def test_transform_orbitals():
"""Test orbtools.partition.OrbitalPartitionTools.transform_orbitals."""
with path("chemtools.data", "naclo4_coeff_ab_mo.npy") as fname:
coeff_ab_mo = np.load(str(fname))
with path("chemtools.data", "naclo4_olp_ab_ab.npy") as fname:
olp_ab_ab = np.load(str(fname))
with path("chemtools.data", "naclo4_occupations.npy") as fname:
occupations = np.load(str(fname))
with path("chemtools.data", "naclo4_ab_atom_indices.npy") as fname:
ab_atom_indices = np.load(str(fname))
coeff_ab_rand = np.linalg.svd(np.random.rand(124, 124))[0].T
rand_atom_indices = (np.random.rand(124) * 6 // 1).astype(int)
# normalize
olp_rand_rand = coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_rand)
coeff_ab_rand *= np.diag(olp_rand_rand)**(-0.5)
olp_rand_rand = coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_rand)
coeff_rand_mo = project(olp_rand_rand,
coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_mo))
orbpart = OrbitalPartitionTools(coeff_ab_mo, occupations, olp_ab_ab, 6,
ab_atom_indices)
neworbpart = orbpart.transform_orbitals(coeff_ab_rand, rand_atom_indices)
assert np.allclose(coeff_ab_rand.dot(coeff_rand_mo), orbpart.coeff_ab_mo)
assert np.allclose(coeff_rand_mo, neworbpart.coeff_ab_mo)
assert np.allclose(olp_rand_rand, neworbpart.olp_ab_ab)
def test_mulliken_populations_newbasis():
"""Test orbstools.partition.OrbitalPartitionTools.mulliken_populations with a new basis."""
# pylint: disable=C0103
with path("chemtools.data", "naclo4_coeff_ab_mo.npy") as fname:
coeff_ab_mo = np.load(str(fname))
with path("chemtools.data", "naclo4_olp_ab_ab.npy") as fname:
olp_ab_ab = np.load(str(fname))
with path("chemtools.data", "naclo4_occupations.npy") as fname:
occupations = np.load(str(fname))
with path("chemtools.data", "naclo4_ab_atom_indices.npy") as fname:
ab_atom_indices = np.load(str(fname))
orbpart = OrbitalPartitionTools(coeff_ab_mo, occupations, olp_ab_ab, 6,
ab_atom_indices)
assert np.allclose(
orbpart.transform_orbitals(np.identity(124),
ab_atom_indices).mulliken_populations(),
orbpart.mulliken_populations(),
)
coeff_ab_rand = np.linalg.svd(np.random.rand(124, 124))[0].T
rand_atom_indices = (np.random.rand(124) * 6 // 1).astype(int)
# normalize
olp_rand_rand = coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_rand)
coeff_ab_rand *= np.diag(olp_rand_rand)**(-0.5)
olp_rand_rand = coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_rand)
coeff_rand_mo = project(olp_rand_rand,
coeff_ab_rand.T.dot(olp_ab_ab).dot(coeff_ab_mo))
orbpart = OrbitalPartitionTools(coeff_ab_mo, occupations, olp_ab_ab, 6,
rand_atom_indices)
assert np.allclose(coeff_ab_rand.dot(coeff_rand_mo), coeff_ab_mo)
assert np.allclose(
orbpart.transform_orbitals(coeff_ab_rand,
rand_atom_indices).mulliken_populations(),
OrbitalPartitionTools(coeff_rand_mo, occupations, olp_rand_rand, 6,
rand_atom_indices).mulliken_populations(),
)
def test_lowdin_populations():
"""Test orbstools.partition.OrbitalPartitionTools.lowdin_populations."""
with path("chemtools.data", "naclo4_coeff_ab_mo.npy") as fname:
coeff_ab_mo = np.load(str(fname))
with path("chemtools.data", "naclo4_olp_ab_ab.npy") as fname:
olp_ab_ab = np.load(str(fname))
with path("chemtools.data", "naclo4_occupations.npy") as fname:
occupations = np.load(str(fname))
with path("chemtools.data", "naclo4_ab_atom_indices.npy") as fname:
ab_atom_indices = np.load(str(fname))
coeff_ab_oab = power_symmetric(olp_ab_ab, -0.5)
orbpart = OrbitalPartitionTools(coeff_ab_mo, occupations, olp_ab_ab, 6,
ab_atom_indices)
assert np.allclose(
coeff_ab_oab.T.dot(olp_ab_ab).dot(coeff_ab_oab), np.identity(124))
assert np.allclose(
orbpart.transform_orbitals(coeff_ab_oab,
ab_atom_indices).mulliken_populations(),
orbpart.lowdin_populations(),
)