Index

A

add_errorbar_data() (stalk.params.EffectiveVariance method) add_image() (stalk.lsi.TransitionPathway method) add_point() (stalk.ls.LineSearchGrid method) (stalk.ls.TargetLineSearchBase method) add_shift() (stalk.ls.LineSearch method) add_sigma() (stalk.params.PesResult method) add_var_eff() (stalk.params.EffectiveVariance method) (stalk.params.EffectiveVarianceMap method)

analyzed (stalk.ls.FittingResult property) angle() (in module stalk.params) args (stalk.ls.FittingFunction attribute) (stalk.util.ArgsContainer property) ArgsContainer (class in stalk.util) axes (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure property)

B

backward (stalk.params.ParameterMapping property) (stalk.params.ParameterStructure property) bias_mix (stalk.ls.TlsSettings property) bias_order (stalk.ls.TlsSettings property) bipolyfit() (in module stalk.util) bipolynomials() (in module stalk.util)

bipolyval() (in module stalk.util) bond_angle() (in module stalk.params) BondAngle (class in stalk.params) BondLength (class in stalk.params) bracket_target_bias() (stalk.ls.TargetLineSearchBase method) bracket_target_biases() (stalk.pls.Surrogate method)

C

calculate_hessian() (stalk.lsi.PathwayImage method) calculate_hessians() (stalk.lsi.TransitionPathway method) calculate_next_params() (stalk.pls.ParallelLineSearch method) check_consistency() (stalk.params.ParameterSet method) check_params_consistency() (stalk.params.ParameterMapping method) check_pos_consistency() (stalk.params.ParameterMapping method) compute_bias() (stalk.ls.TargetLineSearchBase method) compute_bias_of() (stalk.ls.TargetLineSearch method) compute_error() (stalk.ls.TargetLineSearchBase method)

compute_errorbar() (stalk.ls.TargetLineSearchBase method) compute_fdiff() (stalk.params.ParameterHessian method) consistent (stalk.params.ParameterStructure property) copy() (stalk.ls.LsSettings method) (stalk.ls.TlsSettings method) (stalk.params.ParameterSet method) (stalk.params.ParameterStructure method) (stalk.pls.ParallelLineSearch method) (stalk.pls.Surrogate method)

D

d (stalk.ls.LineSearch property) D (stalk.pls.ParallelLineSearch property) D_list (stalk.pls.ParallelLineSearch property) difference (stalk.lsi.TransitionPathway property) dim (stalk.params.ParameterMapping attribute) (stalk.params.ParameterStructure property) direction (stalk.ls.LineSearch property)

directions (stalk.params.ParameterHessian property) directorize() (in module stalk.util) disable_limit (stalk.params.ParameterHessian property) disable_value() (stalk.ls.LineSearchGrid method) distance() (in module stalk.params) (stalk.params.ParameterSet method) distance2() (stalk.params.ParameterSet method)

E

EffectiveVariance (class in stalk.params) EffectiveVarianceMap (class in stalk.params) elem (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure property) enable_value() (stalk.ls.LineSearchGrid method) enabled (stalk.params.LineSearchPoint property) (stalk.params.ParameterHessian property) enabled_directions (stalk.params.ParameterHessian property) enabled_lambdas (stalk.params.ParameterHessian property) epsilon (stalk.ls.TargetLineSearch property) epsilon_d (stalk.pls.Surrogate property) epsilon_p (stalk.pls.Surrogate property) error (stalk.params.LineSearchPoint property) (stalk.params.Parameter property) (stalk.params.PesResult property) error_d (stalk.pls.Surrogate property)

error_data (stalk.params.EffectiveVariance property) error_p (stalk.pls.Surrogate property) error_surface (stalk.ls.TargetLineSearch property) errors (stalk.ls.LineSearchGrid property) evaluate() (stalk.io.FilesPes method) (stalk.ls.LineSearch method) (stalk.lsi.LineSearchIteration method) (stalk.params.PesFunction method) (stalk.pls.ParallelLineSearch method) evaluate_all() (stalk.io.FilesPes method) (stalk.params.PesFunction method) evaluate_eqm() (stalk.lsi.LineSearchIteration method) (stalk.pls.ParallelLineSearch method) evaluate_target() (stalk.ls.TargetLineSearchBase method) evaluated (stalk.ls.LineSearchGrid property) (stalk.pls.ParallelLineSearch property)

F

figure_out_adjusted_offsets() (stalk.ls.TargetLineSearch method) figure_out_offsets() (stalk.ls.LineSearch method) file_path (stalk.params.ParameterSet attribute) FilesPes (class in stalk.io) find_minimum() (stalk.ls.FittingFunction method) find_noisy_minimum() (stalk.ls.FittingFunction method) find_point() (stalk.ls.LineSearchGrid method) fit (stalk.ls.FittingResult attribute) fit_func (stalk.ls.LsSettings property)

fit_res (stalk.ls.LineSearchBase attribute) FittingFunction (class in stalk.ls) FittingResult (class in stalk.ls) forward (stalk.params.ParameterMapping property) (stalk.params.ParameterStructure property) fraction (stalk.ls.FittingResult attribute) (stalk.ls.LsSettings property) func (stalk.ls.FittingFunction attribute) (stalk.util.FunctionCaller property) FunctionCaller (class in stalk.util)

G

generate_error_surface() (stalk.ls.TargetLineSearch method) generate_surrogate() (stalk.lsi.PathwayImage method) generate_surrogates() (stalk.lsi.TransitionPathway method) GeometryLoader (class in stalk.io) GeometryResult (class in stalk.params) GeometryWriter (class in stalk.io) get_all() (stalk.ls.LineSearchGrid method) get_axes() (stalk.params.GeometryResult method) get_distribution() (stalk.ls.FittingFunction method) get_elem() (stalk.params.GeometryResult method) get_errorbar() (stalk.params.EffectiveVariance method) get_force() (stalk.ls.FittingResult method) (stalk.ls.MorseResult method) (stalk.ls.PolynomialResult method) (stalk.ls.SplineResult method) get_fraction_error() (in module stalk.util) get_hessian() (stalk.ls.FittingResult method) (stalk.ls.MorseResult method) (stalk.ls.PolynomialResult method) (stalk.ls.SplineResult method)

get_params_distribution() (stalk.params.ParameterSet method) get_pos() (stalk.params.GeometryResult method) get_result() (stalk.params.GeometryResult method) get_safe_offsets() (stalk.ls.TlsSettings method) get_samples() (stalk.params.EffectiveVariance method) (stalk.params.EffectiveVarianceMap method) get_updated() (stalk.util.ArgsContainer method) get_valid() (stalk.ls.LineSearchGrid method) get_values() (stalk.ls.FittingResult method) (stalk.ls.MorseResult method) (stalk.ls.PolynomialResult method) (stalk.ls.SplineResult method) get_x0_distribution() (stalk.ls.FittingFunction method) get_y0_distribution() (stalk.ls.FittingFunction method) grid (stalk.ls.LineSearchGrid property) grid_opt (stalk.ls.TargetLineSearch property) Gs (stalk.ls.TargetLineSearch property) (stalk.ls.TlsSettings property) (stalk.pls.Surrogate property)

H

hessian (stalk.ls.LineSearch property) (stalk.lsi.PathwayImage property) (stalk.params.ParameterHessian property) (stalk.pls.ParallelLineSearch property)

I

images (stalk.lsi.TransitionPathway property) incomplete (stalk.params.ParameterMapping property) init_from_hessian() (stalk.lsi.LineSearchIteration method) init_from_surrogate() (stalk.lsi.LineSearchIteration method) init_hessian_array() (stalk.params.ParameterHessian method) initialize() (stalk.pls.ParallelLineSearch method)

insert_sigma_data() (stalk.ls.TargetLineSearch method) insert_W_data() (stalk.ls.TargetLineSearch method) intermediate_images (stalk.lsi.TransitionPathway property) interp (stalk.ls.TlsSettings property) interp_kind (stalk.ls.TlsSettings property) interpolate_params() (in module stalk.params) is_eqm (stalk.params.LineSearchPoint property)

J

jacobian() (stalk.params.ParameterStructure method)

K

kind (stalk.ls.FittingFunction property) (stalk.ls.MorseFit property) (stalk.ls.PolynomialFit property) (stalk.ls.SplineFit property)

L

label (stalk.params.Parameter attribute) (stalk.params.ParameterSet attribute) Lambda (stalk.ls.LineSearch property) lambdas (stalk.params.ParameterHessian property) Lambdas (stalk.pls.ParallelLineSearch property) limits (stalk.params.Parameter property) LineSearch (class in stalk.ls) LineSearchBase (class in stalk.ls) LineSearchGrid (class in stalk.ls) LineSearchIteration (class in stalk.lsi) LineSearchPoint (class in stalk.params) load() (stalk.io.GeometryLoader method) (stalk.io.PesLoader method)

load_energy() (in module stalk.io) load_or_relax() (stalk.io.GeometryLoader method) load_pls() (stalk.lsi.LineSearchIteration method) loader (stalk.io.FilesPes attribute) ls() (stalk.pls.ParallelLineSearch method) ls_list (stalk.pls.ParallelLineSearch property) (stalk.pls.Surrogate property) ls_type (stalk.pls.ParallelLineSearch attribute) (stalk.pls.Surrogate attribute) lsi (stalk.lsi.PathwayImage property) LsSettings (class in stalk.ls)

M

M (stalk.ls.TargetLineSearch property) (stalk.ls.TlsSettings property) (stalk.pls.Surrogate property) map_backward() (stalk.params.ParameterMapping method) (stalk.params.ParameterStructure method) map_forward() (stalk.params.ParameterMapping method) (stalk.params.ParameterStructure method) mapping (stalk.params.ParameterStructure property) match_to_tol() (in module stalk.util) mean_bond_angles() (in module stalk.params) mean_distances() (in module stalk.params)

mean_param() (in module stalk.params) module stalk.io stalk.ls stalk.lsi stalk.nexus stalk.params stalk.pls stalk.util morse() (in module stalk.util) MorseFit (class in stalk.ls) MorseResult (class in stalk.ls)

N

N (stalk.ls.LsSettings property) n (stalk.ls.PolynomialFit property) N (stalk.ls.TlsSettings property)

noises (stalk.pls.ParallelLineSearch property) noises_min (stalk.pls.ParallelLineSearch property) noisy (stalk.ls.LineSearchGrid property) (stalk.pls.ParallelLineSearch property)

O

offset (stalk.params.LineSearchPoint property) offsets (stalk.ls.LineSearchGrid property) optimize() (stalk.ls.TargetLineSearch method) (stalk.pls.Surrogate method) optimize_epsilon_d() (stalk.pls.Surrogate method) optimize_epsilon_p() (stalk.pls.Surrogate method)

optimize_surrogate() (stalk.lsi.PathwayImage method) optimize_surrogates() (stalk.lsi.TransitionPathway method) optimize_temperature() (stalk.pls.Surrogate method) optimize_windows_noises() (stalk.pls.Surrogate method) optimized (stalk.ls.TargetLineSearch property) (stalk.pls.Surrogate property)

P

p0 (stalk.ls.MorseFit attribute) ParallelLineSearch (class in stalk.pls) Parameter (class in stalk.params) ParameterHessian (class in stalk.params) ParameterMapping (class in stalk.params) ParameterSet (class in stalk.params) ParameterStructure (class in stalk.params) params (stalk.params.EffectiveVarianceMap property) (stalk.params.ParameterSet property) (stalk.params.ParameterStructure property) (stalk.pls.ParallelLineSearch property) params_err (stalk.params.ParameterSet property) (stalk.pls.ParallelLineSearch property) params_list (stalk.params.ParameterSet property) path (stalk.lsi.LineSearchIteration property) (stalk.lsi.TransitionPathway property) (stalk.pls.ParallelLineSearch property) pathway_final (stalk.lsi.TransitionPathway property) pathway_init (stalk.lsi.TransitionPathway property) PathwayImage (class in stalk.lsi) periodic (stalk.params.ParameterStructure property) periodic_bond_angle() (in module stalk.params) periodic_distance() (in module stalk.params) pes (stalk.pls.ParallelLineSearch property)

PesFunction (class in stalk.params) PesLoader (class in stalk.io) PesResult (class in stalk.params) PhaseAngle (class in stalk.params) plot() (stalk.ls.LineSearch method) (stalk.ls.LineSearchBase method) (stalk.ls.LineSearchGrid method) (stalk.ls.TargetLineSearch method) (stalk.lsi.LineSearchIteration method) (stalk.params.LineSearchPoint method) (stalk.pls.ParallelLineSearch method) plot_convergence() (stalk.lsi.LineSearchIteration method) plot_error_surface() (stalk.ls.TargetLineSearch method) plot_error_surfaces() (stalk.pls.Surrogate method) pls() (stalk.lsi.LineSearchIteration method) pls_list (stalk.lsi.LineSearchIteration property) pointA (stalk.lsi.TransitionPathway property) pointB (stalk.lsi.TransitionPathway property) PolynomialFit (class in stalk.ls) PolynomialResult (class in stalk.ls) pos (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure property) pos_difference() (stalk.params.ParameterStructure method) propagate() (stalk.lsi.LineSearchIteration method) (stalk.pls.ParallelLineSearch method)

R

R_max (stalk.ls.LineSearchGrid property) R_opt (stalk.ls.TargetLineSearch property) reaction_coordinate (stalk.lsi.PathwayImage property) regenerate_Gs() (stalk.ls.TlsSettings method) relax() (stalk.params.PesFunction method) remap_forward() (stalk.params.ParameterStructure method) require_consistent (stalk.params.ParameterHessian property) (stalk.params.ParameterStructure attribute) resampled (stalk.ls.TargetLineSearch property)

rescale() (stalk.params.GeometryResult method) (stalk.params.PesResult method) reset() (stalk.params.ParameterHessian method) reset_interpolation() (stalk.ls.TargetLineSearchBase method) reset_search() (stalk.ls.LineSearchBase method) reset_value() (stalk.params.LineSearchPoint method) rotate_2d() (in module stalk.params) run_linesearch() (stalk.lsi.PathwayImage method) run_linesearches() (stalk.lsi.TransitionPathway method)

S

samples (stalk.params.ParameterSet property) scaling_map (stalk.params.EffectiveVarianceMap attribute) search() (stalk.ls.LineSearchBase method) search_with_error() (stalk.ls.LineSearchBase method) set_backward() (stalk.params.ParameterMapping method) set_forward() (stalk.params.ParameterMapping method) set_grid() (stalk.ls.LineSearch method) set_position() (stalk.params.ParameterStructure method) set_value_error() (stalk.ls.LineSearchGrid method) settings (stalk.ls.LineSearchBase property) setup (stalk.ls.TargetLineSearch property) (stalk.pls.ParallelLineSearch property) setup_optimization() (stalk.ls.TargetLineSearch method) sgn (stalk.ls.LsSettings property) shift() (stalk.params.Parameter method) shift_params() (stalk.params.ParameterSet method) (stalk.params.ParameterStructure method) shifted (stalk.ls.LineSearchGrid property) (stalk.pls.ParallelLineSearch property) shifted_params (stalk.ls.LineSearch property) shifts (stalk.pls.ParallelLineSearch property) sigma (stalk.ls.LineSearch property) sigma_opt (stalk.ls.TargetLineSearch property) (stalk.pls.Surrogate property) SplineFit (class in stalk.ls) SplineResult (class in stalk.ls)

stalk.io module stalk.ls module stalk.lsi module stalk.nexus module stalk.params module stalk.pls module stalk.util module statistical_cost (stalk.pls.Surrogate property) statistical_cost() (stalk.ls.TargetLineSearch method) structure (stalk.ls.LineSearch property) (stalk.lsi.PathwayImage property) (stalk.params.ParameterHessian property) (stalk.pls.ParallelLineSearch property) structure_final (stalk.lsi.LineSearchIteration property) (stalk.lsi.PathwayImage property) structure_init (stalk.lsi.LineSearchIteration property) (stalk.lsi.PathwayImage property) structure_next (stalk.pls.ParallelLineSearch property) Surrogate (class in stalk.pls) surrogate (stalk.lsi.PathwayImage property)

T

target (stalk.ls.TlsSettings property) target_interp (stalk.ls.TargetLineSearchBase property) target_settings (stalk.ls.TargetLineSearch property) (stalk.ls.TargetLineSearchBase property) TargetLineSearch (class in stalk.ls) TargetLineSearchBase (class in stalk.ls)

temperature (stalk.pls.Surrogate property) TlsSettings (class in stalk.ls) to_settings() (stalk.ls.TargetLineSearch method) tol (stalk.params.LineSearchPoint attribute) (stalk.params.ParameterStructure attribute) transient (stalk.lsi.LineSearchIteration property) TransitionPathway (class in stalk.lsi)

U

U (stalk.params.ParameterHessian property)

unit (stalk.params.Parameter attribute) units (stalk.params.ParameterStructure attribute)

V

valid (stalk.ls.LineSearchGrid property) (stalk.params.LineSearchPoint property) valid_errors (stalk.ls.LineSearchGrid property) valid_grid (stalk.ls.LineSearchGrid property) valid_offsets (stalk.ls.LineSearchGrid property) valid_R_max (stalk.ls.LineSearchGrid property) valid_target (stalk.ls.TargetLineSearchBase property) valid_values (stalk.ls.LineSearchGrid property)

valid_W_max (stalk.ls.LineSearch property) validate() (stalk.pls.Surrogate method) value (stalk.params.LineSearchPoint property) (stalk.params.Parameter property) (stalk.params.PesResult property) (stalk.params.PhaseAngle property) values (stalk.ls.LineSearchGrid property) var_eff (stalk.params.EffectiveVariance property) var_eff_map (stalk.lsi.LineSearchIteration property)

W

W_max (stalk.ls.LineSearch property) W_opt (stalk.ls.TargetLineSearch property) (stalk.pls.Surrogate property)

windows (stalk.pls.ParallelLineSearch property) write() (stalk.io.GeometryWriter method) write_to_disk() (stalk.pls.ParallelLineSearch method) write_xyz_sigma() (in module stalk.io)

X

x0 (stalk.ls.FittingResult attribute) (stalk.ls.LineSearchBase property) x0_err (stalk.ls.FittingResult attribute) (stalk.ls.LineSearchBase property)

x_targets (stalk.pls.Surrogate property) XyzGeometry (class in stalk.io)

Y

y0 (stalk.ls.FittingResult attribute) (stalk.ls.LineSearchBase property)

y0_err (stalk.ls.FittingResult attribute) (stalk.ls.LineSearchBase property)