eon.superbasinscheme

Module Contents

Classes

SuperbasinScheme	This poorly-named class handles keeping track of which states belong to which superbasins, the SuperBasin object of those superbasins, and superbasining criteria. It also expands and merges superbasins
TransitionCounting	Implements the transition counting scheme for superbasin detection
EnergyLevel

Data

logger

API

eon.superbasinscheme.logger

‘getLogger(…)’

class eon.superbasinscheme.SuperbasinScheme(superbasin_path, states, kT)

This poorly-named class handles keeping track of which states belong to which superbasins, the SuperBasin object of those superbasins, and superbasining criteria. It also expands and merges superbasins

Initialization

get_containing_superbasin(state)

make_basin_from_sets(start_state, end_state)

make_basin(merge_states)

abstract register_transition(start_state, end_state)

abstract write_data()

abstract read_data()

class eon.superbasinscheme.TransitionCounting(superbasin_path, states, kT, num_transitions)

Bases: eon.superbasinscheme.SuperbasinScheme

Implements the transition counting scheme for superbasin detection

Initialization

register_transition(start_state, end_state)

write_data()

read_data()

get_count(state)

class eon.superbasinscheme.EnergyLevel(superbasin_path, states, kT, energy_increment)

Bases: eon.superbasinscheme.SuperbasinScheme

get_energy_increment(e_min, e_global_min, e_saddle)

get_statelist(state)

register_transition(start_state, end_state)

Increments the energy level of the end state or sets it equal to the energy of the end_state if it hasn’t been visited before.

read_data()

write_data()