pyoptking
stable
Contents:
Getting Started
Convergence
Optimization Algorithms
The Molecular System
General Recommendations
Adding Constraints to the Optimization
Multifragment Optimizations
Keywords and Options
pyoptking
Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
A
A_idx (optking.dimerfrag.DimerFrag attribute)
a_ref_geom() (optking.dimerfrag.DimerFrag method)
active_labels() (optking.dimerfrag.DimerFrag method)
add_cartesian_intcos() (optking.frag.Frag method)
(optking.molsys.Molsys method)
add_converged_point() (optking.IRCfollowing.IntrinsicReactionCoordinate method)
add_h_bonds() (optking.frag.Frag method)
add_intcos_from_connectivity() (optking.frag.Frag method)
alg_error_handler() (optking.optimize.OptimizationManager method)
all_fragments (optking.molsys.Molsys attribute)
apply_external_forces() (optking.molsys.Molsys method)
apply_interfrag_step_scaling() (optking.stepAlgorithms.OptimizationAlgorithm method)
apply_intrafrag_step_scaling() (optking.stepAlgorithms.OptimizationAlgorithm method)
assess_previous_step() (optking.stepAlgorithms.OptimizationAlgorithm method)
atom (optking.dimerfrag.Weight attribute)
atom2frag_index() (optking.molsys.Molsys method)
atom_list2unique_frag_list() (optking.molsys.Molsys method)
atom_symbols (optking.molsys.Molsys attribute)
atoms() (optking.dimerfrag.RefPoint method)
attempt_fromiter() (optking.opt_helper.Helper static method)
augment_connectivity_to_single_fragment() (optking.molsys.Molsys method)
axes_fixed (optking.bend.Bend attribute)
B
B_idx (optking.dimerfrag.DimerFrag attribute)
b_ref_geom() (optking.dimerfrag.DimerFrag method)
backstep() (optking.stepAlgorithms.OptimizationAlgorithm method)
backstep_needed() (optking.stepAlgorithms.OptimizationAlgorithm method)
Bend (class in optking.bend)
bend_type (optking.bend.Bend attribute)
Bmat() (optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
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)
check_maxiter() (optking.optimize.OptimizationManager method)
clear() (optking.molsys.Molsys method)
(optking.optimize.OptimizationManager method)
close() (optking.opt_helper.Helper method)
closest_atoms_between_2_frags() (optking.molsys.Molsys method)
coeffs() (optking.dimerfrag.RefPoint 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)
connectivity_from_distances() (optking.frag.Frag method)
consolidate_fragments() (optking.molsys.Molsys method)
constraint_matrix() (optking.molsys.Molsys method)
converged() (optking.IRCfollowing.IntrinsicReactionCoordinate method)
(optking.optimize.OptimizationManager method)
(optking.stepAlgorithms.OptimizationAlgorithm method)
CustomHelper (class in optking.opt_helper)
D
d_on() (optking.dimerfrag.DimerFrag method)
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 attribute)
dimer_psuedo_frags (optking.molsys.Molsys attribute)
DimerFrag (class in optking.dimerfrag)
dimerfrag_1st_intco() (optking.molsys.Molsys method)
dimerfrag_intco_range() (optking.molsys.Molsys method)
dimerfrag_intco_slice() (optking.molsys.Molsys method)
distance_matrix() (optking.molsys.Molsys method)
Dq2Dx2() (optking.bend.Bend method)
(optking.stre.Stre method)
(optking.tors.Tors method)
dq_discontinuity_correction() (optking.dimerfrag.DimerFrag method)
dq_irc() (optking.IRCfollowing.IntrinsicReactionCoordinate method)
DqDx() (optking.bend.Bend method)
(optking.stre.Stre method)
(optking.tors.Tors method)
E
E (optking.opt_helper.CustomHelper attribute)
(optking.opt_helper.Helper attribute)
EngineHelper (class in optking.opt_helper)
expected_energy() (optking.linesearch.LineSearch method)
(optking.linesearch.ThreePointEnergy method)
(optking.stepAlgorithms.OptimizationAlgorithm method)
(optking.stepAlgorithms.QuasiNewtonOptimization method)
(optking.stepAlgorithms.RFO method)
(optking.stepAlgorithms.SteepestDescent method)
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)
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.optparams.OptParams attribute)
frag_natoms (optking.molsys.Molsys attribute)
fragments (optking.molsys.Molsys attribute)
fragments_atom_list (optking.molsys.Molsys attribute)
freeze() (optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
from_dict() (optking.bend.Bend class method)
(optking.dimerfrag.DimerFrag class method)
(optking.frag.Frag class method)
(optking.IRCfollowing.IntrinsicReactionCoordinate class method)
(optking.linesearch.LineSearch class method)
(optking.molsys.Molsys 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.optparams.OptParams class method)
from_psi4() (optking.molsys.Molsys static method)
from_schema() (optking.molsys.Molsys class method)
fromUserDict() (optking.dimerfrag.DimerFrag class method)
frozen (optking.frag.Frag attribute)
frozen_intco_list (optking.molsys.Molsys attribute)
frozen_list (optking.dimerfrag.DimerFrag attribute)
G
g_convergence (optking.optparams.OptParams attribute)
geom (optking.frag.Frag attribute)
(optking.molsys.Molsys attribute)
(optking.opt_helper.Helper attribute)
get_atom_symbol_list() (optking.frag.Frag method)
get_hess_grad() (in module optking.optimize)
get_hessian_protocol() (optking.optimize.OptimizationManager method)
get_pes_info() (in module optking.optimize)
get_ref_geom() (optking.dimerfrag.DimerFrag method)
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
HBond (class in optking.stre)
Helper (class in optking.opt_helper)
hess_update (optking.optparams.OptParams attribute)
hessian_to_cartesians() (optking.molsys.Molsys method)
hessian_to_internals() (optking.molsys.Molsys method)
HX (optking.opt_helper.CustomHelper attribute)
(optking.opt_helper.Helper attribute)
I
increase_trust_radius() (optking.stepAlgorithms.OptimizationAlgorithm method)
intco_lbls (optking.molsys.Molsys attribute)
intcos (optking.frag.Frag attribute)
intcos_present (optking.molsys.Molsys attribute)
interfrag_dq_discontinuity_correction() (optking.molsys.Molsys method)
intrafrag_hess (optking.optparams.OptParams attribute)
IntrinsicReactionCoordinate (class in optking.IRCfollowing)
inverse (optking.stre.Stre attribute)
irc_de_projected() (in module optking.IRCfollowing)
irc_direction (optking.optparams.OptParams attribute)
is_atom() (optking.frag.Frag method)
is_linear() (optking.frag.Frag method)
L
label2index() (optking.dimerfrag.DimerFrag method)
LineSearch (class in optking.linesearch)
LineSearchStep (class in optking.linesearch)
M
make_internal_coords() (in module optking.optimize)
masses (optking.frag.Frag attribute)
(optking.molsys.Molsys attribute)
module
optking.bend
optking.dimerfrag
optking.frag
optking.IRCfollowing
optking.linesearch
optking.molsys
optking.opt_helper
optking.optimize
optking.optparams
optking.stepAlgorithms
optking.stre
optking.tors
Molsys (class in optking.molsys)
N
n_arefs (optking.dimerfrag.DimerFrag attribute)
n_brefs (optking.dimerfrag.DimerFrag attribute)
natom (optking.frag.Frag attribute)
(optking.molsys.Molsys attribute)
near180 (optking.tors.Tors attribute)
nfragments (optking.molsys.Molsys attribute)
num_intcos (optking.dimerfrag.DimerFrag attribute)
(optking.frag.Frag attribute)
(optking.molsys.Molsys attribute)
num_intrafrag_intcos (optking.molsys.Molsys attribute)
O
opt_coordinates (optking.optparams.OptParams attribute)
opt_error_handler() (optking.optimize.OptimizationManager method)
opt_type (optking.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)
optking.bend
module
optking.dimerfrag
module
optking.frag
module
optking.IRCfollowing
module
optking.linesearch
module
optking.molsys
module
optking.opt_helper
module
optking.optimize
module
optking.optparams
module
optking.stepAlgorithms
module
optking.stre
module
optking.tors
module
OptParams (class in optking.optparams)
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.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
project_redundancies_and_constraints() (optking.molsys.Molsys method)
pseudo_frag (optking.dimerfrag.DimerFrag attribute)
purge_interfragment_connectivity() (optking.molsys.Molsys method)
Q
q() (optking.bend.Bend method)
(optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
(optking.stre.Stre method)
(optking.tors.Tors method)
q_array() (optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
q_show() (optking.bend.Bend method)
(optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
(optking.stre.Stre method)
(optking.tors.Tors method)
q_show_array() (optking.dimerfrag.DimerFrag method)
(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_frozen_intco_list() (optking.molsys.Molsys method)
ranged_intco_list (optking.molsys.Molsys attribute)
RefPoint (class in optking.dimerfrag)
requires() (optking.IRCfollowing.IntrinsicReactionCoordinate method)
(optking.linesearch.ThreePointEnergy 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)
S
set_ref_geom() (optking.dimerfrag.DimerFrag method)
show() (optking.opt_helper.Helper method)
show_geom() (optking.frag.Frag method)
(optking.molsys.Molsys method)
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)
SteepestDescent (class in optking.stepAlgorithms)
step() (optking.linesearch.LineSearch method)
(optking.linesearch.ThreePointEnergy method)
(optking.stepAlgorithms.OptimizationAlgorithm method)
(optking.stepAlgorithms.PartitionedRFO method)
(optking.stepAlgorithms.QuasiNewtonRaphson method)
(optking.stepAlgorithms.RestrictedStepRFO method)
(optking.stepAlgorithms.SteepestDescent method)
step_metrics() (optking.stepAlgorithms.OptimizationInterface method)
step_n_factor() (in module optking.IRCfollowing)
step_size_scalar() (optking.stepAlgorithms.SteepestDescent method)
step_type (optking.optparams.OptParams attribute)
Stre (class in optking.stre)
string_option() (in module optking.optparams)
summarize_result() (optking.opt_helper.Helper 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.dimerfrag.DimerFrag method)
test_Bmat() (optking.molsys.Molsys method)
test_convergence() (optking.opt_helper.Helper method)
test_derivative_Bmat() (optking.molsys.Molsys method)
test_orient() (in module optking.dimerfrag)
ThreePointEnergy (class in optking.linesearch)
to_dict() (optking.bend.Bend method)
(optking.dimerfrag.DimerFrag method)
(optking.frag.Frag method)
(optking.IRCfollowing.IntrinsicReactionCoordinate method)
(optking.linesearch.LineSearch method)
(optking.molsys.Molsys method)
(optking.opt_helper.Helper method)
(optking.optimize.OptimizationManager method)
(optking.stre.Stre method)
(optking.tors.Tors method)
to_schema() (optking.molsys.Molsys method)
Tors (class in optking.tors)
U
unfix_bend_axes() (optking.bend.Bend method)
(optking.frag.Frag method)
(optking.molsys.Molsys method)
unknown_error_handler() (optking.optimize.OptimizationManager method)
update_dihedral_orientations() (optking.frag.Frag method)
(optking.molsys.Molsys method)
update_dimer_intco_reference_points() (optking.molsys.Molsys method)
update_dynamic_level_params() (optking.optparams.OptParams method)
update_history() (optking.stepAlgorithms.OptimizationAlgorithm method)
update_orientation() (optking.tors.Tors method)
update_reference_geometry() (optking.dimerfrag.DimerFrag method)
update_requirements() (optking.optimize.OptimizationManager method)
V
validate_intcos() (optking.dimerfrag.DimerFrag method)
W
Weight (class in optking.dimerfrag)
weight (optking.dimerfrag.Weight attribute)
Z
Z (optking.frag.Frag attribute)
(optking.molsys.Molsys attribute)
zeta() (optking.bend.Bend static method)
(optking.tors.Tors static method)
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