def compare(self, A, B, nnodes=10, nedges=20, weights=None, x=1):
print("")
maker = _MakeRandomGraph(nnodes=nnodes,
nedges=nedges,
node_set=A + B + [x])
graph = maker.run()
graph_backup = graph.copy()
reducer = GraphReduction(maker.rates, A, B, weights=weights)
kmc = KineticMonteCarlo(graph_backup, debug=False)
# test compute_committor_probability()
PxB = reducer.compute_committor_probability(x)
PxB_kmc = kmc.committor_probability(x, A, B, niter=1000)
print("committor probability ", x, "->", B, "=", PxB)
print("committor probability kmc", x, "->", B, "=", PxB_kmc)
self.assertAlmostEqual(PxB, PxB_kmc, delta=.1)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
rAB_SS = reducer.get_rate_AB_SS()
# compute rate via linalg
lin = TwoStateRates(maker.rates, A, B, weights=weights)
lin.compute_rates()
rAB_LA = lin.get_rate_AB()
lin.compute_committors()
rAB_SS_LA = lin.get_rate_AB_SS()
self.assertAlmostEqual(rAB_SS, rAB_SS_LA, 5)
PxB_LA = lin.get_committor(x)
if x not in A and x not in B:
self.assertAlmostEqual(PxB, PxB_LA, 5)
rAB_KMC = kmc.mean_rate(A, B, niter=1000, weights=weights)
print("NGT rate A->B", rAB)
print("KMC rate A->B", rAB_KMC)
print("normalized difference", old_div((rAB - rAB_KMC), rAB))
print("normalized difference to linalg", old_div((rAB - rAB_LA), rAB))
self.assertLess(old_div(abs(rAB - rAB_KMC), rAB), .1)
self.assertLess(old_div(abs(rAB - rAB_LA), rAB), .00001)
rBA_KMC = kmc.mean_rate(B, A, niter=1000, weights=weights)
print("NGT rate B->A", rBA)
print("KMC rate B->A", rBA_KMC)
print("normalized difference", old_div((rBA - rBA_KMC), rBA))
self.assertLess(old_div(abs(rBA - rBA_KMC), rBA), .1)
paB = kmc.committor_probability(A[0], [A[0]], B, niter=1000)
print("the committor probability a->B", paB)
print("graph reduction committor prob",
reducer.get_committor_probabilityAB(A[0]))
self.assertAlmostEqual(paB,
reducer.get_committor_probabilityAB(A[0]),
delta=.1)
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 initialize(self):
self.minima2rates.run()
self.two_state_rates = TwoStateRates(
self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights,
)
def _test_rate(self, i, j):
reducer = TwoStateRates(self.rates, [i], [j])
reducer.compute_rates()
rAB = reducer.get_rate_AB()
self.assertAlmostEqual(rAB, self.final_rate, 7)
reducer.compute_committors()
rAB_ss = reducer.get_rate_AB_SS()
print "kSS", rAB_ss
self.assertAlmostEqual(rAB_ss, 1.5, 7)
def _test_rate(self, A, B):
reducer = TwoStateRates(self.rates, A, B)
reducer.compute_rates()
reducer.compute_committors()
kAB = reducer.get_rate_AB()
self.assertAlmostEqual(kAB, self.true_kAB, 7)
# kBA = reducer.get_rate_BA()
# self.assertAlmostEqual(kBA, self.true_kBA, 7)
rAB_SS = reducer.get_rate_AB_SS()
self.assertAlmostEqual(rAB_SS, self.true_kAB_SS, 7)
def compare(self, A, B, nnodes=10, nedges=20, weights=None, x=1):
print("")
maker = _MakeRandomGraph(nnodes=nnodes, nedges=nedges, node_set=A+B+[x])
graph = maker.run()
graph_backup = graph.copy()
reducer = GraphReduction(maker.rates, A, B, weights=weights)
kmc = KineticMonteCarlo(graph_backup, debug=False)
# test compute_committor_probability()
PxB = reducer.compute_committor_probability(x)
PxB_kmc = kmc.committor_probability(x, A, B, niter=1000)
print("committor probability ", x, "->", B, "=", PxB)
print("committor probability kmc", x, "->", B, "=", PxB_kmc)
self.assertAlmostEqual(PxB, PxB_kmc, delta=.1)
reducer.compute_rates()
rAB = reducer.get_rate_AB()
rBA = reducer.get_rate_BA()
rAB_SS = reducer.get_rate_AB_SS()
# compute rate via linalg
lin = TwoStateRates(maker.rates, A, B, weights=weights)
lin.compute_rates()
rAB_LA = lin.get_rate_AB()
lin.compute_committors()
rAB_SS_LA = lin.get_rate_AB_SS()
self.assertAlmostEqual(rAB_SS, rAB_SS_LA, 5)
PxB_LA = lin.get_committor(x)
if x not in A and x not in B:
self.assertAlmostEqual(PxB, PxB_LA, 5)
rAB_KMC = kmc.mean_rate(A, B, niter=1000, weights=weights)
print("NGT rate A->B", rAB)
print("KMC rate A->B", rAB_KMC)
print("normalized difference", (rAB - rAB_KMC)/rAB)
print("normalized difference to linalg", (rAB - rAB_LA)/rAB)
self.assertLess(abs(rAB - rAB_KMC)/rAB, .1)
self.assertLess(abs(rAB - rAB_LA)/rAB, .00001)
rBA_KMC = kmc.mean_rate(B, A, niter=1000, weights=weights)
print("NGT rate B->A", rBA)
print("KMC rate B->A", rBA_KMC)
print("normalized difference", (rBA - rBA_KMC)/rBA)
self.assertLess(abs(rBA - rBA_KMC)/rBA, .1)
paB = kmc.committor_probability(A[0], [A[0]], B, niter=1000)
print("the committor probability a->B", paB)
print("graph reduction committor prob", reducer.get_committor_probabilityAB(A[0]))
self.assertAlmostEqual(paB, reducer.get_committor_probabilityAB(A[0]), delta=.1)
def _test_rate(self, i, j):
reducer = TwoStateRates(self.rates, [i], [j])
reducer.compute_rates()
rAB = reducer.get_rate_AB()
self.assertAlmostEqual(rAB, self.final_rate, 7)
reducer.compute_committors()
rAB_ss = reducer.get_rate_AB_SS()
print("kSS", rAB_ss)
self.assertAlmostEqual(rAB_ss, 1.5, 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)
def _test_rate(self, A, B):
reducer = TwoStateRates(self.rates, A, B)
reducer.compute_rates()
reducer.compute_committors()
kAB = reducer.get_rate_AB()
self.assertAlmostEqual(kAB, self.true_kAB, 7)
# kBA = reducer.get_rate_BA()
# self.assertAlmostEqual(kBA, self.true_kBA, 7)
rAB_SS = reducer.get_rate_AB_SS()
self.assertAlmostEqual(rAB_SS, self.true_kAB_SS, 7)
class RatesLinalg(object):
"""this class duplicates the behavior in RateCalculation, but with the linalg solver"""
_initialized = False
_times_computed = False
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 initialize(self):
self.minima2rates.run()
self.two_state_rates = TwoStateRates(self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights)
def compute_rates(self):
if not self._initialized:
self.initialize()
if not self._times_computed:
self.two_state_rates.compute_rates()
self._times_computed = True
return old_div(self.two_state_rates.get_rate_AB(),
self.minima2rates.rate_norm)
def get_mfptimes(self):
if not self._initialized:
self.initialize()
if not self._times_computed:
self.two_state_rates.compute_rates()
times = self.two_state_rates.mfpt_computer.mfpt_dict
self.mfpt_dict = dict(
((m, t * self.minima2rates.rate_norm) for m, t in times.items()))
for m in self.minima2rates.B:
self.mfpt_dict[m] = 0.
return self.mfpt_dict
def compute_committors(self):
if not self._initialized:
self.initialize()
self.two_state_rates.compute_committors()
self.committors = self.two_state_rates.committor_dict
for m in self.minima2rates.A:
self.committors[m] = 0.
for m in self.minima2rates.B:
self.committors[m] = 1.
return self.committors
def get_committors(self):
return self.committors
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 RatesLinalg(object):
"""this class duplicates the behavior in RateCalculation, but with the linalg solver"""
_initialized = False
_times_computed = False
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 initialize(self):
self.minima2rates.run()
self.two_state_rates = TwoStateRates(
self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights,
)
def compute_rates(self):
if not self._initialized:
self.initialize()
if not self._times_computed:
self.two_state_rates.compute_rates()
self._times_computed = True
return self.two_state_rates.get_rate_AB() / self.minima2rates.rate_norm
def get_mfptimes(self):
if not self._initialized:
self.initialize()
if not self._times_computed:
self.two_state_rates.compute_rates()
times = self.two_state_rates.mfpt_computer.mfpt_dict
self.mfpt_dict = dict(((m, t * self.minima2rates.rate_norm) for m, t in times.iteritems()))
for m in self.minima2rates.B:
self.mfpt_dict[m] = 0.0
return self.mfpt_dict
def compute_committors(self):
if not self._initialized:
self.initialize()
self.two_state_rates.compute_committors()
self.committors = self.two_state_rates.committor_dict
for m in self.minima2rates.A:
self.committors[m] = 0.0
for m in self.minima2rates.B:
self.committors[m] = 1.0
return self.committors
def get_committors(self):
return self.committors
def initialize(self):
self.minima2rates.run()
self.two_state_rates = TwoStateRates(self.minima2rates.rate_constants,
self.minima2rates.A,
self.minima2rates.B,
weights=self.minima2rates.weights)