def _basis_offset_for_atoms(atoms, basis_tab):
basoff = [0]
n = 0
for at in atoms:
symb = _symbol(at[0])
if symb in basis_tab:
bas0 = basis_tab[symb]
else:
bas0 = basis_tab[_rm_digit(symb)]
for b in bas0:
angl = b[0]
n += _num_contract(b) * (angl * 2 + 1)
basoff.append(n)
return n, basoff
def _basis_offset_for_atoms(atoms, basis_tab):
basoff = [0]
n = 0
for at in atoms:
symb = _symbol(at[0])
if symb in basis_tab:
bas0 = basis_tab[symb]
else:
bas0 = basis_tab[_rm_digit(symb)]
for b in bas0:
angl = b[0]
n += _num_contract(b) * (angl*2+1)
basoff.append(n)
return n, basoff
def _make_mindo_mol(mol):
assert (not mol.has_ecp())
def make_sto_6g(n, l, zeta):
es = mopac_param.gexps[(n, l)]
cs = mopac_param.gcoefs[(n, l)]
return [l] + [(e * zeta**2, c) for e, c in zip(es, cs)]
def principle_quantum_number(charge):
if charge < 3:
return 1
elif charge < 10:
return 2
elif charge < 18:
return 3
else:
return 4
mindo_mol = copy.copy(mol)
atom_charges = mindo_mol.atom_charges()
atom_types = set(atom_charges)
basis_set = {}
for charge in atom_types:
n = principle_quantum_number(charge)
l = 0
sto_6g_function = make_sto_6g(n, l, mopac_param.ZS3[charge])
basis = [sto_6g_function]
if charge > 2: # include p functions
l = 1
sto_6g_function = make_sto_6g(n, l, mopac_param.ZP3[charge])
basis.append(sto_6g_function)
basis_set[_symbol(int(charge))] = basis
mindo_mol.basis = basis_set
z_eff = mopac_param.CORE[atom_charges]
mindo_mol.nelectron = int(z_eff.sum() - mol.charge)
mindo_mol.build(0, 0)
return mindo_mol
