def test_normal_modes(self):
coordinates = [[0.00000, 0.0000000, -0.0808819],
[-1.43262, 0.0000000, -1.2823700],
[1.43262, 0.0000000, -1.2823700]]
symbols = ['O', 'H', 'H']
normal_modes = [
[[0., 0., -0.075], [-0.381, -0., 0.593], [0.381, -0.,
0.593]], # mode 1
[[-0., -0., 0.044], [-0.613, -0., -0.35], [0.613, 0.,
-0.35]], # mode 2
[[-0.073, -0., -0.], [0.583, 0., 0.397], [0.583, 0., -0.397]]
] # mode 3
sym_modes_gs = SymmetryModes(group='c2v',
coordinates=coordinates,
modes=normal_modes,
symbols=symbols)
a1 = SymmetryBase(group='c2v', rep='A1')
a2 = SymmetryBase(group='c2v', rep='A2')
b1 = SymmetryBase(group='c2v', rep='B1')
b2 = SymmetryBase(group='c2v', rep='B2')
for i, ref in enumerate([a1, a1, b1]):
nm = sym_modes_gs.get_state_mode(i)
self.assertCountEqual(
np.round(nm.get_ir_representation(), decimals=2),
np.round(ref.get_ir_representation(), decimals=2))
def test_mo_symmetry(self):
mo_sym = [
SymmetryFunction('C2v', mo) for mo in self.molecular_orbitals
]
# print(mo_sym)
a1 = SymmetryBase(group='c2v', rep='A1')
a2 = SymmetryBase(group='c2v', rep='A2')
b1 = SymmetryBase(group='c2v', rep='B1')
b2 = SymmetryBase(group='c2v', rep='B2')
for mo, ref in zip(mo_sym, [a1, a1, b1, a1, b2, a1, b1]):
self.assertCountEqual(
np.round(mo.get_ir_representation(), decimals=6),
np.round(ref.get_ir_representation(), decimals=6))
def get_symmetry_wf(occupation_alpha, occupation_beta):
state_wf = SymmetryBase(group='D2h', rep='Ag')
for orbital_a, occupation in zip(molsym.mo_SOEVs_a, occupation_alpha):
if abs(occupation) > 0.1:
state_orb = SymmetryBase(group='D2h',
rep=pd.Series(np.array(orbital_a),
index=[ "E", "C2", "C2'", "C2''", "sh", "i", "sv", "sd"]))
state_wf = state_wf * state_orb
for orbital_b, occupation in zip(molsym.mo_SOEVs_a, occupation_beta):
if abs(occupation) > 0.1:
state_orb = SymmetryBase(group='D2h',
rep=pd.Series(np.array(orbital_b),
index=[ "E", "C2", "C2'", "C2''", "sh", "i", "sv", "sd"]))
state_wf = state_wf * state_orb
return state_wf
def test_algebra(self):
a1 = SymmetryBase(group='Td', rep='A1')
a2 = SymmetryBase(group='Td', rep='A2')
e = SymmetryBase(group='Td', rep='E')
t1 = SymmetryBase(group='Td', rep='T1')
t2 = SymmetryBase(group='Td', rep='T2')
prod_1 = e * e + 2 * a1
result_1 = 3 * a1 + a2 + e
prod_2 = t1 * t1
result_2 = a1 + e + t1 + t2
self.assertCountEqual(prod_1.get_ir_representation(),
result_1.get_ir_representation())
self.assertCountEqual(prod_2.get_ir_representation(),
result_2.get_ir_representation())
def test_functions(self):
a1 = SymmetryBase(group='Td', rep='A1')
a2 = SymmetryBase(group='Td', rep='A2')
e = SymmetryBase(group='Td', rep='E')
t1 = SymmetryBase(group='Td', rep='T1')
t2 = SymmetryBase(group='Td', rep='T2')
print('A1 . A1: ', dot(a1, a1))
self.assertAlmostEqual(dot(e, e), 4)
self.assertAlmostEqual(dot(t1, e), 0)
self.assertAlmostEqual(dot(t1, t1 + e), 9.0)
self.assertAlmostEqual(dot(t1, t1 + e, normalize=True), 0.6)
self.assertAlmostEqual(dot(t1 + e, t1 + e), 25.0)
self.assertAlmostEqual(dot(t1 + e, t1 + e, normalize=True), 1.0)
self.assertAlmostEqual(dot(0.6 * t1 + e, t1), 5.4)
self.assertAlmostEqual(dot(t1, t1, normalize=True), 1.0)
self.assertAlmostEqual(norm(t1 + e), 5.0)
self.assertAlmostEqual(norm(t1), 3.0)
self.assertAlmostEqual(norm(e), 2.0)
self.assertAlmostEqual(norm(a1), 1.0)
self.assertAlmostEqual(norm(a1 + a2 + e + t1 + t2), 10.0)
def get_orbital_state(orbital_soev):
state_orb = SymmetryBase(group='c2v',
rep=pd.Series(orbital_soev,
index=["E", "C2", "sv_xz",
"sd_yz"]))
return state_orb
def check_transition(transition):
if al.dot(transition, SymmetryBase(group='C2h', rep='Ag')) > 0.1:
return 'Allowed'
else:
return 'Forbidden'
cis_wf_0 = get_wf_symm(
cis_orbitals_sym,
alpha=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
beta=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0])
cis_wf_1 = get_wf_symm(
cis_orbitals_sym,
alpha=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
beta=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0])
cis_wf_2 = get_wf_symm(
cis_orbitals_sym,
alpha=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0],
beta=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0])
# print(cis_wf_0, cis_wf_1, cis_wf_2)
cis_dm = SymmetryBase(group='C2v', rep='B1') + \
SymmetryBase(group='C2v', rep='B2') + \
SymmetryBase(group='C2v', rep='A1')
def check_transition(transtion):
if al.dot(transtion, SymmetryBase(group='C2v', rep='A1')) > 0.1:
return 'Allowed'
else:
return 'Forbidden'
print('wf_0 -> wf_1: ', cis_wf_0 * cis_dm * cis_wf_1,
check_transition(cis_wf_0 * cis_dm * cis_wf_1))
print('wf_0 -> wf_2: ', cis_wf_0 * cis_dm * cis_wf_2,
check_transition(cis_wf_0 * cis_dm * cis_wf_2))
from posym import PointGroup, SymmetryBase
pg = PointGroup(group='C2h')
print('\nTest Point group table')
print(pg)
bu = SymmetryBase(group='C2h', rep='Bu')
bg = SymmetryBase('C2h', 'Bg')
ag = SymmetryBase('C2h', 'Ag')
print('\nTest symmetry object operation')
print('bu * bg:', 2 * bu * bg)
print('(bu + bg) * (bu + bu + ag):', (bu + bg) * (bu + bu + ag))
state1 = (bu + bg) * (bu + bu + ag)
print('\nTest symmetry object representation')
pg = PointGroup(group='Td')
print(pg)
bg = SymmetryBase('C2h', 'Bg')
a1 = SymmetryBase(group='Td', rep='A1')
a2 = SymmetryBase(group='Td', rep='A2')
e = SymmetryBase(group='Td', rep='E')
t1 = SymmetryBase(group='Td', rep='T1')
print('e*e + a1:', e * e + 2 * a1)
print('t1*t1:', t1 * t1)
pg = PointGroup(group='C2v')