def test_sitestatsfingerprint(self):
# Test matrix.
op_struct_fp = SiteStatsFingerprint.from_preset("OPSiteFingerprint",
stats=None)
opvals = op_struct_fp.featurize(self.diamond)
oplabels = op_struct_fp.feature_labels()
self.assertAlmostEqual(opvals[10][0], 0.9995, places=7)
self.assertAlmostEqual(opvals[10][1], 0.9995, places=7)
opvals = op_struct_fp.featurize(self.nacl)
self.assertAlmostEqual(opvals[18][0], 0.9995, places=7)
self.assertAlmostEqual(opvals[18][1], 0.9995, places=7)
opvals = op_struct_fp.featurize(self.cscl)
self.assertAlmostEqual(opvals[22][0], 0.9995, places=7)
self.assertAlmostEqual(opvals[22][1], 0.9995, places=7)
# Test stats.
op_struct_fp = SiteStatsFingerprint.from_preset("OPSiteFingerprint")
opvals = op_struct_fp.featurize(self.diamond)
print(opvals, '**')
self.assertAlmostEqual(opvals[0], 0.0005, places=7)
self.assertAlmostEqual(opvals[1], 0, places=7)
self.assertAlmostEqual(opvals[2], 0.0005, places=7)
self.assertAlmostEqual(opvals[3], 0.0, places=7)
self.assertAlmostEqual(opvals[4], 0.0005, places=7)
self.assertAlmostEqual(opvals[18], 0.0805, places=7)
self.assertAlmostEqual(opvals[20], 0.9995, places=7)
self.assertAlmostEqual(opvals[21], 0, places=7)
self.assertAlmostEqual(opvals[22], 0.0075, places=7)
self.assertAlmostEqual(opvals[24], 0.2355, places=7)
self.assertAlmostEqual(opvals[-1], 0.0, places=7)
# Test coordination number
cn_fp = SiteStatsFingerprint.from_preset("JmolNN", stats=("mean", ))
cn_vals = cn_fp.featurize(self.diamond)
self.assertEqual(cn_vals[0], 4.0)
# Test the covariance
prop_fp = SiteStatsFingerprint(
SiteElementalProperty(properties=["Number", "AtomicWeight"]),
stats=["mean"],
covariance=True)
# Test the feature labels
labels = prop_fp.feature_labels()
self.assertEqual(3, len(labels))
# Test a structure with all the same type (cov should be zero)
features = prop_fp.featurize(self.diamond)
self.assertArrayAlmostEqual(features, [6, 12.0107, 0])
# Test a structure with only one atom (cov should be zero too)
features = prop_fp.featurize(self.sc)
self.assertArrayAlmostEqual([13, 26.9815386, 0], features)
# Test a structure with nonzero covariance
features = prop_fp.featurize(self.nacl)
self.assertArrayAlmostEqual([14, 29.22138464, 37.38969216], features)
def test_site_elem_prop(self):
f = SiteElementalProperty.from_preset("seko-prb-2017")
# Make sure it does the B1 structure correctly
feat_labels = f.feature_labels()
feats = f.featurize(self.b1, 0)
self.assertAlmostEqual(1, feats[feat_labels.index("site Number")])
feats = f.featurize(self.b1, 1)
self.assertAlmostEqual(2, feats[feat_labels.index("site Number")])
# Test the citations
citations = f.citations()
self.assertEqual(1, len(citations))
self.assertIn("Seko2017", citations[0])
def test_site_elem_prop(self):
f = SiteElementalProperty.from_preset("seko-prb-2017")
# Make sure it does the B1 structure correctly
feat_labels = f.feature_labels()
feats = f.featurize(self.b1, 0)
self.assertAlmostEqual(1, feats[feat_labels.index("site Number")])
feats = f.featurize(self.b1, 1)
self.assertAlmostEqual(2, feats[feat_labels.index("site Number")])
# Test the citations
citations = f.citations()
self.assertEqual(1, len(citations))
self.assertIn("Seko2017", citations[0])