def test_mfpt_between_sets(self):
x = mfpt(self.P, [1, 2], origin=0)
assert_allclose(x, self.o0t12)
x = mfpt(self.P, [0, 1], origin=2)
assert_allclose(x, self.o2t01)
x = mfpt(self.P, 2, origin=[0, 1])
assert_allclose(x, self.o01t2)
x = mfpt(self.P, 0, origin=[1, 2])
assert_allclose(x, self.o12t0)
def test_mfpt(self):
x = mfpt(self.P, 0)
assert_allclose(x, self.m0)
x = mfpt(self.P, 1)
assert_allclose(x, self.m1)
x = mfpt(self.P, 2)
assert_allclose(x, self.m2)
x = mfpt(self.P, [0, 1])
assert_allclose(x, self.m01)
x = mfpt(self.P, [1, 2])
assert_allclose(x, self.m12)
def test_time_units():
dtraj = np.random.randint(0, 4, 1000)
tau = 12
dt = 0.456
msmobj = estimate_markov_model(dtraj, lag=tau, dt_traj='%f ns' % dt)
# check MFPT consistency
mfpt_ref = msmobj.mfpt([0], [1])
tptobj = tpt(msmobj, [0], [1])
assert_allclose(tptobj.mfpt, mfpt_ref)
assert_allclose(mfpt(msmobj.P, [1], [0], tau=tau) * dt, mfpt_ref)
assert_allclose(
np.dot(msmobj.stationary_distribution, tptobj.backward_committor) /
tptobj.total_flux, mfpt_ref)
# check flux consistency
total_flux_ref = tptobj.total_flux
A = tptobj.A
B = tptobj.B
I = tptobj.I
assert_allclose(
tptobj.gross_flux[A, :][:, B].sum() +
tptobj.gross_flux[A, :][:, I].sum(), total_flux_ref)
assert_allclose(
tptobj.net_flux[A, :][:, B].sum() + tptobj.net_flux[A, :][:, I].sum(),
total_flux_ref)
assert_allclose(
tptobj.flux[A, :][:, B].sum() + tptobj.flux[A, :][:, I].sum(),
total_flux_ref)
mf = tptobj.major_flux(1.0)
assert_allclose(mf[A, :][:, B].sum() + mf[A, :][:, I].sum(),
total_flux_ref)
# check that the coarse-grained version is consistent too
_, tptobj2 = tptobj.coarse_grain([A, I, B])
assert_allclose(tptobj2.total_flux, total_flux_ref)
assert_allclose(tptobj2.mfpt, mfpt_ref)