def test_simple_cubic(self):
"""Test with an easy structure"""
# Make sure direction-dependent fingerprints are zero
agni = AGNIFingerprints(directions=['x', 'y', 'z'])
features = agni.featurize(self.sc, 0)
self.assertEqual(8 * 3, len(features))
self.assertEqual(8 * 3, len(set(agni.feature_labels())))
self.assertArrayAlmostEqual([
0,
] * 24, features)
# Compute the "atomic fingerprints"
agni.directions = [None]
agni.cutoff = 3.75 # To only get 6 neighbors to deal with
features = agni.featurize(self.sc, 0)
self.assertEqual(8, len(features))
self.assertEqual(8, len(set(agni.feature_labels())))
self.assertEqual(0.8, agni.etas[0])
self.assertAlmostEqual(
6 * np.exp(-(3.52 / 0.8)**2) * 0.5 *
(np.cos(np.pi * 3.52 / 3.75) + 1), features[0])
self.assertAlmostEqual(
6 * np.exp(-(3.52 / 16)**2) * 0.5 *
(np.cos(np.pi * 3.52 / 3.75) + 1), features[-1])
# Test that passing etas to constructor works
new_etas = np.logspace(-4, 2, 6)
agni = AGNIFingerprints(directions=['x', 'y', 'z'], etas=new_etas)
self.assertArrayAlmostEqual(new_etas, agni.etas)
def test_simple_cubic(self):
"""Test with an easy structure"""
# Make sure direction-dependent fingerprints are zero
agni = AGNIFingerprints(directions=['x', 'y', 'z'])
features = agni.featurize(self.sc, 0)
self.assertEqual(8 * 3, len(features))
self.assertEqual(8 * 3, len(set(agni.feature_labels())))
self.assertArrayAlmostEqual([0, ] * 24, features)
# Compute the "atomic fingerprints"
agni.directions = [None]
agni.cutoff = 3.75 # To only get 6 neighbors to deal with
features = agni.featurize(self.sc, 0)
self.assertEqual(8, len(features))
self.assertEqual(8, len(set(agni.feature_labels())))
self.assertEqual(0.8, agni.etas[0])
self.assertAlmostEqual(6 * np.exp(-(3.52 / 0.8) ** 2) * 0.5 * (np.cos(np.pi * 3.52 / 3.75) + 1), features[0])
self.assertAlmostEqual(6 * np.exp(-(3.52 / 16) ** 2) * 0.5 * (np.cos(np.pi * 3.52 / 3.75) + 1), features[-1])
# Test that passing etas to constructor works
new_etas = np.logspace(-4, 2, 6)
agni = AGNIFingerprints(directions=['x', 'y', 'z'], etas=new_etas)
self.assertArrayAlmostEqual(new_etas, agni.etas)
def test_off_center_cscl(self):
agni = AGNIFingerprints(directions=[None, 'x', 'y', 'z'], cutoff=4)
# Compute the features on both sites
site1 = agni.featurize(self.cscl, 0)
site2 = agni.featurize(self.cscl, 1)
# The atomic attributes should be equal
self.assertArrayAlmostEqual(site1[:8], site2[:8])
# The direction-dependent ones should be equal and opposite in sign
self.assertArrayAlmostEqual(-1 * site1[8:], site2[8:])
# Make sure the site-ones are as expected.
right_dist = 4.209 * np.sqrt(0.45 ** 2 + 2 * 0.5 ** 2)
right_xdist = 4.209 * 0.45
left_dist = 4.209 * np.sqrt(0.55 ** 2 + 2 * 0.5 ** 2)
left_xdist = 4.209 * 0.55
self.assertAlmostEqual(4 * (
right_xdist / right_dist * np.exp(-(right_dist / 0.8) ** 2) * 0.5 * (np.cos(np.pi * right_dist / 4) + 1) -
left_xdist / left_dist * np.exp(-(left_dist / 0.8) ** 2) * 0.5 * (np.cos(np.pi * left_dist / 4) + 1)),
site1[8])
def test_off_center_cscl(self):
agni = AGNIFingerprints(directions=[None, 'x', 'y', 'z'], cutoff=4)
# Compute the features on both sites
site1 = agni.featurize(self.cscl, 0)
site2 = agni.featurize(self.cscl, 1)
# The atomic attributes should be equal
self.assertArrayAlmostEqual(site1[:8], site2[:8])
# The direction-dependent ones should be equal and opposite in sign
self.assertArrayAlmostEqual(-1 * site1[8:], site2[8:])
# Make sure the site-ones are as expected.
right_dist = 4.209 * np.sqrt(0.45 ** 2 + 2 * 0.5 ** 2)
right_xdist = 4.209 * 0.45
left_dist = 4.209 * np.sqrt(0.55 ** 2 + 2 * 0.5 ** 2)
left_xdist = 4.209 * 0.55
self.assertAlmostEqual(4 * (
right_xdist / right_dist * np.exp(-(right_dist / 0.8) ** 2) * 0.5 * (np.cos(np.pi * right_dist / 4) + 1) -
left_xdist / left_dist * np.exp(-(left_dist / 0.8) ** 2) * 0.5 * (np.cos(np.pi * left_dist / 4) + 1)),
site1[8])
