def test_ensure_umbrella_center_from_ndarray(self):
# dimension=1
us_center = util._ensure_umbrella_center(np.array([1.0]), 1)
self._assert_us_center(us_center, 1)
np.testing.assert_array_equal(us_center,
np.array([1.0], dtype=np.float64))
# dimension=3, uniform
us_center = util._ensure_umbrella_center(np.array([1.0, 1.0, 1.0]), 3)
self._assert_us_center(us_center, 3)
np.testing.assert_array_equal(
us_center, np.array([1.0, 1.0, 1.0], dtype=np.float64))
# dimension=4, not uniform
us_center = util._ensure_umbrella_center(
np.array([1.0, 2.0, 3.0, 4.0]), 4)
self._assert_us_center(us_center, 4)
np.testing.assert_array_equal(
us_center, np.array([1.0, 2.0, 3.0, 4.0], dtype=np.float64))
# dimension=4x1, not uniform
us_center = util._ensure_umbrella_center(
np.array([
[1.0, 2.0, 3.0, 4.0],
]), 4)
self._assert_us_center(us_center, 4)
np.testing.assert_array_equal(
us_center, np.array([1.0, 2.0, 3.0, 4.0], dtype=np.float64))
def test_ensure_umbrella_center_from_scalar(self):
# dimension=1
us_center = util._ensure_umbrella_center(1.0, 1)
self._assert_us_center(us_center, 1)
np.testing.assert_array_equal(us_center,
np.array([1.0], dtype=np.float64))
# dimension=3
us_center = util._ensure_umbrella_center(1.0, 3)
self._assert_us_center(us_center, 3)
np.testing.assert_array_equal(
us_center, np.array([1.0, 1.0, 1.0], dtype=np.float64))
def test_umbrella_sampling_bias_sequences_1x1(self):
trajs = [np.array([[0.0], [0.5], [1.0]])]
umbrella_centers = np.array([
util._ensure_umbrella_center(0.0, 1),
util._ensure_umbrella_center(1.0, 1)
],
dtype=np.float64)
force_constants = np.array([
util._ensure_force_constant(1.0, 1),
util._ensure_force_constant(2.0, 1)
],
dtype=np.float64)
self._assert_bias_sequences(
util._get_umbrella_bias_sequences(trajs, umbrella_centers,
force_constants),
[np.array([[0.0, 1.0], [0.125, 0.25], [0.5, 0.0]])])
def test_umbrella_sampling_bias_sequences_1x0(self):
trajs = [np.array([0.0, 0.5, 1.0])]
umbrella_centers = np.array([
util._ensure_umbrella_center(0.0, 1),
util._ensure_umbrella_center(1.0, 1)
],
dtype=np.float64)
force_constants = np.array([
util._ensure_force_constant(1.0, 1),
util._ensure_force_constant(2.0, 1)
],
dtype=np.float64)
width = np.zeros(shape=(umbrella_centers.shape[1], ), dtype=np.float64)
self._assert_bias_sequences(
util._get_umbrella_bias_sequences(trajs, umbrella_centers,
force_constants, width),
[np.array([[0.0, 1.0], [0.125, 0.25], [0.5, 0.0]])])
def test_ensure_umbrella_center_catches_unmatching_dimension(self):
with self.assertRaises(ValueError):
util._ensure_umbrella_center([1.0, 1.0], 1)
with self.assertRaises(ValueError):
util._ensure_umbrella_center([1.0, 1.0, 1.0], 2)
with self.assertRaises(ValueError):
util._ensure_umbrella_center([1.0, 1.0], 3)
with self.assertRaises(ValueError):
util._ensure_umbrella_center([[1.0], [1.0]], 1)
with self.assertRaises(ValueError):
util._ensure_umbrella_center([[1.0], [1.0]], 3)
with self.assertRaises(ValueError):
util._ensure_umbrella_center([[1.0, 1.0], [1.0]], 3)