def get_symmetry_le(electronic_structure,
data_rasci,
fragment_atoms=(0),
tol=0.1,
group='D2h'):
# This only works for singlets on close shell calculations
types = classify_diabatic_states_of_fragment(
data_rasci['diabatization']['diabatic_states'],
fragment_atoms,
tol=0.1)
functions_range = get_basis_functions_ranges_by_atoms(
electronic_structure['basis'], atoms_range=fragment_atoms)
coordinates_frag = np.array(
electronic_structure['structure'].get_coordinates())[fragment_atoms]
labels_frag = electronic_structure['structure'].get_symbols(
)[fragment_atoms]
inertia_moments, inertia_axis = get_inertia(
Structure(coordinates=coordinates_frag, symbols=labels_frag))
center_frag, normal_frag = get_plane(coordinates_frag)
# print(np.array(inertia_axis))
# print(inertia_moments)
# print(inertia_axis[0])
# print(inertia_axis[1])
# print(inertia_axis[2])
if 'LE' in types:
indices = [i for i, x in enumerate(types) if x == "LE"]
symmetry_labels = []
for index in indices:
print('\nLE state found at diabat {}!'.format(index + 1))
coefficients = electronic_structure['nato_coefficients_multi'][
index + 1]
occupation = electronic_structure['nato_occupancies_multi'][index +
1]
overlap_matrix = np.array(electronic_structure['overlap'])
functions_indices = _indices_from_ranges(functions_range)
overlap_matrix = np.array([
ovm[functions_indices]
for ovm in overlap_matrix[functions_indices]
])
c_alpha = np.array(coefficients['alpha'])
oc_alpha = np.array(occupation['alpha'])
orbitals = []
alpha = 0
beta = 0
coefficients_new = {'alpha': [], 'beta': []}
for i, (va, o) in enumerate(zip(c_alpha, oc_alpha)):
va_frag = va[functions_indices]
frag_dot = np.dot(va_frag, np.dot(overlap_matrix, va_frag))
if np.abs(frag_dot - 0.5) > tol:
if frag_dot > 0.5:
orbitals.append((i, np.round(o)))
orbital = np.zeros(len(c_alpha))
for j, val in zip(functions_indices, va_frag):
orbital[j] = val / np.sqrt(frag_dot)
if np.abs(o - 1) < tol and o < 2 - tol:
if alpha == beta:
alpha += 1
coefficients_new['alpha'].append(list(orbital))
else:
beta += 1
coefficients_new['beta'].append(list(orbital))
else:
pass
if alpha == beta:
multiplicity = 1
else:
multiplicity = 3
n_electrons = alpha + beta
try:
# This only works for singlets
molsym = get_wf_symmetry(electronic_structure['structure'],
electronic_structure['basis'],
coefficients_new,
center=center_frag,
orientation=inertia_axis[0],
orientation2=inertia_axis[1],
group=group)
#molsym.print_alpha_mo_IRD()
#molsym.print_beta_mo_IRD()
molsym.print_wf_mo_IRD()
symmetry_labels.append(molsym.IRLab[np.argmax(molsym.wf_IRd)])
except:
pass
return symmetry_labels
return None
# get orbital type
orbital_types = get_orbital_classification(electronic_structure,
center=[0.0, 0.0, 0.0],
orientation=[0.0, 0.0, 1.0])
# print results
print(' {:5} {:5} {:5}'.format('num', 'type', 'overlap'))
for i, ot in enumerate(orbital_types):
print('{:5}: {:5} {:5.3f}'.format(i + 1, ot[0], ot[1]))
# print(molecule.alpha_electrons, molecule.beta_electrons)
print('\nAdiabatic states\n--------------------')
print_excited_states(parsed_data['excited_states'], include_conf_rasci=True)
inertia_moments, inertia_axis = get_inertia(electronic_structure['structure'])
#print(im)
#print(ivec[0])
#print(ivec[1])
#print(ivec[2])
print('\nInertia\n----------')
print(inertia_moments)
print(np.array(inertia_axis))
print(electronic_structure['structure'])
symmetry_measures = get_state_symmetry(electronic_structure,
parsed_data['excited_states'],
center=[0, 0, 0],
orientation=inertia_axis[0],