pele.rates._rates

Module source

routines to compute rates from a database of minima

pele.rates._rates.log_sum2()

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def log_sum2(a, b):

return log( exp(a) + exp(b) )

pele.rates._rates.log_equilibrium_occupation_probability()

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def log_equilibrium_occupation_probability(minimum, T):

return the log equilibrium occupation probability

This is computed from the harmonic superposition approximation. Some constants that are the same for all minima have been left out.

class pele.rates._rates.RateCalculation

Source

class RateCalculation:

compute transition rates from a database of minima and transition states

Parameters:

transition_states: iteratable

list (or iterator) of transition states that define the rate network

A, Biterables

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

Tfloat

temperature at which to do the the calculation. Should be in units of energy, i.e. include the factor of k_B if necessary.

RateCalculation.compute_rates()

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def compute_rates(self):

compute the rates from A to B and vice versa

RateCalculation.compute_rates_and_committors()

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def compute_rates_and_committors(self):

compute the rates from A to B and vice versa

class pele.rates._rates.RatesLinalg

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class RatesLinalg:

this class duplicates the behavior in RateCalculation, but with the linalg solver

pele.rates._rates.compute_committors()

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def compute_committors(transition_states, A, B, T=1.0):

compute and return the committor probabilites between A and B

First try the linear algebra method. If it fails, then use NGT