def do_check_committors(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates_and_committors()
committors = rcalc.get_committors()
rla = RatesLinalg(self.db.transition_states(), A, B)
cla = rla.compute_committors()
for m, qla in cla.iteritems():
self.assertAlmostEqual(committors[m], qla, 7)
def do_check_committors(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates_and_committors()
committors = rcalc.get_committors()
rla = RatesLinalg(self.db.transition_states(), A, B)
cla = rla.compute_committors()
for m, qla in cla.items():
self.assertAlmostEqual(committors[m], qla, 7)
def do_check_rates(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates()
rAB = rcalc.get_rate_AB()
rBA = rcalc.get_rate_BA()
rla = RatesLinalg(self.db.transition_states(), A, B)
rAB_la = rla.compute_rates()
self.assertAlmostEqual(rAB, rAB_la, 7)
def test1(self):
m1 = self.db.getMinimum(1)
m2 = self.db.getMinimum(2)
m3 = self.db.getMinimum(3)
m4 = self.db.getMinimum(4)
rcalc = RateCalculation(self.db.transition_states(), [m1], [m2], T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 7106337458., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 1955395816., delta=1e4)
rcalc = RateCalculation(self.db.transition_states(), [m1,m3], [m2, m4], T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 8638736600., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 3499625167., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1], [m2], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 7106337458., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1, m3], [m2, m4], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 8638736600., delta=1e4)
def do_check_rates(self, A, B):
rcalc = RateCalculation(self.db.transition_states(), A, B)
rcalc.compute_rates()
rAB = rcalc.get_rate_AB()
rBA = rcalc.get_rate_BA()
rla = RatesLinalg(self.db.transition_states(), A, B)
rAB_la = rla.compute_rates()
self.assertAlmostEqual(rAB, rAB_la, 7)
def _compute_rates(self):
self.ui.label_status.setText("computing rates %s <-> %s" % (self.A, self.B))
T = float(self.ui.lineEdit_T.text())
calculator = RateCalculation(self.transition_states, self.A, self.B,
T=T, use_fvib=True)
calculator.compute_rates()
rAB = calculator.get_rate_AB()
rBA = calculator.get_rate_BA()
self._add_result(self.A, self.B, rAB, rBA)
self.ui.label_status.setText("")
print len(A), "A minima"
print len(B), "B minima"
print A[0].energy
print B[0].energy
#rate_constants = reduce_rates(rate_constants, B, A=A)
print "computing rates from minima data"
T = .05
print "temperature", T
pele_rates = RateCalculation(db.transition_states(), A, B, T=T, use_fvib=True)
pele_rates._make_kmc_graph()
rates = pele_rates.rate_constants
weights = pele_rates._get_equilibrium_occupation_probabilities()
rate_norm = np.exp(-pele_rates.max_log_rate)
#Peq = pele_rates._get_equilibrium_occupation_probabilities()
print "reducing rates"
rate_constants = reduce_rates(rates, B, A=A)
print "max rate constant", max(rates.itervalues())
print "min rate constant", min(rates.itervalues())
if False:
def test1(self):
m1 = self.db.getMinimum(1)
m2 = self.db.getMinimum(2)
m3 = self.db.getMinimum(3)
m4 = self.db.getMinimum(4)
rcalc = RateCalculation(self.db.transition_states(), [m1], [m2],
T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 7106337458., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 1955395816., delta=1e4)
rcalc = RateCalculation(self.db.transition_states(), [m1, m3],
[m2, m4],
T=0.592)
rcalc.compute_rates()
self.assertAlmostEqual(rcalc.get_rate_AB(), 8638736600., delta=1e4)
self.assertAlmostEqual(rcalc.get_rate_BA(), 3499625167., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1], [m2], T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 7106337458., delta=1e4)
rla = RatesLinalg(self.db.transition_states(), [m1, m3], [m2, m4],
T=0.592)
rAB = rla.compute_rates()
self.assertAlmostEqual(rAB, 8638736600., delta=1e4)