def test_step_uncoupled(self):
from math import sqrt
# test uncoupled
V0 = 2.0
V1 = 3.0
uncoupled_matrix = dynq.NonadiabaticMatrix([[V0, 0.0], [0.0, V1]])
# DEBUG
#uncoupled_matrix = dynq.NonadiabaticMatrix([[0.0, 0.0], [0.0, 3.0]])
uncoupled = dynq.potentials.MMSTHamiltonian(uncoupled_matrix)
uncoupled_topology = dynq.Topology(masses=[], potential=uncoupled)
uncoupled_snap = dynq.MMSTSnapshot(
coordinates=np.array([]), momenta=np.array([]),
electronic_coordinates=np.array([1.0, 1.0]),
electronic_momenta=np.array([1.0, 1.0]),
topology=uncoupled_topology
)
uncoupled_integ = CandyRozmus4MMST(0.01, uncoupled)
import dynamiq_engine.features as dynq_f
import openpathsampling.engines.features as paths_f
uncoupled_integ.prepare([paths_f.coordinates, dynq_f.momenta,
dynq_f.electronic_coordinates,
dynq_f.electronic_momenta,
dynq_f.action])
explicit_T = lambda pes, snap : (
np.dot(snap.momenta, pes.dHdp(snap))
+ np.dot(snap.electronic_momenta, pes.electronic_dHdp(snap))
#- pes.H(snap) + pes.V(snap)
)
uncoupled_integ.reset(uncoupled_snap)
for i in range(10):
uncoupled_integ.step(uncoupled, uncoupled_snap, uncoupled_snap)
t=0.01*(i+1)
ho1 = exact_ho(time=t, omega=2.0, m=1.0/2.0, q0=1.0, p0=1.0)
ho2 = exact_ho(time=t, omega=3.0, m=1.0/3.0, q0=1.0, p0=1.0)
T = uncoupled.T(uncoupled_snap)
V = uncoupled.V(uncoupled_snap)
assert_almost_equal(ho1['L'] + ho2['L'] + 0.5*(V0+V1), T-V)
# TODO: note that there's some question about the correctness of
# the action here. However, we DO have the correct Lagrangian,
# and we get the correct action for other HO systems. So it is
# possible that the problem is a fundamental issue with this
# integration approach for the action.
# For future work to test this, the starting point should be
#print ho1['S']+ho2['S']+0.5*(V0+V1)*t, uncoupled_snap.action
exact_1 = exact_ho(time=0.1, omega=2.0, m=1.0/2.0, q0=1.0, p0=1.0)
exact_2 = exact_ho(time=0.1, omega=3.0, m=1.0/3.0, q0=1.0, p0=1.0)
predicted_coordinates = [exact_1['q'][0], exact_2['q'][0]]
predicted_momenta = [exact_1['p'][0], exact_2['p'][0]]
assert_array_almost_equal(uncoupled_snap.electronic_coordinates,
np.array(predicted_coordinates))
assert_array_almost_equal(uncoupled_snap.electronic_momenta,
np.array(predicted_momenta))
assert_almost_equal(explicit_T(uncoupled, uncoupled_snap),
uncoupled.T(uncoupled_snap))
def test_T(self):
# Definition of T is $L + V = p * dH/dp - H + V$; test this directly.
# Use a lambda rather than nested def because nested def screws with
# my in-editor test runner
explicit_T = lambda pes, snap : (
np.dot(snap.momenta, pes.dHdp(snap))
+ np.dot(snap.electronic_momenta, pes.electronic_dHdp(snap))
- pes.H(snap) + pes.V(snap)
)
pes_T = self.tully.T(self.tully_snap)
assert_almost_equal(pes_T, explicit_T(self.tully, self.tully_snap))
assert_almost_equal(explicit_T(self.four_state, self.four_state_snap),
self.four_state.T(self.four_state_snap))
