API Reference

Modules

• stochkin.workflows
  • stochkin.workflows
  • run_1d_ctmc()
  • run_1d_ctmc_from_plumed()
  • run_1d_ctmc_with_hummer_D()
  • run_mfep_ctmc()
  • run_multi_mfep_ctmc()
  • interface_to_centers()
  • interpolate_D_to_grid()
• stochkin.uncertainty
  • Key functions
  • Detailed API
• stochkin.potentials
  • stochkin.potentials
  • StringPotential
  • make_potential_from_string()
  • double_well_2d()
  • mexican_hat_potential()
  • central_well_barrier_ring_potential()
  • muller_potential()
  • simple_double_well_2d()
  • double_well_1d()
  • make_double_well_1d()
  • Basin
  • BasinNetwork
  • Basin1D
  • BasinNetwork1D
  • sample_potential_grid()
  • build_basin_network_from_fes_1d()
  • build_basin_network_from_potential_1d()
  • detect_basins_for_mfpt_1d()
  • build_core_labels_from_full_labels()
  • build_basin_network_from_potential()
  • detect_basins_for_mfpt()
• stochkin.integrators
  • stochkin.integrators
  • velocity_update()
  • position_update()
  • random_velocity_update()
  • baobab_step()
  • baobab_2d()
  • GammaToDiffusion
  • apply_bounds()
  • finite_difference_grad_scalar()
  • eval_diffusion_and_grad()
  • overdamped_step_euler()
  • overdamped_bd()
• stochkin.fes
  • stochkin.fes
  • load_plumed_fes_2d()
  • load_plumed_scalar_field_2d()
  • load_diffusion_scalar_2d_from_plumed()
  • load_plumed_fes_1d()
  • FESPotential
  • FESPotential1D
  • make_fes_potential_from_grid()
  • make_fes_potential_from_plumed()
  • make_fes_potential_from_plumed_1d()
  • plot_fes_colormap()
• stochkin.fpe
  • stochkin.fpe
  • solve_fp_steady_state()
  • build_fp_generator_from_fes()
  • solve_fp_1d_from_fes()
  • mfpt_1d_smolu_integral()
  • solve_committor_1d_from_fes()
  • solve_exit_time_1d_from_fes()
  • compute_ctmc_generator_fpe_1d()
  • build_mesh_2d_from_edges()
  • make_backward_coefficient_A_face_from_cell_values()
  • solve_committor_fipy()
  • solve_exit_time_fipy()
  • compute_ctmc_generator_fpe_fipy()
• stochkin.mfep
  • MFEPPath
  • GridMFEP
  • NEBMFEP
  • compute_mfep_profile_1d()
• stochkin.mfpt
  • stochkin.mfpt
  • single_passage_time()
  • generate_basin_position()
  • generate_basin_position_1d()
  • compute_mfpt()
  • compute_mfpt_1d()
  • compute_bidirectional_mfpt()
  • compute_bidirectional_mfpt_1d()
  • plot_mfpt_statistics()
  • estimate_transition_rates()
  • basinA_mfpt()
  • basinB_mfpt()
  • dw1d_basin_left_mfpt()
  • dw1d_basin_right_mfpt()
  • compute_mfpt_network()
  • compute_mfpt_network_fpe()
  • estimate_rate_matrix()
• stochkin.committor
  • stochkin.committor
  • run_short_trajectory()
  • committor_point()
  • committor_map_parallel()
  • committor_profile_1d()
  • basinA()
  • basinB()
  • committor_map_fpe()
• stochkin.replicas
  • stochkin.replicas
  • single_replica()
  • run_replicas()
  • single_replica_1d()
  • run_replicas_1d()
• stochkin.plotting
  • plot_results()
  • plot_mfpt_matrix()
  • plot_fp_solution_vs_boltzmann()
  • plot_basin_network()
  • plot_central_well_barrier_ring()
  • plot_2d_fes()
  • draw_barrier_arrows()
• stochkin.boundaries
  • Why this module exists
  • reflect_scalar()
  • apply_bounds()
  • reflect_position_velocity()
• stochkin.style
  • set_publication_style()
  • publication_style()