def test_momentum_getter(self):
momentum = self.engine.momentum
state = self.engine.simulation.context.getState(getVelocities=True)
velocities = state.getVelocities(asNumpy=True)
assert_equal_array_array(
momentum.velocities / (u.nanometers / u.picoseconds),
velocities / (u.nanometers / u.picoseconds))
def test_configuration_getter(self):
config = self.engine.configuration
state = self.engine.simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True)
assert_equal_array_array(
config.coordinates / u.nanometers,
positions / u.nanometers
)
def test_momentum_getter(self):
momentum = self.engine.momentum
state = self.engine.simulation.context.getState(getVelocities=True)
velocities = state.getVelocities(asNumpy=True)
assert_equal_array_array(
momentum.velocities / (u.nanometers / u.picoseconds),
velocities / (u.nanometers / u.picoseconds)
)
def test_snapshot_get(self):
snap = self.engine.current_snapshot
state = self.engine.simulation.context.getState(getVelocities=True,
getPositions=True)
pos = state.getPositions(asNumpy=True) / u.nanometers
vel = state.getVelocities(asNumpy=True) / (u.nanometers / u.picoseconds)
assert_equal_array_array(snap.coordinates / u.nanometers, pos)
assert_equal_array_array(snap.velocities / (u.nanometers / u.picoseconds),
vel)
def test_snapshot_get(self):
snap = self.engine.current_snapshot
state = self.engine.simulation.context.getState(getVelocities=True,
getPositions=True)
pos = state.getPositions(asNumpy=True) / u.nanometers
vel = state.getVelocities(asNumpy=True) / (u.nanometers / u.picoseconds)
assert_equal_array_array(snap.coordinates / u.nanometers, pos)
assert_equal_array_array(snap.velocities / (u.nanometers / u.picoseconds),
vel)
def test_convert_to_3Ndim(v):
assert_equal_array_array(convert_to_3Ndim([1.0, 2.0]),
np.array([[1.0, 2.0, 0.0]]))
assert_equal_array_array(convert_to_3Ndim([1.0, 2.0, 3.0]),
np.array([[1.0, 2.0, 3.0]]))
assert_equal_array_array(convert_to_3Ndim([1.0, 2.0, 3.0, 4.0]),
np.array([[1.0, 2.0, 3.0], [4.0, 0.0, 0.0]]))
def test_convert_to_3Ndim(v):
raise SkipTest
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0]),
np.array([[1.0, 2.0, 0.0]]))
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0, 3.0]),
np.array([[1.0, 2.0, 3.0]]))
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0, 3.0, 4.0]),
np.array([[1.0, 2.0, 3.0], [4.0, 0.0, 0.0]]))
def test_convert_to_3Ndim(v):
raise SkipTest
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0]),
np.array([[1.0, 2.0, 0.0]]))
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0, 3.0]),
np.array([[1.0, 2.0, 3.0]]))
assert_equal_array_array(toy.convert_to_3Ndim([1.0, 2.0, 3.0, 4.0]),
np.array([[1.0, 2.0, 3.0], [4.0, 0.0, 0.0]]))
def test_list_even(self):
result = make_list_of_pairs([0, 1, 2, 3, 4, 5])
assert_equal_array_array(result, self.correct)
def test_list_of_list_pairs(self):
result = make_list_of_pairs([[0, 1], [2, 3], [4, 5]])
assert_equal_array_array(result, self.correct)
def test_list_even(self):
result = make_list_of_pairs([0, 1, 2, 3, 4, 5])
assert_equal_array_array(result, self.correct)
def test_list_of_list_pairs(self):
result = make_list_of_pairs([[0, 1], [2, 3], [4, 5]])
assert_equal_array_array(result, self.correct)
def test_configuration_getter(self):
config = self.engine.configuration
state = self.engine.simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True)
assert_equal_array_array(config.coordinates / u.nanometers,
positions / u.nanometers)