pele.rates._rate_calculations.GraphReduction

class pele.rates._rate_calculations.GraphReduction(rate_constants, A, B, debug=False, weights=None)

class to apply the graph reduction method for finding transition rates between two groups of nodes

Parameters:

rate_constantsdict

a dictionary of rates. the keys are tuples of nodes (u,v), the values are the rate constants from u to v.

A, Biterables

Groups of nodes specifying the reactant and product groups. The rates returned will be the rate from A to B and vice versa.

weightsdict

Dictionary with nodes as keys and weights as values. The weights are the equilibrium occupation probabilities of the nodes in A and B. They are used to do the weighted mean for the final average over inverse mean first passage times.

Notes

This follows the new graph transformation procedure (NGT) described by David Wales, J. Chem. Phys., 2009 http://dx.doi.org/10.1063/1.3133782

The rate, rAB computed by this calculation (returned by self.get_final_rates) is the inverse mean first passage time averaged over the states in A

Methods

check_graph()
compute_committor_probabilities(nodes)	compute the committor probability for each node in nodes
compute_committor_probability(x)	compute the probability that trajectory starting from x reaches B before it reaches A
compute_rates()	do the computation to compute the rates
get_committor_probabilityAB(x)	return the committor probability for node x
get_rate_AB()	Return the transition rate from A to B
get_rate_AB_SS()
get_rate_BA()	Return the transition rate from B to A
initial_check_graph()

Attributes