def test_fail_without_lambdas(self):
fake_ifaceA = paths.InterfaceSet(cv=self.ifacesA.cv,
volumes=self.ifacesA.volumes,
direction=self.ifacesA.direction)
network = paths.MISTISNetwork([(self.stateA, fake_ifaceA, self.stateB)
])
network.sampling_transitions[0].tcp = self.tcp_A
bias = paths.SRTISBiasFromNetwork(network)
def test_bias_from_ms_network(self):
ms_outer = paths.MSOuterTISInterface.from_lambdas({
self.ifacesA: -0.1,
self.ifacesB: 0.1
})
network = paths.MISTISNetwork(
[(self.stateA, self.ifacesA, self.stateB),
(self.stateB, self.ifacesB, self.stateA)],
ms_outers=[ms_outer])
transition_AB = None
transition_BA = None
for t in network.sampling_transitions:
if t.stateA == self.stateA:
t.tcp = self.tcp_A
transition_AB = t
elif t.stateA == self.stateB:
t.tcp = self.tcp_B
transition_BA = t
else:
print([t.stateA, t.stateB])
print([self.stateA, self.stateB])
raise RuntimeError("Weird states in test transition")
bias = paths.SRTISBiasFromNetwork(network)
n_ensembles = len(bias.dataframe.index)
for i in range(n_ensembles):
for j in range(i, n_ensembles):
if not np.isnan(bias.dataframe.loc[i, j]):
np.testing.assert_almost_equal(
bias.dataframe.loc[i, j],
old_div(1.0, bias.dataframe.loc[j, i]))
for i in range(len(transition_AB.ensembles) - 1):
ens_to = transition_AB.ensembles[i]
ens_from = transition_AB.ensembles[i + 1]
assert_almost_equal(bias.bias_value(ens_from, ens_to), 0.5)
for i in range(len(transition_BA.ensembles) - 1):
ens_to = transition_BA.ensembles[i]
ens_from = transition_BA.ensembles[i + 1]
assert_almost_equal(bias.bias_value(ens_from, ens_to), 0.2)
for ensA in transition_AB.ensembles:
for ensB in transition_BA.ensembles:
assert_equal(np.isnan(bias.bias_value(ensA, ensB)), True)
assert_equal(np.isnan(bias.bias_value(ensB, ensA)), True)
assert_almost_equal(
bias.bias_value(transition_BA.ensembles[-1], network.ms_outers[0]),
old_div(5.0, 2))
assert_almost_equal(
bias.bias_value(transition_AB.ensembles[-1], network.ms_outers[0]),
old_div(2.0, 2))
raise SkipTest
def test_bias_from_network(self):
# force the TCP in
network = paths.MISTISNetwork([(self.stateA, self.ifacesA, self.stateB)
])
network.sampling_transitions[0].tcp = self.tcp_A
bias = paths.SRTISBiasFromNetwork(network)
transition = list(network.transitions.values())[0] # only one
# check reciprocal of symmetric partners
for i in range(4):
for j in range(i, 4):
assert_equal(bias.dataframe.loc[i, j],
old_div(1.0, bias.dataframe.loc[j, i]))
for i in range(len(transition.ensembles) - 1):
ens_to = transition.ensembles[i]
ens_from = transition.ensembles[i + 1]
assert_equal(bias.bias_value(ens_from, ens_to), 0.5)
for i in range(len(transition.ensembles) - 2):
ens_to = transition.ensembles[i]
ens_from = transition.ensembles[i + 2]
assert_equal(bias.bias_value(ens_from, ens_to), 0.25)
def test_fail_without_tcp(self):
network = paths.MISTISNetwork([(self.stateA, self.ifacesA, self.stateB)
])
bias = paths.SRTISBiasFromNetwork(network)