() (a3fe.run._virtual_queue.VirtualQueue method) (a3fe.run.LamWindow method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

L

lam_val_weights (a3fe.run.Stage property) LamWindow (class in a3fe.run) Leg (class in a3fe.run) lighten() (a3fe.run.Leg method) (a3fe.run.Simulation method)

load() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method)

M

minimise_input() (in module a3fe.run.system_prep) model_config (a3fe.configuration.engine_config.SomdConfig attribute) (a3fe.configuration.slurm_config.SlurmConfig attribute) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig attribute) model_construct() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_copy() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method) model_dump() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method) model_dump_json() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method) model_extra (a3fe.configuration.engine_config.SomdConfig property) (a3fe.configuration.slurm_config.SlurmConfig property) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig property) model_fields_set (a3fe.configuration.engine_config.SomdConfig property) (a3fe.configuration.slurm_config.SlurmConfig property) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig property) model_json_schema() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_parametrized_name() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_post_init() (a3fe.configuration.engine_config.SomdConfig method) (a3fe.configuration.slurm_config.SlurmConfig method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig method)

model_rebuild() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_validate() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_validate_json() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) model_validate_strings() (a3fe.configuration.engine_config.SomdConfig class method) (a3fe.configuration.slurm_config.SlurmConfig class method) (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig class method) module a3fe.analyse a3fe.analyse.analyse_set a3fe.analyse.compare a3fe.analyse.detect_equil a3fe.analyse.mbar a3fe.analyse.plot a3fe.analyse.rmsd a3fe.analyse.waters a3fe.configuration a3fe.configuration.engine_config a3fe.configuration.slurm_config a3fe.configuration.system_prep_config a3fe.run a3fe.run._simulation_runner a3fe.run._utils a3fe.run._virtual_queue a3fe.run.system_prep

N

ncycles (a3fe.configuration.engine_config.SomdConfig property)

nmoves (a3fe.configuration.engine_config.SomdConfig property)

P

p_plot() (in module a3fe.analyse.plot) parameterise_input() (in module a3fe.run.system_prep) plot_against_exp() (in module a3fe.analyse.plot) plot_av_waters() (in module a3fe.analyse.plot) plot_comparitive_convergence() (in module a3fe.analyse.plot) plot_comparitive_convergence_on_ax() (in module a3fe.analyse.plot) plot_comparitive_convergence_sem() (in module a3fe.analyse.plot) plot_comparitive_convergence_sem_on_ax() (in module a3fe.analyse.plot)

plot_equilibration_time() (in module a3fe.analyse.plot) plot_gelman_rubin_rhat() (in module a3fe.analyse.plot) plot_gradient_hists() (in module a3fe.analyse.plot) plot_gradient_stats() (in module a3fe.analyse.plot) plot_gradient_timeseries() (in module a3fe.analyse.plot) plot_mbar_pmf() (in module a3fe.analyse.plot) plot_normality() (in module a3fe.analyse.plot) plot_overlap_mat() (in module a3fe.analyse.plot) plot_overlap_mats() (in module a3fe.analyse.plot)

Q

queue (a3fe.run._virtual_queue.VirtualQueue property)

R

read_gradients() (a3fe.run.Simulation method) recursively_get_attr() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) recursively_set_attr() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) required_legs (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig property) required_stages (a3fe.configuration.system_prep_config.SomdSystemPreparationConfig property) reset() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

retry() (in module a3fe.run._utils) run() (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) run_ensemble_equilibration() (a3fe.run.Leg method) (in module a3fe.run.system_prep) run_mbar() (in module a3fe.analyse.mbar) running (a3fe.run.Simulation property) (a3fe.run.Stage property)

S

save() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) set_equilibration_time() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method) setup() (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.Leg method) setup_stages() (a3fe.run.Leg method)

Simulation (class in a3fe.run) SimulationRunner (class in a3fe.run._simulation_runner) SimulationRunnerIterator (class in a3fe.run._utils) slurm_file_base (a3fe.run.Simulation property) slurm_output_files (a3fe.run.Simulation property) SlurmConfig (class in a3fe.configuration.slurm_config) solvate_input() (in module a3fe.run.system_prep) SomdConfig (class in a3fe.configuration.engine_config) SomdSystemPreparationConfig (class in a3fe.configuration.system_prep_config) Stage (class in a3fe.run) stream_log_level (a3fe.run._simulation_runner.SimulationRunner property) (a3fe.run._virtual_queue.VirtualQueue property) (a3fe.run.CalcSet property) (a3fe.run.Calculation property) (a3fe.run.LamWindow property) (a3fe.run.Leg property) (a3fe.run.Simulation property) (a3fe.run.Stage property) submit() (a3fe.run._virtual_queue.VirtualQueue method)

T

TmpWorkingDir() (in module a3fe.run._utils)

tot_gpu_time (a3fe.run.Simulation property) tot_simtime (a3fe.run.Simulation property)

U

update() (a3fe.run._virtual_queue.VirtualQueue method) (a3fe.run.Stage method) update_engine_config_option() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

update_paths() (a3fe.run._simulation_runner.SimulationRunner method) (a3fe.run.CalcSet method) (a3fe.run.Calculation method) (a3fe.run.LamWindow method) (a3fe.run.Leg method) (a3fe.run.Simulation method) (a3fe.run.Stage method)

V

VirtualQueue (class in a3fe.run._virtual_queue)

W

wait() (a3fe.run._virtual_queue.VirtualQueue method) (a3fe.run.Stage method)

write_config() (a3fe.configuration.engine_config.SomdConfig method)