Index

A

add_point() (stalk.ls.LineSearchGrid method) (stalk.ls.TargetLineSearchBase method) add_shift() (stalk.ls.LineSearch method) analyzed (stalk.ls.FittingResult property)

args (stalk.io.FilesFunction attribute) (stalk.io.GeometryWriter attribute) (stalk.ls.FittingFunction attribute) axes (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure attribute)

B

backward_args (stalk.params.ParameterStructure attribute) backward_func (stalk.params.ParameterStructure attribute) 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) bracket_target_bias() (stalk.ls.TargetLineSearchBase method) bracket_target_biases() (stalk.pls.TargetParallelLineSearch method)

C

calculate_next_params() (stalk.pls.ParallelLineSearch method) check_consistency() (stalk.params.ParameterSet method) (stalk.params.ParameterStructure 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.TargetParallelLineSearch method)

D

d (stalk.ls.LineSearch property) D (stalk.params.ParameterHessian attribute) (stalk.pls.ParallelLineSearch property) dim (stalk.params.ParameterStructure attribute)

direction (stalk.ls.LineSearch property) directions (stalk.params.ParameterHessian property) directorize() (in module stalk.util) disable_value() (stalk.ls.LineSearchGrid method) distance() (in module stalk.params)

E

EffectiveVariance (class in stalk.util) elem (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure attribute) enable_value() (stalk.ls.LineSearchGrid method) enabled (stalk.ls.LineSearch property) (stalk.params.LineSearchPoint property) enabled_ls (stalk.pls.ParallelLineSearch property) epsilon (stalk.ls.TargetLineSearch property) epsilon_d (stalk.pls.TargetParallelLineSearch property) epsilon_p (stalk.pls.TargetParallelLineSearch attribute) error (stalk.params.LineSearchPoint property) (stalk.params.Parameter property) error_d (stalk.pls.TargetParallelLineSearch attribute)

error_p (stalk.pls.TargetParallelLineSearch attribute) error_surface (stalk.ls.TargetLineSearch property) errorbar (stalk.util.EffectiveVariance attribute) errors (stalk.ls.LineSearchGrid property) evaluate() (stalk.ls.LineSearch method) (stalk.lsi.LineSearchIteration method) (stalk.params.PesFunction method) (stalk.pls.ParallelLineSearch method) evaluate_all() (stalk.params.PesFunction method) evaluate_eqm() (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) FilesFunction (class in stalk.io) FilesLoader (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_args (stalk.params.ParameterStructure attribute) forward_func (stalk.params.ParameterStructure attribute) fraction (stalk.ls.FittingResult attribute) (stalk.ls.LsSettings property) func (stalk.io.FilesFunction attribute) (stalk.ls.FittingFunction attribute)

G

generate() (stalk.io.FilesFunction method) generate_error_surface() (stalk.ls.TargetLineSearch 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.util.EffectiveVariance method) get_force() (stalk.ls.FittingResult method) get_fraction_error() (in module stalk.util) get_hessian() (stalk.ls.FittingResult method) (stalk.params.ParameterHessian method)

get_min_params() (in module stalk.util) get_params_distribution() (stalk.params.ParameterStructure method) get_pos() (stalk.params.GeometryResult method) get_result() (stalk.params.GeometryResult method) get_samples() (stalk.util.EffectiveVariance method) get_shifted_params() (stalk.ls.LineSearch method) get_valid() (stalk.ls.LineSearchGrid method) get_values() (stalk.ls.FittingResult 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.TargetParallelLineSearch property)

H

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

hessian_set (stalk.params.ParameterHessian property)

I

init_from_hessian() (stalk.lsi.LineSearchIteration method) init_from_surrogate() (stalk.lsi.LineSearchIteration method) init_hessian_array() (stalk.params.ParameterHessian method) init_hessian_real() (stalk.params.ParameterHessian method) init_hessian_structure() (stalk.params.ParameterHessian method) init_params() (stalk.params.ParameterSet method)

initialize() (stalk.pls.ParallelLineSearch method) insert_sigma_data() (stalk.ls.TargetLineSearch method) insert_W_data() (stalk.ls.TargetLineSearch method) interp (stalk.ls.TlsSettings property) interp_kind (stalk.ls.TlsSettings property) is_eqm (stalk.params.LineSearchPoint property)

J

jacobian() (stalk.params.ParameterStructure method)

L

label (stalk.params.Parameter attribute) (stalk.params.ParameterSet attribute) Lambda (stalk.ls.LineSearch property) (stalk.params.ParameterHessian attribute) lambdas (stalk.params.ParameterHessian property) Lambdas (stalk.pls.ParallelLineSearch 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) (stalk.params.ParameterStructure method) load_pls() (stalk.lsi.LineSearchIteration method) ls() (stalk.pls.ParallelLineSearch method) (stalk.pls.TargetParallelLineSearch method) ls_list (stalk.pls.ParallelLineSearch property) (stalk.pls.TargetParallelLineSearch property) ls_type (stalk.pls.ParallelLineSearch attribute) (stalk.pls.TargetParallelLineSearch attribute) LsSettings (class in stalk.ls)

M

M (stalk.ls.TargetLineSearch property) (stalk.ls.TlsSettings property) (stalk.pls.TargetParallelLineSearch property) map_backward() (stalk.params.ParameterStructure method) map_forward() (stalk.params.ParameterStructure method) match_to_tol() (in module stalk.util) 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

N

N (stalk.ls.LsSettings property) (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.TargetParallelLineSearch method) optimize_epsilon_d() (stalk.pls.TargetParallelLineSearch method)

optimize_epsilon_p() (stalk.pls.TargetParallelLineSearch method) optimize_temperature() (stalk.pls.TargetParallelLineSearch method) optimize_windows_noises() (stalk.pls.TargetParallelLineSearch method) optimized (stalk.ls.TargetLineSearch property) (stalk.pls.TargetParallelLineSearch property)

P

P (stalk.params.ParameterHessian attribute) ParallelLineSearch (class in stalk.pls) Parameter (class in stalk.params) ParameterHessian (class in stalk.params) ParameterSet (class in stalk.params) ParameterStructure (class in stalk.params) params (stalk.params.ParameterSet 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.pls.ParallelLineSearch property) periodic (stalk.params.ParameterStructure property) pes (stalk.pls.ParallelLineSearch property) PesFunction (class in stalk.params)

PesLoader (class in stalk.io) plot() (stalk.ls.LineSearch method) (stalk.ls.LineSearchBase method) (stalk.ls.LineSearchGrid method) (stalk.ls.TargetLineSearch 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.TargetParallelLineSearch method) pls() (stalk.lsi.LineSearchIteration method) pls_list (stalk.lsi.LineSearchIteration property) pos (stalk.params.GeometryResult attribute) (stalk.params.ParameterStructure attribute) 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) regenerate_Gs() (stalk.ls.TlsSettings method) relax() (stalk.params.PesFunction method)

remap_forward() (stalk.params.ParameterStructure method) resampled (stalk.ls.TargetLineSearch property) reset_interpolation() (stalk.ls.TargetLineSearchBase method) reset_search() (stalk.ls.LineSearchBase method) reset_value() (stalk.params.LineSearchPoint method)

S

samples (stalk.util.EffectiveVariance attribute) search() (stalk.ls.LineSearchBase method) search_with_error() (stalk.ls.LineSearchBase method) set_axes() (stalk.params.ParameterStructure method) set_backward_func() (stalk.params.ParameterStructure method) set_elem() (stalk.params.ParameterStructure method) set_forward_func() (stalk.params.ParameterStructure method) set_grid() (stalk.ls.LineSearch method) set_params() (stalk.params.ParameterSet method) (stalk.params.ParameterStructure method) set_position() (stalk.params.ParameterStructure method) set_structure() (stalk.params.ParameterHessian 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) shift_pos() (stalk.params.ParameterStructure method) shifted (stalk.ls.LineSearchGrid property) (stalk.pls.ParallelLineSearch property)

shifts (stalk.pls.ParallelLineSearch property) sigma (stalk.ls.LineSearch property) sigma_opt (stalk.ls.TargetLineSearch property) (stalk.pls.TargetParallelLineSearch property) 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.TargetParallelLineSearch property) statistical_cost() (stalk.ls.TargetLineSearch method) structure (stalk.ls.LineSearch property) (stalk.params.ParameterHessian attribute) (stalk.pls.ParallelLineSearch property) structure_next (stalk.pls.ParallelLineSearch 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)

TargetParallelLineSearch (class in stalk.pls) temperature (stalk.pls.TargetParallelLineSearch property) TlsSettings (class in stalk.ls) to_settings() (stalk.ls.TargetLineSearch method) tol (stalk.params.LineSearchPoint attribute) (stalk.params.ParameterStructure attribute)

U

U (stalk.params.ParameterHessian attribute) unit (stalk.params.Parameter attribute)

units (stalk.params.ParameterStructure attribute) update_hessian() (stalk.params.ParameterHessian method)

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.TargetParallelLineSearch method) value (stalk.params.LineSearchPoint property) (stalk.params.Parameter property) values (stalk.ls.LineSearchGrid property)

W

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

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

X

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

x_targets (stalk.pls.TargetParallelLineSearch 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)