def test_mol_basis_data(self, basis_data):
"""Test that correct basis set parameters are generated for a given molecule represented as
a list of atoms."""
basis, symbols, n_ref, params_ref = basis_data
n_basis, params = mol_basis_data(basis, symbols)
assert n_basis == n_ref
assert np.allclose(params, params_ref)
def __init__(
self,
symbols,
coordinates,
charge=0,
mult=1,
basis_name="sto-3g",
l=None,
alpha=None,
coeff=None,
):
if basis_name not in ["sto-3g", "STO-3G"]:
raise ValueError("Currently, the only supported basis set is 'sto-3g'.")
if set(symbols) - set(atomic_numbers):
raise ValueError(f"Atoms in {set(symbols) - set(atomic_numbers)} are not supported.")
self.symbols = symbols
self.coordinates = coordinates
self.charge = charge
self.mult = mult
self.basis_name = basis_name
self.n_basis, self.basis_data = mol_basis_data(self.basis_name, self.symbols)
if l is None:
l = [i[0] for i in self.basis_data]
if alpha is None:
alpha = [pnp.array(i[1], requires_grad=False) for i in self.basis_data]
if coeff is None:
coeff = [pnp.array(i[2], requires_grad=False) for i in self.basis_data]
r = list(
itertools.chain(
*[[self.coordinates[i]] * self.n_basis[i] for i in range(len(self.n_basis))]
)
)
self.l = l
self.alpha = alpha
self.coeff = coeff
self.r = r
self.basis_set = [
BasisFunction(self.l[i], self.alpha[i], self.coeff[i], self.r[i]) for i in range(len(l))
]
self.n_orbitals = len(self.l)
self.nuclear_charges = [atomic_numbers[s] for s in self.symbols]
self.n_electrons = sum(np.array(self.nuclear_charges)) - self.charge