Linesearch iteration

Surrogate Hessian accelerated parallel line-search: line-search iteration

class stalk.lsi.LineSearchIteration(path='', surrogate=None, structure=None, hessian=None, pes=None, pes_func=None, pes_args={}, var_eff_map=None, **pls_args)

Bases: object

evaluate(add_sigma=False)

evaluate_eqm(**kwargs)

init_from_hessian(hessian, structure=None, pes=None, **pls_args)

init_from_surrogate(surrogate: ParallelLineSearch, structure=None, pes=None)

load_pls()

property path

plot(target: ParameterSet = None, bundle=True, **kwargs)

plot_convergence(P_list=None, targets=None, colors=None, markers=None, **kwargs)

pls(i=None)

property pls_list

propagate(i=None, write=True, overwrite=True, fname='pls.p', add_sigma=False, interactive=False, **kwargs)

property structure_final

property structure_init

property transient

property var_eff_map

class stalk.lsi.PathwayImage(structure: ParameterSet, reaction_coordinate=0)

Bases: object

calculate_hessian(tangent, pes: PesFunction, path='', **hessian_args)

generate_surrogate(pes: PesFunction = None, overwrite=False, **surrogate_args)

property hessian

property lsi

optimize_surrogate(overwrite=True, **optimize_args)

property reaction_coordinate

run_linesearch(num_iter=3, path='lsi', pes: PesFunction = None, add_sigma=False, **lsi_args)

property structure

property structure_final

property structure_init

property surrogate

class stalk.lsi.TransitionPathway(path='', images: list[ParameterSet] = None)

Bases: object

add_image(image: ParameterSet, rc=None)

calculate_hessians(**hessian_args)

property difference

generate_surrogates(**surrogate_args)

property images

property intermediate_images

optimize_surrogates(**optimize_args)

property path

property pathway_final

property pathway_init

property pointA

property pointB

run_linesearches(**lsi_args)