def compute_rates_and_committors(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(self.minima2rates.rate_constants,
self.minima2rates.A, self.minima2rates.B,
weights=self.minima2rates.weights)
self.reducer.compute_rates_and_committors()
def do_check(self, A, B, nnodes=20, nedges=20):
np.random.seed(0)
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A + B)
maker.run()
reducer = NGT(maker.rates, A, B, debug=False)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
def do_check(self, A, B, nnodes=20, nedges=20):
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A+B)
rates = maker.make_rates()
reducer = TwoStateRates(rates, A, B)
reducer.compute_rates()
reducer.compute_committors()
from pele.rates._ngt_cpp import NGT
ngt = NGT(rates, A, B)
ngt.compute_rates()
self.assertAlmostEqual(reducer.get_rate_AB(), ngt.get_rate_AB(), 7)
self.assertAlmostEqual(reducer.get_rate_AB_SS(), ngt.get_rate_AB_SS(), 7)
class RateCalculation(object):
"""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, B : iterables
groups of minima specifying the reactant and product groups. The rates
returned will be the rate from A to B and vice versa.
T : float
temperature at which to do the the calculation. Should be in units of
energy, i.e. include the factor of k_B if necessary.
"""
def __init__(self, transition_states, A, B, T=1., use_fvib=True):
self.minima2rates = _Minima2Rates(transition_states,
A,
B,
T=T,
use_fvib=use_fvib)
def compute_rates(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights)
self.reducer.compute_rates()
def compute_rates_and_committors(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights)
self.reducer.compute_rates_and_committors()
def get_rate_AB(self):
return old_div(self.reducer.get_rate_AB(), self.minima2rates.rate_norm)
def get_rate_BA(self):
return old_div(self.reducer.get_rate_BA(), self.minima2rates.rate_norm)
def get_rate_AB_SS(self):
return old_div(self.reducer.get_rate_AB_SS(),
self.minima2rates.rate_norm)
def get_rate_BA_SS(self):
return old_div(self.reducer.get_rate_BA_SS(),
self.minima2rates.rate_norm)
def get_committors(self):
committors = self.reducer.get_committors()
return committors
class RateCalculation(object):
"""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, B : iterables
groups of minima specifying the reactant and product groups. The rates
returned will be the rate from A to B and vice versa.
T : float
temperature at which to do the the calculation. Should be in units of
energy, i.e. include the factor of k_B if necessary.
"""
def __init__(self, transition_states, A, B, T=1.0, use_fvib=True):
self.minima2rates = _Minima2Rates(transition_states, A, B, T=T, use_fvib=use_fvib)
def compute_rates(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(
self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights,
)
self.reducer.compute_rates()
def compute_rates_and_committors(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(
self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights,
)
self.reducer.compute_rates_and_committors()
def get_rate_AB(self):
return self.reducer.get_rate_AB() / self.minima2rates.rate_norm
def get_rate_BA(self):
return self.reducer.get_rate_BA() / self.minima2rates.rate_norm
def get_rate_AB_SS(self):
return self.reducer.get_rate_AB_SS() / self.minima2rates.rate_norm
def get_rate_BA_SS(self):
return self.reducer.get_rate_BA_SS() / self.minima2rates.rate_norm
def get_committors(self):
committors = self.reducer.get_committors()
return committors
def compare_linalg(self, A, B, nnodes=20, nedges=20):
from pele.rates._rates_linalg import TwoStateRates
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A + B)
maker.run()
reducer = NGT(maker.rates, A, B)
reducer.compute_rates_and_committors()
committors = reducer.get_committors()
la = TwoStateRates(maker.rates, A, B)
# la.compute_rates()
la.compute_committors()
qla = la.committor_dict
for n, qla in la.committor_dict.items():
self.assertAlmostEqual(qla, committors[n], 7)
def compare_linalg(self, A, B, nnodes=20, nedges=20):
from pele.rates._rates_linalg import TwoStateRates
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A+B)
maker.run()
reducer = NGT(maker.rates, A, B)
reducer.compute_rates_and_committors()
committors = reducer.get_committors()
la = TwoStateRates(maker.rates, A, B)
# la.compute_rates()
la.compute_committors()
qla = la.committor_dict
for n, qla in la.committor_dict.iteritems():
self.assertAlmostEqual(qla, committors[n], 7)
def compute_rates_and_committors(self):
"""compute the rates from A to B and vice versa"""
self.minima2rates.run()
self.reducer = NGT(self.minima2rates.rate_constants,
self.minima2rates.A, self.minima2rates.B,
weights=self.minima2rates.weights)
self.reducer.compute_rates_and_committors()
def _test_rate(self, A, B):
reducer = NGT(self.rates, A, B, debug=False)
reducer.compute_rates()
kAB = reducer.get_rate_AB()
kBA = reducer.get_rate_BA()
self.assertAlmostEqual(kAB, self.true_kAB, 7)
self.assertAlmostEqual(kBA, self.true_kBA, 7)
rAB_SS = reducer.get_rate_AB_SS()
rBA_SS = reducer.get_rate_BA_SS()
self.assertAlmostEqual(rAB_SS, self.true_kAB_SS, 7)
self.assertAlmostEqual(rBA_SS, self.true_kBA_SS, 7)
def _test_rate(self, i, j):
reducer = NGT(self.rates, [i], [j], debug=False)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
self.assertAlmostEqual(rAB, self.final_rate, 7)
self.assertAlmostEqual(rBA, self.final_rate, 7)
rAB_SS = reducer.get_rate_AB_SS()
rBA_SS = reducer.get_rate_BA_SS()
self.assertAlmostEqual(rAB_SS, self.final_rate_SS, 7)
self.assertAlmostEqual(rBA_SS, self.final_rate_SS, 7)
def do_check(self, A, B, nnodes=20, nedges=20):
np.random.seed(0)
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A + B)
maker.run()
reducer = NGT(maker.rates, A, B, debug=False)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
def _test_rate(self, i, j):
reducer = NGT(self.rates, [i], [j], debug=False)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
self.assertAlmostEqual(rAB, self.final_rate, 7)
self.assertAlmostEqual(rBA, self.final_rate, 7)
rAB_SS = reducer.get_rate_AB_SS()
rBA_SS = reducer.get_rate_BA_SS()
self.assertAlmostEqual(rAB_SS, self.final_rate_SS, 7)
self.assertAlmostEqual(rBA_SS, self.final_rate_SS, 7)
def _test_rate(self, A, B):
reducer = NGT(self.rates, A, B, debug=False)
reducer.compute_rates()
kAB = reducer.get_rate_AB()
kBA = reducer.get_rate_BA()
self.assertAlmostEqual(kAB, self.true_kAB, 7)
self.assertAlmostEqual(kBA, self.true_kBA, 7)
rAB_SS = reducer.get_rate_AB_SS()
rBA_SS = reducer.get_rate_BA_SS()
self.assertAlmostEqual(rAB_SS, self.true_kAB_SS, 7)
self.assertAlmostEqual(rBA_SS, self.true_kBA_SS, 7)
def do_check(self, A, B, nnodes=20, nedges=20):
maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A + B)
rates = maker.make_rates()
reducer = TwoStateRates(rates, A, B)
reducer.compute_rates()
reducer.compute_committors()
from pele.rates._ngt_cpp import NGT
ngt = NGT(rates, A, B)
ngt.compute_rates()
self.assertAlmostEqual(reducer.get_rate_AB(), ngt.get_rate_AB(), 7)
self.assertAlmostEqual(reducer.get_rate_AB_SS(), ngt.get_rate_AB_SS(),
7)