pele.rates._rates_linalg

class pele.rates._rates_linalg.LinalgError

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class LinalgError(Exception):

raised when a the linear algebra solver fails

class pele.rates._rates_linalg.CommittorLinalg

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class CommittorLinalg:

compute committor probabilites using sparse linear algebra

class pele.rates._rates_linalg.MfptLinalgSparse

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class MfptLinalgSparse:

compute mean first passage times using sparse linear algebra

class pele.rates._rates_linalg.TwoStateRates

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class TwoStateRates:

compute committors and several different rates between two groups

TwoStateRates.get_rate_AB()

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def get_rate_AB(self):

return the rate from A to B

the rate is the inverse mean first passage time averaged over the nodes in A

TwoStateRates.get_rate_AB_SS()

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def get_rate_AB_SS(self):

return the steady state rate from A to B

TwoStateRates.get_committor()

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def get_committor(self, x):

return the probability that a trajectory starting from x reaches B before A

TwoStateRates.compute_rates()

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def compute_rates(
    self,
    use_umfpack=True,
    subgroups=False,
    symmetric=False,
    Peq=None,
    cg=False,
    mfpt_estimates=None,
):

compute the mean first passage times.

TwoStateRates.compute_committors()

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def compute_committors(self):

compute the committors