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_umbrella_sampling_bias_sequences_catches_unmatching_dimension(
self):
# wrong centers + constants
with self.assertRaises(TypeError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0, 1.0]]), [[[1.0, 0.0], [1.0, 0.0]]])
with self.assertRaises(TypeError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])], [[1.0, 1.0]],
np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([1.0, 1.0]), np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0, 1.0]]), np.array([[1.0, 0.0], [1.0, 0.0]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[[1.0, 1.0]]]), np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0, 1.0]]), np.array([[[[1.0, 0.0], [1.0, 0.0]]]]))
# conflicting centers + constants
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0, 1.0, 1.0]]),
np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0]]), np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences(
[np.array([[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]])],
np.array([[1.0, 1.0], [2.0, 2.0]]),
np.array([[[1.0, 0.0], [1.0, 0.0]]]))
# traj does not match valid centers + constants
with self.assertRaises(TypeError):
util._get_umbrella_bias_sequences(
[[[0.0, 0.0], [0.5, 0.1], [1.0, 0.2]]], np.array([[1.0, 1.0]]),
np.array([[[1.0, 0.0], [1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences([np.array([0.0, 0.5, 1.0])],
np.array([[1.0, 1.0]]),
np.array([[[1.0, 0.0],
[1.0, 0.0]]]))
with self.assertRaises(ValueError):
util._get_umbrella_bias_sequences([
np.array([[0.0, 1.0, 2.0], [0.5, 1.0, 2.0], [1.0, 1.0, 2.0]])
], np.array([[1.0, 1.0]]), np.array([[[1.0, 0.0], [1.0, 0.0]]]))