mo_coeff_f1 = _set_zero_to_coefficients(
electronic_structure['basis'],
electronic_structure['nato_coefficients_multi'][1], range_f2)
# get symmetry classification
electronic_structure['coefficients'] = mo_coeff_f1
electronic_structure['mo_energies'] = electronic_structure['nato_occupancies']
# save test fchk file with new coefficients
open('test_f1.fchk', 'w').write(build_fchk(electronic_structure))
# get plane from coordinates
coordinates_f1 = np.array(
electronic_structure['structure'].get_coordinates())[range_f1]
center_f1, normal_f1 = get_plane(coordinates_f1)
mulliken = output['diabatization']['mulliken_analysis'][1]
a = np.sum(np.array(mulliken['attach'])[range_f1])
print(a)
print(electronic_structure['overlap'])
print(mulliken)
def orbital_localization(coefficients, overlap_matrix):
for a_orbital, b_orbital in zip(coefficients['alpha'],
coefficients['beta']):
a_dot = np.dot(np.dot(a_orbital, overlap_matrix), a_orbital)
b_dot = np.dot(np.dot(b_orbital, overlap_matrix), b_orbital)
basis='6-311(2+,2+)G**',
ras_roots=10,
ras_do_hole=False,
ras_do_part=False)
# get data from Q-Chem calculation
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
parser=parser_rasci,
store_full_output=True)
# get plane from coordinates to determine orientation using the plane of the molecule
coordinates_mat = np.array(electronic_structure['structure'].get_coordinates())
center, normal = get_plane(coordinates_mat)
symmetry_measures = get_state_symmetry(
electronic_structure,
output['excited_states'],
center=center, # if not provided use center of electronic charge
orientation=normal, # if not provided auto-search best orientation
group=point_group,
extra_print=False)
energies = [state['excitation_energy'] for state in output['excited_states']]
print('Symmetry of RASCI excited states\n--------------------------------')
for i, (energy, state) in enumerate(zip(energies, symmetry_measures)):
print('{:2} {:6} {:5.3f}'.format(i + 1, state[0], state[1]) +
' {:5.3f} eV'.format(energy))
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
orientation=(1, 0, 0),
orientation2=(0, 1, 0),
)
# Analysis of diabatic states to use in diabatization
print('\nSymmetry of the electronic states of the dimer')
list_diabatic = []
for i, state in enumerate(parsed_data['excited_states']):
sym_lab = symmetry_measures[i][0]
energy = state['excitation_energy']
print('State {}: {:3}'.format(i+1, sym_lab))
range_frag = list(range(0, 6))
coordinates_frag = ee['structure'].get_coordinates(fragment=range_frag)
center_frag, normal_frag = get_plane(coordinates_frag)
electronic_structure_frag = crop_electronic_structure(ee, range_frag, renormalize=True)
# save test fchk file with new coefficients
write_to_fchk(electronic_structure_frag, filename='fragment.fchk')
molsym = get_wf_symmetry(electronic_structure_frag['structure'],
electronic_structure_frag['basis'],
electronic_structure_frag['coefficients'],
center=center_frag,
orientation=(1, 0, 0),
orientation2=(0, 1, 0),
group='D2h')
molsym.print_alpha_mo_IRD()
