class TestTptFunctionsSparse(unittest.TestCase):
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = BirthDeathChain(q, p)
T_dense = self.bdc.transition_matrix()
T_sparse = csr_matrix(T_dense)
self.T = T_sparse
self.mu = self.bdc.stationary_distribution()
self.qminus = self.bdc.committor_backward(self.a, self.b)
self.qplus = self.bdc.committor_forward(self.a, self.b)
# present results
self.fluxn = flux.flux_matrix(self.T,
self.mu,
self.qminus,
self.qplus,
netflux=False)
self.netfluxn = flux.flux_matrix(self.T,
self.mu,
self.qminus,
self.qplus,
netflux=True)
self.totalfluxn = flux.total_flux(self.netfluxn, self.A)
self.raten = flux.rate(self.totalfluxn, self.mu, self.qminus)
def test_tpt_flux(self):
flux = self.bdc.flux(self.a, self.b)
assert_allclose(self.fluxn.toarray(), flux)
def test_tpt_netflux(self):
netflux = self.bdc.netflux(self.a, self.b)
assert_allclose(self.netfluxn.toarray(), netflux)
def test_tpt_totalflux(self):
totalflux = self.bdc.totalflux(self.a, self.b)
assert_allclose(self.totalfluxn, totalflux)
def test_tpt_rate(self):
rate = self.bdc.rate(self.a, self.b)
assert_allclose(self.raten, rate)
class TestTPT(unittest.TestCase):
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = BirthDeathChain(q, p)
self.T = self.bdc.transition_matrix()
"""Use precomputed mu, qminus, qplus"""
self.mu = self.bdc.stationary_distribution()
self.qplus = self.bdc.committor_forward(self.a, self.b)
self.qminus = self.bdc.committor_backward(self.a, self.b)
# self.qminus = committor.backward_committor(self.T, self.A, self.B, mu=self.mu)
# self.qplus = committor.forward_committor(self.T, self.A, self.B)
self.fluxn = tpt.flux_matrix(self.T,
self.mu,
self.qminus,
self.qplus,
netflux=False)
self.netfluxn = tpt.to_netflux(self.fluxn)
self.Fn = tpt.total_flux(self.fluxn, self.A)
self.kn = tpt.rate(self.Fn, self.mu, self.qminus)
def test_flux(self):
flux = self.bdc.flux(self.a, self.b)
assert_allclose(self.fluxn, flux)
def test_netflux(self):
netflux = self.bdc.netflux(self.a, self.b)
assert_allclose(self.netfluxn, netflux)
def test_totalflux(self):
F = self.bdc.totalflux(self.a, self.b)
assert_allclose(self.Fn, F)
def test_rate(self):
k = self.bdc.rate(self.a, self.b)
assert_allclose(self.kn, k)
class TestTPTDense(unittest.TestCase):
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = BirthDeathChain(q, p)
self.T = self.bdc.transition_matrix()
"""Compute mu, qminus, qplus in constructor"""
self.tpt = flux.tpt(self.T, self.A, self.B)
"""Use precomputed mu, qminus, qplus"""
self.mu = self.bdc.stationary_distribution()
self.qminus = self.bdc.committor_backward(self.a, self.b)
self.qplus = self.bdc.committor_forward(self.a, self.b)
self.tpt_fast = flux.tpt(self.T,
self.A,
self.B,
mu=self.mu,
qminus=self.qminus,
qplus=self.qplus)
def test_grossflux(self):
flux = self.bdc.flux(self.a, self.b)
fluxn = self.tpt.gross_flux
assert_allclose(fluxn, flux)
fluxn = self.tpt_fast.gross_flux
assert_allclose(fluxn, flux)
def test_netflux(self):
netflux = self.bdc.netflux(self.a, self.b)
netfluxn = self.tpt.net_flux
assert_allclose(netfluxn, netflux)
netfluxn = self.tpt_fast.net_flux
assert_allclose(netfluxn, netflux)
def test_totalflux(self):
F = self.bdc.totalflux(self.a, self.b)
Fn = self.tpt.total_flux
assert_allclose(Fn, F)
Fn = self.tpt_fast.total_flux
assert_allclose(Fn, F)
def test_rate(self):
k = self.bdc.rate(self.a, self.b)
kn = self.tpt.rate
assert_allclose(kn, k)
kn = self.tpt_fast.rate
assert_allclose(kn, k)
def test_backward_committor(self):
qminus = self.qminus
qminusn = self.tpt.backward_committor
assert_allclose(qminusn, qminus)
qminusn = self.tpt_fast.backward_committor
assert_allclose(qminusn, qminus)
def test_forward_committor(self):
qplus = self.qplus
qplusn = self.tpt.forward_committor
assert_allclose(qplusn, qplus)
qplusn = self.tpt_fast.forward_committor
assert_allclose(qplusn, qplus)
def test_stationary_distribution(self):
mu = self.mu
mun = self.tpt.stationary_distribution
assert_allclose(mun, mu)
mun = self.tpt_fast.stationary_distribution
assert_allclose(mun, mu)
