Index A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | U | V | W | X | Y A apply_bounds() (in module stochkin.boundaries) (in module stochkin.integrators) as_xy() (stochkin.mfep.MFEPPath method) B baobab_2d() (in module stochkin.integrators) baobab_step() (in module stochkin.integrators) Basin (class in stochkin.potentials) Basin1D (class in stochkin.potentials) basinA() (in module stochkin.committor) basinA_mfpt() (in module stochkin.mfpt) basinB() (in module stochkin.committor) basinB_mfpt() (in module stochkin.mfpt) BasinNetwork (class in stochkin.potentials) BasinNetwork1D (class in stochkin.potentials) basins (stochkin.potentials.BasinNetwork attribute), [1] (stochkin.potentials.BasinNetwork1D attribute), [1] bootstrap_ctmc_1d() (in module stochkin.uncertainty) bootstrap_ctmc_with_hummer_D() (in module stochkin.uncertainty) bounds (stochkin.potentials.Basin attribute), [1] (stochkin.potentials.Basin1D attribute), [1] build_basin_network_from_fes_1d() (in module stochkin.potentials) build_basin_network_from_potential() (in module stochkin.potentials) build_basin_network_from_potential_1d() (in module stochkin.potentials) build_core_labels_from_full_labels() (in module stochkin.potentials) build_fp_generator_from_fes() (in module stochkin.fpe) build_mesh_2d_from_edges() (in module stochkin.fpe) C central_well_barrier_ring_potential() (in module stochkin.potentials) coarse_subsample() (stochkin.fes.FESPotential method) committor_map_fpe() (in module stochkin.committor) committor_map_parallel() (in module stochkin.committor) committor_point() (in module stochkin.committor) committor_profile_1d() (in module stochkin.committor) compute_bidirectional_mfpt() (in module stochkin.mfpt) compute_bidirectional_mfpt_1d() (in module stochkin.mfpt) compute_ctmc_generator_fpe_1d() (in module stochkin.fpe) compute_ctmc_generator_fpe_fipy() (in module stochkin.fpe) compute_mfep_profile_1d() (in module stochkin.mfep) compute_mfpt() (in module stochkin.mfpt) compute_mfpt_1d() (in module stochkin.mfpt) compute_mfpt_network() (in module stochkin.mfpt) compute_mfpt_network_fpe() (in module stochkin.mfpt) confidence_level (stochkin.uncertainty.UncertaintyResult attribute), [1] coordinate_to_index() (stochkin.mfep.GridMFEP method) core_labels (stochkin.potentials.BasinNetwork attribute), [1] D detect_basins_for_mfpt() (in module stochkin.potentials) detect_basins_for_mfpt_1d() (in module stochkin.potentials) double_well_1d() (in module stochkin.potentials) double_well_2d() (in module stochkin.potentials) draw_barrier_arrows() (in module stochkin.plotting) dw1d_basin_left_mfpt() (in module stochkin.mfpt) dw1d_basin_right_mfpt() (in module stochkin.mfpt) E estimate_rate_matrix() (in module stochkin.mfpt) estimate_transition_rates() (in module stochkin.mfpt) eval_diffusion_and_grad() (in module stochkin.integrators) evaluate_U_on_grid() (stochkin.fes.FESPotential method) exit_mean_ci_hi (stochkin.uncertainty.UncertaintyResult attribute) exit_mean_ci_lo (stochkin.uncertainty.UncertaintyResult attribute) exit_mean_mean (stochkin.uncertainty.UncertaintyResult attribute) exit_mean_samples (stochkin.uncertainty.UncertaintyResult attribute), [1] exit_mean_std (stochkin.uncertainty.UncertaintyResult attribute) F F (stochkin.mfep.MFEPPath attribute), [1] f_min (stochkin.potentials.Basin attribute), [1] (stochkin.potentials.Basin1D attribute), [1] FESPotential (class in stochkin.fes) FESPotential1D (class in stochkin.fes) find_path() (stochkin.mfep.GridMFEP method) finite_difference_grad_scalar() (in module stochkin.integrators) from_plumed() (stochkin.mfep.GridMFEP class method) G GammaToDiffusion (class in stochkin.integrators) generate_basin_position() (in module stochkin.mfpt) generate_basin_position_1d() (in module stochkin.mfpt) GridMFEP (class in stochkin.mfep) I id (stochkin.potentials.Basin attribute), [1] (stochkin.potentials.Basin1D attribute), [1] indices (stochkin.mfep.MFEPPath attribute), [1] interface_to_centers() (in module stochkin.workflows) interpolate_D_to_grid() (in module stochkin.workflows) K K_ci_hi (stochkin.uncertainty.UncertaintyResult attribute) K_ci_lo (stochkin.uncertainty.UncertaintyResult attribute) K_mean (stochkin.uncertainty.UncertaintyResult attribute) k_out_ci_hi (stochkin.uncertainty.UncertaintyResult attribute) k_out_ci_lo (stochkin.uncertainty.UncertaintyResult attribute) k_out_mean (stochkin.uncertainty.UncertaintyResult attribute) k_out_samples (stochkin.uncertainty.UncertaintyResult attribute), [1] k_out_std (stochkin.uncertainty.UncertaintyResult attribute) K_ps_ci_hi (stochkin.uncertainty.UncertaintyResult attribute) K_ps_ci_lo (stochkin.uncertainty.UncertaintyResult attribute) K_ps_mean (stochkin.uncertainty.UncertaintyResult attribute) K_ps_std (stochkin.uncertainty.UncertaintyResult attribute) K_samples (stochkin.uncertainty.UncertaintyResult attribute), [1] K_std (stochkin.uncertainty.UncertaintyResult attribute) L labels (stochkin.potentials.BasinNetwork attribute), [1] (stochkin.potentials.BasinNetwork1D attribute), [1] labels_full (stochkin.potentials.BasinNetwork attribute), [1] load_diffusion_scalar_2d_from_plumed() (in module stochkin.fes) load_plumed_fes_1d() (in module stochkin.fes) load_plumed_fes_2d() (in module stochkin.fes) load_plumed_scalar_field_2d() (in module stochkin.fes) M make_backward_coefficient_A_face_from_cell_values() (in module stochkin.fpe) make_double_well_1d() (in module stochkin.potentials) make_fes_potential_from_grid() (in module stochkin.fes) make_fes_potential_from_plumed() (in module stochkin.fes) make_fes_potential_from_plumed_1d() (in module stochkin.fes) make_potential_from_string() (in module stochkin.potentials) metadata (stochkin.mfep.MFEPPath attribute), [1] method (stochkin.mfep.MFEPPath attribute), [1] mexican_hat_potential() (in module stochkin.potentials) MFEPPath (class in stochkin.mfep) mfpt_1d_smolu_integral() (in module stochkin.fpe) minimum (stochkin.potentials.Basin attribute), [1] (stochkin.potentials.Basin1D attribute), [1] module stochkin.boundaries stochkin.committor stochkin.fes stochkin.fpe stochkin.integrators stochkin.mfep stochkin.mfpt stochkin.plotting stochkin.potentials stochkin.replicas stochkin.style stochkin.uncertainty stochkin.workflows muller_potential() (in module stochkin.potentials) N n_basins (stochkin.potentials.BasinNetwork property) (stochkin.potentials.BasinNetwork1D property) n_bootstrap (stochkin.uncertainty.UncertaintyResult attribute), [1] n_failed (stochkin.uncertainty.UncertaintyResult attribute), [1] NEBMFEP (class in stochkin.mfep) O objective (stochkin.mfep.MFEPPath attribute), [1] overdamped_bd() (in module stochkin.integrators) overdamped_step_euler() (in module stochkin.integrators) P p_branch_ci_hi (stochkin.uncertainty.UncertaintyResult attribute) p_branch_ci_lo (stochkin.uncertainty.UncertaintyResult attribute) p_branch_mean (stochkin.uncertainty.UncertaintyResult attribute) p_branch_samples (stochkin.uncertainty.UncertaintyResult attribute), [1] p_branch_std (stochkin.uncertainty.UncertaintyResult attribute) plot() (stochkin.fes.FESPotential method) (stochkin.fes.FESPotential1D method) plot_2d_fes() (in module stochkin.plotting) plot_basin_network() (in module stochkin.plotting) plot_central_well_barrier_ring() (in module stochkin.plotting) plot_fes_colormap() (in module stochkin.fes) plot_fp_solution_vs_boltzmann() (in module stochkin.plotting) plot_interpolated() (stochkin.fes.FESPotential method) plot_mfpt_matrix() (in module stochkin.plotting) plot_mfpt_statistics() (in module stochkin.mfpt) plot_results() (in module stochkin.plotting) position_update() (in module stochkin.integrators) publication_style() (in module stochkin.style) R radius (stochkin.potentials.Basin attribute), [1] (stochkin.potentials.Basin1D attribute), [1] random_velocity_update() (in module stochkin.integrators) reference (stochkin.uncertainty.UncertaintyResult attribute), [1] refine() (stochkin.mfep.NEBMFEP method) refine_between() (stochkin.mfep.NEBMFEP method) refine_fire() (stochkin.mfep.NEBMFEP method) reflect_position_velocity() (in module stochkin.boundaries) reflect_scalar() (in module stochkin.boundaries) run_1d_ctmc() (in module stochkin.workflows) run_1d_ctmc_from_plumed() (in module stochkin.workflows) run_1d_ctmc_with_hummer_D() (in module stochkin.workflows) run_mfep_ctmc() (in module stochkin.workflows) run_multi_mfep_ctmc() (in module stochkin.workflows) run_replicas() (in module stochkin.replicas) run_replicas_1d() (in module stochkin.replicas) run_short_trajectory() (in module stochkin.committor) S s (stochkin.mfep.MFEPPath attribute), [1] (stochkin.potentials.BasinNetwork1D attribute), [1] sample_point_in_basin() (stochkin.potentials.BasinNetwork method) (stochkin.potentials.BasinNetwork1D method) sample_potential_grid() (in module stochkin.potentials) save_path_xyf() (stochkin.mfep.MFEPPath method) save_profile_1d() (stochkin.mfep.MFEPPath method) set_publication_style() (in module stochkin.style) simple_double_well_2d() (in module stochkin.potentials) single_passage_time() (in module stochkin.mfpt) single_replica() (in module stochkin.replicas) single_replica_1d() (in module stochkin.replicas) solve_committor_1d_from_fes() (in module stochkin.fpe) solve_committor_fipy() (in module stochkin.fpe) solve_exit_time_1d_from_fes() (in module stochkin.fpe) solve_exit_time_fipy() (in module stochkin.fpe) solve_fp_1d_from_fes() (in module stochkin.fpe) solve_fp_steady_state() (in module stochkin.fpe) stochkin.boundaries module stochkin.committor module stochkin.fes module stochkin.fpe module stochkin.integrators module stochkin.mfep module stochkin.mfpt module stochkin.plotting module stochkin.potentials module stochkin.replicas module stochkin.style module stochkin.uncertainty module stochkin.workflows module StringPotential (class in stochkin.potentials) summary() (stochkin.uncertainty.UncertaintyResult method) U U (stochkin.potentials.BasinNetwork attribute), [1] (stochkin.potentials.BasinNetwork1D attribute), [1] UncertaintyResult (class in stochkin.uncertainty) V velocity_update() (in module stochkin.integrators) W which_basin() (stochkin.potentials.BasinNetwork method) (stochkin.potentials.BasinNetwork1D method) X x (stochkin.mfep.MFEPPath attribute) xs (stochkin.potentials.BasinNetwork attribute) Y y (stochkin.mfep.MFEPPath attribute) ys (stochkin.potentials.BasinNetwork attribute)