def test_mo_map(self):
mol1 = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='6-31g')
mol2 = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo1 = numpy.random.random((mol1.nao_nr(), 10))*.2
mo2 = numpy.random.random((mol2.nao_nr(), 15))*.2
idx,s = mo_mapping.mo_map(mol1, mo1, mol2, mo2)
self.assertTrue(numpy.allclose(idx,
[[1,11], [2,11], [7,11], [8,11], [9,11],]))
self.assertAlmostEqual(abs(s).sum(), 54.5514791873481, 9)
def test_mo_map(self):
mol1 = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='6-31g')
mol2 = gto.M(atom = '''O 0 0 0; O 0 0 1''', basis='ccpvdz')
numpy.random.seed(1)
mo1 = numpy.random.random((mol1.nao_nr(), 10))*.2
mo2 = numpy.random.random((mol2.nao_nr(), 15))*.2
idx,s = mo_mapping.mo_map(mol1, mo1, mol2, mo2)
self.assertTrue(numpy.allclose(idx,
[[1,11], [2,11], [7,11], [8,11], [9,11],]))
self.assertAlmostEqual(abs(s).sum(), 54.5514791873481, 9)
def ovp_check(mol1: gto.mole.Mole,
mol2: gto.mole.Mole,
mo1: np.ndarray,
mo2: np.ndarray,
tol: float = 0.35,
mo_range: list = None) -> list:
r"""Compare two sets of orbitals then return the list of orbital indices
where orbitals of the same index match whith each other.
Args:
mol1 (object): mol of system 1.
mol2 (object): mol of system 2.
mo1 (np.ndarray): molecular orbitals of system 1.
mo2 (np.ndarray): molecular orbitals of system 2.
tol (float): tolerance.
mo_range (list): range of orbitals to check.
Returns:
match (list): List of matched orbital indices.
raises:
TypeError: MO both should be of the same size.
"""
from pyscf.tools import mo_mapping
if not mo1.shape[0] == mo2.shape[0]:
raise TypeError('Both MOs should be of the same dimensions')
if mo_range is None:
mo_range = list(range(mo1.shape[0]))
match = []
idx = np.array(mo_mapping.mo_map(mol1, mo1, mol2, mo2, tol=tol)[0])
for i in mo_range:
idxi = idx[idx[:, 0] == i]
for j in idxi:
if set(j) == set([i, i]):
match.append(i)
return match