def test_compute_weights(self):
"""Tes compute weights function."""
# generate random points
npoint = 50
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2],
[2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
indices = [0, 13, 29, 50]
# compute with old generate_weights method
weights_ref = becke.generate_weights(points,
centers,
nums,
pt_ind=indices)
# compute with compute_weights
weights_compute = becke.compute_weights(points,
centers,
nums,
pt_ind=indices)
assert_allclose(weights_ref, weights_compute)
# compute with one selected atom weights
weights_ref2 = becke.generate_weights(points, centers, nums, select=1)
weights_compute2 = becke.compute_weights(points,
centers,
nums,
select=1)
assert_allclose(weights_ref2, weights_compute2)
def test_becke_sum3_one(self):
"""Test becke weights add up to one with three centers."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2], [2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
weights0 = becke.generate_weights(points, centers, nums, select=[0])
weights1 = becke.generate_weights(points, centers, nums, select=[1])
weights2 = becke.generate_weights(points, centers, nums, select=2)
assert_allclose(weights0 + weights1 + weights2, np.ones(100))
def test_becke_compute_atom_weight(self):
"""Test becke compute pa function."""
npoint = 10
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2], [2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
weights0 = becke.generate_weights(points, centers, nums, select=[0])
weights1 = becke.generate_weights(points, centers, nums, select=[1])
weights2 = becke.generate_weights(points, centers, nums, select=[2])
aw_0 = becke.compute_atom_weight(points, centers, nums, 0)
aw_1 = becke.compute_atom_weight(points, centers, nums, 1)
aw_2 = becke.compute_atom_weight(points, centers, nums, 2)
assert_allclose(weights0, aw_0)
assert_allclose(weights1, aw_1)
assert_allclose(weights2, aw_2)
def test_raise_errors(self):
"""Test errors raise."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2]])
# error of select and pt_ind
becke = BeckeWeights({1: 0.5, 2: 0.8})
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, select=[])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, pt_ind=[3])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, pt_ind=[3, 6])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, select=[], pt_ind=[])
with self.assertRaises(ValueError):
becke.generate_weights(points,
centers,
nums,
select=[0, 1],
pt_ind=[0, 10, 50, 99])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, select=[])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, pt_ind=[3])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, pt_ind=[3, 6])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, select=[], pt_ind=[])
with self.assertRaises(ValueError):
becke.compute_weights(points,
centers,
nums,
select=[0, 1],
pt_ind=[0, 10, 50, 99])
# error of order
with self.assertRaises(ValueError):
BeckeWeights({1: 0.5, 2: 0.8}, order=3.0)
# error of radii
with self.assertRaises(TypeError):
BeckeWeights({1.0: 0.5, 2: 0.8}, order=3)
with self.assertRaises(TypeError):
BeckeWeights(np.array([0.5, 0.8]), order=3)
def test_becke_special_points(self):
"""Test becke weights for special cases."""
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2], [2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
weights = becke.generate_weights(centers, centers, nums, select=0)
assert_allclose(weights, [1, 0, 0])
weights = becke.generate_weights(centers, centers, nums, select=1)
assert_allclose(weights, [0, 1, 0])
weights = becke.generate_weights(centers, centers, nums, select=2)
assert_allclose(weights, [0, 0, 1])
# each point in seperate sectors.
weights = becke.generate_weights(centers, centers, nums, pt_ind=[0, 1, 2, 3])
assert_allclose(weights, [1, 1, 1])
weights = becke.generate_weights(
centers, centers, nums, select=[0, 1], pt_ind=[0, 1, 3]
)
assert_allclose(weights, [1, 1, 0])
weights = becke.generate_weights(
centers, centers, nums, select=[2, 0], pt_ind=[0, 2, 3]
)
assert_allclose(weights, [0, 0, 0])
def test_noble_gas_radius(self):
"""Test np.nan value to be handled properly."""
noble_list = [2, 10, 18, 36, 54, 85, 86]
for i in noble_list:
nums = np.array([i, i - 1]) if i != 86 else np.array([i, i - 2])
centers = np.array([[0.5, 0.0, 0.0], [-0.5, 0.0, 0.0]])
pts = np.zeros((10, 3), dtype=float)
pts[:, 1:] += np.random.rand(10, 2)
becke = BeckeWeights(order=3)
wts = becke.generate_weights(pts, centers, nums, pt_ind=[0, 5, 10])
assert_allclose(wts, 0.5)
wts = becke.compute_weights(pts, centers, nums, pt_ind=[0, 5, 10])
assert_allclose(wts, 0.5)
