def rotational_symmetry_number(mol):
'''Number of unique orientations of the rigid molecule that only
interchange identical atoms.
Source http://cccbdb.nist.gov/thermo.asp (search "symmetry number")
'''
from pyscf import symm
group = symm.detect_symm(mol._atom)[0]
if group in ['SO3', 'C1', 'Ci', 'Cs', 'Coov']:
sigma = 1
elif group == 'Dooh':
sigma = 2
elif group in ['T', 'Td']:
sigma = 12
elif group == 'Oh':
sigma = 24
elif group == 'Ih':
sigma = 60
elif group[0] == 'C': # 'Cn', 'Cnv', 'Cnh'
sigma = int(''.join([x for x in group if x.isdigit()]))
elif group[0] == 'D': # 'Dn', 'Dnd', 'Dnh'
sigma = 2 * int(''.join([x for x in group if x.isdigit()]))
elif group[0] == 'S': # 'Sn'
sigma = int(''.join([x for x in group if x.isdigit()])) / 2
else:
raise RuntimeError("symmetry group: " + group)
return sigma
def get_so(atoms, basis):
atoms = gto.mole.format_atom(atoms)
gpname, origin, axes = symm.detect_symm(atoms)
gpname, axes = symm.subgroup(gpname, axes)
atoms = gto.mole.format_atom(atoms, origin, axes)
eql_atoms = symm.symm_identical_atoms(gpname, atoms)
so = symm.basis.symm_adapted_basis(gpname, eql_atoms, atoms, basis)[0]
n = 0
for c in so:
if c.size > 0:
n += c.shape[1]
return n, so
def get_so(atoms, basis):
atoms = gto.mole.format_atom(atoms)
gpname, origin, axes = symm.detect_symm(atoms)
gpname, axes = symm.subgroup(gpname, axes)
atoms = gto.mole.format_atom(atoms, origin, axes)
eql_atoms = symm.symm_identical_atoms(gpname, atoms)
so = symm.basis.symm_adapted_basis(gpname, eql_atoms, atoms, basis)[0]
n = 0
for c in so:
if c.size > 0:
n += c.shape[1]
return n, so
def get_so(atoms, basis, cart=False):
atoms = gto.mole.format_atom(atoms)
gpname, origin, axes = symm.detect_symm(atoms)
gpname, axes = symm.subgroup(gpname, axes)
atoms = gto.mole.format_atom(atoms, origin, axes, 'Bohr')
mol = gto.M(atom=atoms, basis=basis, unit='Bohr', spin=None)
mol.cart = cart
so = symm.basis.symm_adapted_basis(mol, gpname)[0]
n = 0
for c in so:
if c.size > 0:
n += c.shape[1]
assert(n == mol.nao_nr())
return n, so
def get_so(atoms, basis, cart=False):
atoms = gto.mole.format_atom(atoms)
gpname, origin, axes = symm.detect_symm(atoms)
gpname, axes = symm.subgroup(gpname, axes)
atoms = gto.mole.format_atom(atoms, origin, axes)
try:
mol = gto.M(atom=atoms, basis=basis)
except RuntimeError:
mol = gto.M(atom=atoms, basis=basis, spin=1)
mol.cart = cart
so = symm.basis.symm_adapted_basis(mol, gpname)[0]
n = 0
for c in so:
if c.size > 0:
n += c.shape[1]
assert(n == mol.nao_nr())
return n, so