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
RateThreshold	Implements a superbasin scheme where states are merged if the transition rate between them is faster than a specified threshold.

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()

class eon.superbasinscheme.RateThreshold(superbasin_path, states, kT, rate_threshold)

Bases: eon.superbasinscheme.SuperbasinScheme

Implements a superbasin scheme where states are merged if the transition rate between them is faster than a specified threshold.

Initialization

Initializes the RateThreshold scheme.

Args: superbasin_path (str): The path to the superbasin directory. states (States): The global states object. kT (float): The thermal energy (k_B * T) in the appropriate units. rate_threshold (float): The rate (in 1/time) above which states will be merged into a superbasin.

register_transition(start_state, end_state)

Checks if the transition rate between start_state and end_state exceeds the defined threshold. If it does, it merges them.

write_data()

This scheme is stateless, so no data needs to be written. The creation of superbasins is handled by the base class and the Superbasin objects, which persist their own state.

read_data()

This scheme is stateless, so no data needs to be read on startup.