def test_atomic_pair_maks_O_self_overlap(self):
from SCFInitialGuess.construction.utilities import make_atom_pair_mask
# test hydrogen
expected = np.zeros((7, 7))
expected[0:5, 0:5] = 1
expected = expected.astype("bool")
actual = make_atom_pair_mask(self.mol, 0, 0)
np.testing.assert_allclose(actual, expected)
def _assert_results_ok(self, G, T, pair):
"""pair marks the expected regions. With descritor and target matrix mock
the expected results are clear."""
from SCFInitialGuess.construction.utilities import \
make_atom_pair_mask
# check symmetry vector G
self.assertListEqual(G, self._make_expected_symmetry_vector(pair))
# check matrix
for (p, t) in zip(pair, T):
if isinstance(p, int):
mask = make_atom_pair_mask(self.mol, p, p)
np.testing.assert_equal(
extract_triu(self.T.copy()[mask],
N_BASIS[self.mol.basis][self.mol.species[p]]),
t)
else:
# exptract block from LOWER triu (thus min/max)
mask = make_atom_pair_mask(self.mol, np.max(p), np.min(p))
np.testing.assert_equal(self.T[mask], t)
def make_target_matrix_mock(mol):
"""This function creates a matrix of strings that can be used to
debug matrix block extractions. Its values e.g. for element (i,j) are
<spies_i><i>-<species_j><j>.
"""
from SCFInitialGuess.construction.utilities import make_atom_pair_mask
dim = mol.dim
T = np.zeros((dim, dim), dtype="object")
for i, atom_i in enumerate(mol.species):
for j, atom_j in enumerate(mol.species):
mask = make_atom_pair_mask(mol, i, j)
m = atom_i + str(i) + "-" + atom_j + str(j)
if N_BASIS[mol.basis][atom_i] * N_BASIS[mol.basis][atom_j]:
T[mask] = m
else:
T[mask] = np.array([[m] * N_BASIS[mol.basis][atom_j]] *
N_BASIS[mol.basis][atom_i],
dtype="object")
return T