Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | Z A accept_symmetry_breaking (optking.v2.optparams.OptParams attribute) add_auxiliary_bonds (optking.v2.optparams.OptParams attribute) add_auxiliary_bonds() (optking.frag.Frag method) add_cartesian_intcos() (optking.frag.Frag method) add_converged_point() (optking.IRCfollowing.IntrinsicReactionCoordinate method) add_h_bonds() (optking.frag.Frag method) add_intcos_from_connectivity() (optking.frag.Frag method) adjust_unmet_constraints() (in module optking.displace) alg_error_handler() (optking.optimize.OptimizationManager method) alg_geom_maxiter (optking.v2.optparams.OptParams attribute) all_fragments (optking.molsys.Molsys property) apply_interfrag_step_scaling() (optking.stepAlgorithms.OptimizationAlgorithm method) apply_intrafrag_step_scaling() (optking.stepAlgorithms.OptimizationAlgorithm method) assess_previous_step() (optking.stepAlgorithms.ImageRFO method) (optking.stepAlgorithms.OptimizationAlgorithm method) atom2frag_index() (optking.molsys.Molsys method) atom_list2unique_frag_list() (optking.molsys.Molsys method) attempt_fromiter() (optking.opt_helper.Helper static method) augment_connectivity_to_single_fragment() (optking.molsys.Molsys method) auxiliary_bond_factor (optking.v2.optparams.OptParams attribute) axes_fixed (optking.bend.Bend attribute) B back_transformation() (in module optking.displace) backstep() (optking.stepAlgorithms.OptimizationAlgorithm method) backstep_needed() (optking.stepAlgorithms.OptimizationAlgorithm method) Bend (class in optking.bend) bend_type (optking.bend.Bend attribute) bends (optking.tors.Tors attribute) Bmat() (optking.dimerfrag.DimerFrag method) (optking.frag.Frag method) (optking.molsys.Molsys method) bt_dx_conv (optking.v2.optparams.OptParams attribute) bt_dx_rms_change_conv (optking.v2.optparams.OptParams attribute) bt_max_iter (optking.v2.optparams.OptParams attribute) bt_pinv_rcond (optking.v2.optparams.OptParams attribute) build_coordinates() (optking.opt_helper.Helper method) build_rfo_matrix() (optking.stepAlgorithms.RFO static method) C calc_arc_dist_step() (optking.IRCfollowing.IntrinsicReactionCoordinate method) calc_lagrangian() (optking.IRCfollowing.IntrinsicReactionCoordinate method) calc_lagrangian_derivs() (optking.IRCfollowing.IntrinsicReactionCoordinate method) calc_line_dist_step() (optking.IRCfollowing.IntrinsicReactionCoordinate method) calculations_needed() (optking.opt_helper.CustomHelper method) cart_hess_read (optking.v2.optparams.OptParams attribute) check_maxiter() (optking.optimize.OptimizationManager method) clear() (optking.optimize.OptimizationManager method) close() (optking.opt_helper.Helper method) compute() (optking.opt_helper.Helper method) compute_axes() (optking.bend.Bend method) compute_distance() (optking.linesearch.LineSearch method) (optking.linesearch.ThreePointEnergy method) compute_pivot_and_guess_points() (optking.IRCfollowing.IntrinsicReactionCoordinate method) conjugate_gradient_type (optking.v2.optparams.OptParams attribute) ConjugateGradient (class in optking.stepAlgorithms) connectivity_from_distances() (optking.frag.Frag method) consecutive_backsteps_allowed (optking.v2.optparams.OptParams attribute) constraint_matrix() (optking.molsys.Molsys method) conv_criteria() (optking.v2.optparams.OptParams method) conv_max_DE (optking.v2.optparams.OptParams attribute) conv_max_disp (optking.v2.optparams.OptParams attribute) conv_max_force (optking.v2.optparams.OptParams attribute) conv_rms_disp (optking.v2.optparams.OptParams attribute) conv_rms_force (optking.v2.optparams.OptParams attribute) converged() (optking.IRCfollowing.IntrinsicReactionCoordinate method) (optking.optimize.OptimizationManager method) (optking.stepAlgorithms.OptimizationAlgorithm method) covalent_connect (optking.v2.optparams.OptParams attribute) CustomHelper (class in optking.opt_helper) D decrease_trust_radius() (optking.stepAlgorithms.OptimizationAlgorithm method) diagonal_hessian_guess() (optking.bend.Bend method) (optking.stre.HBond method) (optking.stre.Stre method) (optking.tors.Tors method) dimer_intcos (optking.molsys.Molsys property) dimer_psuedo_frags (optking.molsys.Molsys property) DimerFrag (class in optking.dimerfrag) displace_frag() (in module optking.displace) displace_molsys() (in module optking.displace) Dq2Dx2() (optking.bend.Bend method) (optking.stre.Stre method) (optking.tors.Tors method) dq_irc() (optking.IRCfollowing.IntrinsicReactionCoordinate method) dq_to_dx() (in module optking.displace) DqDx() (optking.bend.Bend method) (optking.stre.Stre method) (optking.tors.Tors method) dynamic_level (optking.v2.optparams.OptParams attribute) dynamic_lvl_max (optking.v2.optparams.OptParams attribute) E E (optking.opt_helper.CustomHelper attribute) (optking.opt_helper.Helper attribute) EngineHelper (class in optking.opt_helper) ensure_bt_convergence (optking.v2.optparams.OptParams attribute) expected_energy() (optking.linesearch.LineSearch method) (optking.linesearch.ThreePointEnergy method) (optking.stepAlgorithms.ConjugateGradient method) (optking.stepAlgorithms.OptimizationAlgorithm method) (optking.stepAlgorithms.QuasiNewtonOptimization method) (optking.stepAlgorithms.RFO method) (optking.stepAlgorithms.SteepestDescent method) ext_force_bend (optking.v2.optparams.OptParams attribute) ext_force_cartesian (optking.v2.optparams.OptParams attribute) ext_force_dihedral (optking.v2.optparams.OptParams attribute) ext_force_distance (optking.v2.optparams.OptParams attribute) ext_force_oofp (optking.v2.optparams.OptParams attribute) F f_show_factor (optking.bend.Bend attribute) (optking.stre.Stre attribute) (optking.tors.Tors attribute) finish() (optking.optimize.OptimizationManager method) fit() (optking.linesearch.LineSearch method) (optking.linesearch.ThreePointEnergy method) fix_bend_axes() (optking.bend.Bend method) (optking.frag.Frag method) (optking.molsys.Molsys method) fix_val_near_pi (optking.v2.optparams.OptParams attribute) flexible_g_convergence (optking.v2.optparams.OptParams attribute) Frag (class in optking.frag) frag_1st_atom() (optking.molsys.Molsys method) frag_1st_intco() (optking.molsys.Molsys method) frag_atom_range() (optking.molsys.Molsys method) frag_atom_slice() (optking.molsys.Molsys method) frag_geom() (optking.molsys.Molsys method) frag_intco_range() (optking.molsys.Molsys method) frag_intco_slice() (optking.molsys.Molsys method) frag_mode (optking.v2.optparams.OptParams attribute) frag_natoms (optking.molsys.Molsys property) frag_ref_atoms (optking.v2.optparams.OptParams attribute) fragments (optking.molsys.Molsys property) freeze() (optking.frag.Frag method) freeze_all_dihedrals (optking.v2.optparams.OptParams attribute) freeze_intrafrag (optking.v2.optparams.OptParams attribute) from_dict() (in module optking.opt_helper) (optking.bend.Bend class method) (optking.IRCfollowing.IntrinsicReactionCoordinate class method) (optking.linesearch.LineSearch class method) (optking.opt_helper.CustomHelper class method) (optking.opt_helper.EngineHelper class method) (optking.opt_helper.Helper class method) (optking.optimize.OptimizationManager class method) (optking.stre.Stre class method) (optking.tors.Tors class method) from_internal_dict() (optking.v2.optparams.OptParams class method) from_psi4() (in module optking.opt_helper) (optking.molsys.Molsys static method) from_schema() (in module optking.opt_helper) (optking.molsys.Molsys class method) from_user_dict() (optking.dimerfrag.DimerFrag class method) frozen (optking.frag.Frag property) frozen_bend (optking.v2.optparams.OptParams attribute) frozen_cartesian (optking.v2.optparams.OptParams attribute) frozen_dihedral (optking.v2.optparams.OptParams attribute) frozen_distance (optking.v2.optparams.OptParams attribute) frozen_intco_list (optking.molsys.Molsys property) frozen_oofp (optking.v2.optparams.OptParams attribute) full_hess_every (optking.v2.optparams.OptParams attribute) G g_convergence (optking.v2.optparams.OptParams attribute) geom (optking.frag.Frag property) (optking.molsys.Molsys property) (optking.opt_helper.Helper attribute) geom_maxiter (optking.v2.optparams.OptParams attribute) get_hess_grad() (in module optking.optimize) get_hessian_protocol() (optking.optimize.OptimizationManager method) get_pes_info() (in module optking.optimize) get_unmet_constraints() (in module optking.displace) Gmat() (optking.molsys.Molsys method) gradient_to_cartesians() (optking.molsys.Molsys method) gradient_to_internals() (optking.molsys.Molsys method) gX (optking.opt_helper.CustomHelper attribute) (optking.opt_helper.Helper attribute) H h_bond_connect (optking.v2.optparams.OptParams attribute) h_guess_every (optking.v2.optparams.OptParams attribute) HBond (class in optking.stre) Helper (class in optking.opt_helper) hess_update (optking.v2.optparams.OptParams attribute) hess_update_den_tol (optking.v2.optparams.OptParams attribute) hess_update_dq_tol (optking.v2.optparams.OptParams attribute) hess_update_limit (optking.v2.optparams.OptParams attribute) hess_update_limit_max (optking.v2.optparams.OptParams attribute) hess_update_limit_scale (optking.v2.optparams.OptParams attribute) hess_update_use_last (optking.v2.optparams.OptParams attribute) hessian_file (optking.v2.optparams.OptParams attribute) hessian_to_internals() (optking.molsys.Molsys method) History (class in optking.history) HX (optking.opt_helper.CustomHelper attribute) (optking.opt_helper.Helper attribute) I ImageRFO (class in optking.stepAlgorithms) include_oofp (optking.v2.optparams.OptParams attribute) increase_trust_radius() (optking.stepAlgorithms.OptimizationAlgorithm method) initialize_from_psi4() (in module optking.optwrapper) initialize_options() (in module optking.optwrapper) intcos (optking.frag.Frag property) interfrag_collinear_tol (optking.v2.optparams.OptParams attribute) interfrag_coords (optking.v2.optparams.OptParams attribute) interfrag_dist_inv (optking.v2.optparams.OptParams attribute) interfrag_hess (optking.v2.optparams.OptParams attribute) interfrag_mode (optking.v2.optparams.OptParams attribute) interfrag_trust (optking.v2.optparams.OptParams attribute) interfrag_trust_max (optking.v2.optparams.OptParams attribute) interfrag_trust_min (optking.v2.optparams.OptParams attribute) interfragment_connect (optking.v2.optparams.OptParams attribute) intrafrag_hess (optking.v2.optparams.OptParams attribute) intrafrag_trust (optking.v2.optparams.OptParams attribute) intrafrag_trust_max (optking.v2.optparams.OptParams attribute) intrafrag_trust_min (optking.v2.optparams.OptParams attribute) IntrinsicReactionCoordinate (class in optking.IRCfollowing) inverse (optking.stre.Stre attribute) irc_convergence (optking.v2.optparams.OptParams attribute) irc_de_projected() (in module optking.IRCfollowing) irc_direction (optking.v2.optparams.OptParams attribute) irc_mode (optking.v2.optparams.OptParams attribute) irc_points (optking.v2.optparams.OptParams attribute) irc_step_size (optking.v2.optparams.OptParams attribute) is_linear() (optking.frag.Frag method) L linear_algebra_tol (optking.v2.optparams.OptParams attribute) linear_bend_threshold (optking.v2.optparams.OptParams attribute) LineSearch (class in optking.linesearch) linesearch (optking.v2.optparams.OptParams attribute) linesearch_step (optking.v2.optparams.OptParams attribute) LineSearchStep (class in optking.linesearch) M make_computer() (in module optking.optwrapper) make_internal_coords() (in module optking.optimize) masses (optking.frag.Frag property) (optking.molsys.Molsys property) model_post_init() (optking.v2.optparams.OptParams method) module optking.bend optking.displace optking.IRCfollowing optking.linesearch optking.opt_helper optking.optimize optking.optwrapper optking.stepAlgorithms optking.stre optking.tors Molsys (class in optking.molsys) N natom (optking.frag.Frag property) (optking.molsys.Molsys property) near180 (optking.tors.Tors attribute) nfragments (optking.molsys.Molsys property) num_intcos (optking.frag.Frag property) (optking.molsys.Molsys property) num_intrafrag_intcos (optking.molsys.Molsys property) O opt_coordinates (optking.v2.optparams.OptParams attribute) opt_error_handler() (optking.optimize.OptimizationManager method) opt_type (optking.v2.optparams.OptParams attribute) optimization_factory() (in module optking.optimize) OptimizationAlgorithm (class in optking.stepAlgorithms) OptimizationInterface (class in optking.stepAlgorithms) OptimizationManager (class in optking.optimize) optimize() (in module optking.optimize) (optking.opt_helper.EngineHelper method) optimize_psi4() (in module optking.optwrapper) optimize_qcengine() (in module optking.optwrapper) optking.bend module optking.displace module optking.IRCfollowing module optking.linesearch module optking.opt_helper module optking.optimize module optking.optwrapper module optking.stepAlgorithms module optking.stre module optking.tors module orient_fragment() (optking.dimerfrag.DimerFrag method) P PartitionedRFO (class in optking.stepAlgorithms) post_step_str() (optking.opt_helper.Helper method) pre_step_str() (optking.opt_helper.Helper method) prepare_opt_output() (in module optking.optimize) print_geom() (optking.molsys.Molsys method) print_intcos() (optking.frag.Frag method) print_lvl (optking.v2.optparams.OptParams attribute) print_trajectory_xyz_file (optking.v2.optparams.OptParams attribute) program (optking.v2.optparams.OptParams attribute) project_redundancies_and_constraints() (optking.molsys.Molsys method) Q q() (optking.bend.Bend method) (optking.frag.Frag method) (optking.molsys.Molsys method) (optking.stre.Stre method) (optking.tors.Tors method) q_array() (optking.frag.Frag method) (optking.molsys.Molsys method) q_show() (optking.bend.Bend method) (optking.frag.Frag method) (optking.molsys.Molsys method) (optking.stre.Stre method) (optking.tors.Tors method) q_show_array() (optking.frag.Frag method) (optking.molsys.Molsys method) q_show_factor (optking.bend.Bend attribute) (optking.stre.Stre attribute) (optking.tors.Tors attribute) q_show_forces() (optking.molsys.Molsys method) QuasiNewtonOptimization (class in optking.stepAlgorithms) QuasiNewtonRaphson (class in optking.stepAlgorithms) R ranged_bend (optking.v2.optparams.OptParams attribute) ranged_cartesian (optking.v2.optparams.OptParams attribute) ranged_dihedral (optking.v2.optparams.OptParams attribute) ranged_distance (optking.v2.optparams.OptParams attribute) ranged_frozen_intco_list() (optking.molsys.Molsys method) ranged_oofp (optking.v2.optparams.OptParams attribute) redundant_eval_tol (optking.v2.optparams.OptParams attribute) requires() (optking.IRCfollowing.IntrinsicReactionCoordinate method) (optking.linesearch.ThreePointEnergy method) (optking.stepAlgorithms.ConjugateGradient method) (optking.stepAlgorithms.OptimizationAlgorithm method) (optking.stepAlgorithms.QuasiNewtonOptimization method) (optking.stepAlgorithms.SteepestDescent method) reset() (optking.linesearch.LineSearch method) (optking.linesearch.ThreePointEnergy method) RestrictedStepRFO (class in optking.stepAlgorithms) RFO (class in optking.stepAlgorithms) rfo_follow_root (optking.v2.optparams.OptParams attribute) rfo_normalization_max (optking.v2.optparams.OptParams attribute) rfo_root (optking.v2.optparams.OptParams attribute) rsrfo_alpha_max (optking.v2.optparams.OptParams attribute) S sd_hessian (optking.v2.optparams.OptParams attribute) show() (optking.opt_helper.Helper method) show_geom() (optking.molsys.Molsys method) simple_step_scaling (optking.v2.optparams.OptParams attribute) small_bend_fix_threshold (optking.v2.optparams.OptParams attribute) split_fragments_by_connectivity() (optking.molsys.Molsys method) start() (optking.linesearch.LineSearch method) start_step() (optking.optimize.OptimizationManager method) status() (optking.opt_helper.Helper method) steepest_descent_type (optking.v2.optparams.OptParams attribute) SteepestDescent (class in optking.stepAlgorithms) Step (class in optking.history) step() (optking.linesearch.LineSearch method) (optking.linesearch.ThreePointEnergy method) (optking.stepAlgorithms.ConjugateGradient method) (optking.stepAlgorithms.ImageRFO method) (optking.stepAlgorithms.OptimizationAlgorithm method) (optking.stepAlgorithms.PartitionedRFO method) (optking.stepAlgorithms.QuasiNewtonRaphson method) (optking.stepAlgorithms.RestrictedStepRFO method) (optking.stepAlgorithms.SteepestDescent method) step_matches_forces() (in module optking.stepAlgorithms) step_metrics() (optking.stepAlgorithms.OptimizationInterface method) step_n_factor() (in module optking.IRCfollowing) step_size_scalar() (optking.stepAlgorithms.SteepestDescent method) step_type (optking.v2.optparams.OptParams attribute) Stre (class in optking.stre) summarize_result() (optking.opt_helper.Helper method) supports_trust_region() (optking.stepAlgorithms.ConjugateGradient method) (optking.stepAlgorithms.ImageRFO method) (optking.stepAlgorithms.OptimizationAlgorithm method) (optking.stepAlgorithms.PartitionedRFO method) (optking.stepAlgorithms.QuasiNewtonOptimization method) (optking.stepAlgorithms.SteepestDescent method) T take_step() (optking.IRCfollowing.IntrinsicReactionCoordinate method) (optking.linesearch.LineSearch method) (optking.opt_helper.Helper method) (optking.optimize.OptimizationManager method) (optking.stepAlgorithms.OptimizationAlgorithm method) (optking.stepAlgorithms.OptimizationInterface method) (optking.stepAlgorithms.QuasiNewtonOptimization method) test_B (optking.v2.optparams.OptParams attribute) test_Bmat() (optking.molsys.Molsys method) test_convergence() (optking.opt_helper.Helper method) test_derivative_B (optking.v2.optparams.OptParams attribute) test_derivative_Bmat() (optking.molsys.Molsys method) ThreePointEnergy (class in optking.linesearch) to_dict() (optking.bend.Bend method) (optking.IRCfollowing.IntrinsicReactionCoordinate method) (optking.linesearch.LineSearch method) (optking.opt_helper.Helper method) (optking.optimize.OptimizationManager method) (optking.stre.Stre method) (optking.tors.Tors method) (optking.v2.optparams.OptParams method) Tors (class in optking.tors) U unfix_bend_axes() (optking.bend.Bend method) (optking.frag.Frag method) (optking.molsys.Molsys method) unfreeze_dihedrals (optking.v2.optparams.OptParams attribute) unknown_error_handler() (optking.optimize.OptimizationManager method) update_dihedral_orientations() (optking.frag.Frag method) (optking.molsys.Molsys method) update_dynamic_level_params() (optking.v2.optparams.OptParams method) update_history() (optking.stepAlgorithms.OptimizationAlgorithm method) update_orientation() (optking.tors.Tors method) update_requirements() (optking.optimize.OptimizationManager method) V v3d_tors_angle_lim (optking.v2.optparams.OptParams attribute) v3d_tors_cos_tol (optking.v2.optparams.OptParams attribute) W write_trajectory (optking.v2.optparams.OptParams attribute) Z Z (optking.frag.Frag property) zeta() (optking.bend.Bend static method) (optking.tors.Tors static method)
