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Changing rasci and tddft parsers
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@acebreiro
acebreiro committed Oct 31, 2024
1 parent 4b94769 commit fe4967e
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203 changes: 114 additions & 89 deletions pyqchem/parsers/parser_cis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def basic_cis(output):
# Molecule
data_dict['structure'] = read_input_structure(output)
n_atoms = data_dict['structure'].get_number_of_atoms()

# scf_energy
enum = output.find('Total energy in the final basis set')
try:
Expand Down Expand Up @@ -99,6 +99,7 @@ def basic_cis(output):
# old version of qchem (< 5.01)
state_cis_words = output_cis[m.end():].split()
mul = state_cis_words[13]
print(mul)
trans_mom = [float(mom) for mom in [state_cis_words[16],
state_cis_words[18],
state_cis_words[20]]]
Expand Down Expand Up @@ -175,95 +176,119 @@ def basic_cis(output):

data_dict['excited_states'] = excited_states

# Spin-Orbit coupling
initial = output.find('*********SPIN-ORBIT COUPLING JOB BEGINS HERE*********')
final = output.find('*********SOC CODE ENDS HERE*********')

data_interstate = {}
if initial > 0:
soc_section = output[initial:final]

def label_states(excited_states):
labels = []
ns = 1
nt = 1
for state in excited_states:
if state['multiplicity'].lower() == 'singlet':
labels.append('S{}'.format(ns))
ns += 1
elif state['multiplicity'].lower() == 'triplet':
labels.append('T{}'.format(nt))
nt += 1
else:
try:
m = float(state['multiplicity'])
if abs(m - 1) < 0.1:
labels.append('S{}'.format(ns))
ns += 1
if abs(m - 3) < 0.1:
labels.append('T{}'.format(nt))
nt += 1
state['multiplicity'] = m

except ValueError:
raise ParserError('basic_cis', 'State multiplicity error', output)

return labels, nt-1, ns-1

labels, n_triplet, n_singlet = label_states(excited_states)

for i, label in enumerate(labels):
data_interstate[(i+1, 0)] = {'1e_soc_mat': [0j, 0j, 0j], 'soc_units': 'cm-1'}
data_interstate[(0, i+1)] = {'1e_soc_mat': [0j, 0j, 0j], 'soc_units': 'cm-1'}
for j, label2 in enumerate(labels):
if (label[0] == 'S' or label2[0] == 'S') and (label[0] != label2[0]):
data_interstate[(i+1, j+1)] = {'1e_soc_mat': [[0j, 0j, 0j]], 'soc_units': 'cm-1'}
elif label[0] == 'T' and label2[0] == 'T':
data_interstate[(i+1, j+1)] = {'1e_soc_mat': [[0j, 0j, 0j], [0j, 0j, 0j], [0j, 0j, 0j]], 'soc_units': 'cm-1'}
elif label[0] == 'S' and label2[0] == 'S':
data_interstate[(i+1, j+1)] = {'1e_soc_mat': [[0j]], 'soc_units': 'cm-1'}
# Multiplicity mapping for singlets, triplets... where multiplicity is indicated as "S1", "T1" in SOC section

try:
test = float(data_dict['excited_states'][0]['multiplicity'])
except ValueError:
multiplicity_mapping = {'0': 0}
count_multiplicity = {'Singlet': 0, 'Triplet': 0, 'Quintet': 0, 'Heptet': 0}
for i, state in enumerate(data_dict['excited_states']):
count_multiplicity[state['multiplicity']] += 1
multiplicity_mapping.update({state['multiplicity'][0]+str(count_multiplicity[state['multiplicity']]): i+1})

# SPIN-ORBIT COUPLINGS

done_interstate_soc = bool(output.find('SPIN-ORBIT COUPLING JOB USING WIGNER–ECKART THEOREM BEGINS HERE')+1)

if done_interstate_soc:
ini_section = output.find('SPIN-ORBIT COUPLING JOB USING WIGNER–ECKART THEOREM BEGINS HERE')
end_section = output.find('SPIN-ORBIT COUPLING JOB ENDS HERE')
soc_section = output[ini_section: end_section]
section_sizes = search_bars(soc_section, bar_type=r'\*'*50+'\n')

interstate_dict = {}

for i, m in enumerate(re.finditer('State A:', soc_section)):
section_length = section_sizes[i+1] - section_sizes[i]
section_pair = soc_section[m.start():m.start() + section_length]

lines = section_pair.split('\n')

try: # In doublets, where states can be taken as integers (0, 1..)
state_a = int(lines[0].split()[-1])
state_b = int(lines[1].split()[-1])

except ValueError: # In singlets, where states cannot be taken as integers (S1, T1...)
if 'Ground state' in lines[0]:
state_a = 0
else:
raise ParserError('basic_cis', 'State multiplicity error', output)

for i, label in enumerate(labels):
for k2, ms2 in enumerate([-1, 0, 1]):
for j, label2 in enumerate(labels):
if label[0] == 'T':
for k, ms in enumerate([-1, 0, 1]):
enum = soc_section.find('SOC between the {} (ms={}) state and excited triplet states (ms={})'.format(label, ms2, ms))
for line in soc_section[enum:enum+80*(n_triplet+1)].split('\n'):
if len(line.split()) == 0:
break
if line.split()[0] == '{}(ms={})'.format(label2, ms):
data_interstate[(i+1, j+1)]['1e_soc_mat'][k2][k] = _list_to_complex(line.split()[1:4])
data_interstate[(i+1, j+1)]['1e_soc_mat'][k][k2] = _list_to_complex(line.split()[1:4])
data_interstate[(j+1, i+1)]['1e_soc_mat'][k2][k] = _list_to_complex(line.split()[1:4])
data_interstate[(j+1, i+1)]['1e_soc_mat'][k][k2] = _list_to_complex(line.split()[1:4])
break

elif label[0] == 'S':
for k, ms in enumerate([-1, 0, 1]):
enum = soc_section.find('SOC between the {} state and excited triplet states (ms={})'.format(label, ms))
for line in soc_section[enum:enum+80*(n_triplet+1)].split('\n'):
if len(line.split()) == 0:
break
if line.split()[0] == '{}(ms={})'.format(label2, ms):
data_interstate[(i+1, j+1)]['1e_soc_mat'][0][k] = _list_to_complex(line.split()[1:4])
data_interstate[(j+1, i+1)]['1e_soc_mat'][0][k] = _list_to_complex(line.split()[1:4])
break
else:
raise ParserError('basic_cis', 'SOC reading error', output)

enum = soc_section.find('SOC between the singlet ground state and excited triplet states (ms={})'.format(ms2))
for line in soc_section[enum:enum+80*(n_triplet+1)].split('\n'):
if len(line.split()) == 0:
break
if line.split()[0] == '{}(ms={})'.format(label, ms2):
data_interstate[(i+1, 0)]['1e_soc_mat'][k2] = _list_to_complex(line.split()[1:4])
data_interstate[(0, i+1)]['1e_soc_mat'][k2] = _list_to_complex(line.split()[1:4])
break

data_dict['interstate_properties'] = data_interstate
state_a = multiplicity_mapping[lines[0].split()[-1]]
state_b = multiplicity_mapping[lines[1].split()[-1]]

pair_dict = {}
for j, line in enumerate(lines):
if 'Ket state' in line and state_a == 0 and 'scf_multiplicity' not in data_dict:
data_dict['scf_multiplicity'] = int(float(line.split()[5]))

if 'WARNING! Clebsh-Gordon coefficient is too small' in line:
pair_dict['1e_socc'] = 0
pair_dict['1e_soc_mat'] = [0]
pair_dict['mf_socc'] = 0
pair_dict['mf_soc_mat'] = [0]

if 'One-electron SO (cm-1)' in line:
soc_keyword = '1e_socc'
soc_matrix_keyword = '1e_soc_mat'
elif 'Mean-field SO (cm-1)' in line:
soc_keyword = 'mf_socc'
soc_matrix_keyword = 'mf_soc_mat'

if 'SOCC' in line:
pair_dict[soc_keyword] = float(line.split()[2])

if 'Actual matrix elements:' in line:
soc_matrix = []
for soc_line in lines[j:]:

if '<Sz=' in soc_line:
matches = re.findall(r"\(([^)]+)\)", soc_line)
soc_matrix.append([list(map(float, match.split(','))) for match in matches])

if r'_'*30 in soc_line:
break

pair_dict[soc_matrix_keyword] = soc_matrix

interstate_dict[(state_a, state_b)] = pair_dict

data_dict['interstate_socs'] = interstate_dict

# ANGULAR MOMENTUMS

done_interstate_angmom = bool(output.find(' STATE-TO-STATE TRANSITION ANGULAR MOMENTS')+1)

if done_interstate_angmom:
ini_section = output.find('STATE-TO-STATE TRANSITION ANGULAR MOMENTS')
end_section = output.find('END OF TRANSITION MOMENT CALCULATION')
angmom_section = output[ini_section: end_section]
section_sizes = search_bars(angmom_section, bar_type='Transition Angular Moments') # r'-'*40)

interstate_dict = {}

for i, m in enumerate(re.finditer('Transition Angular Moments', angmom_section)):
try:
section_length = section_sizes[i+1] - section_sizes[i]
except IndexError:
section_length = len(angmom_section) - section_sizes[i]
section_pair = angmom_section[m.start():m.start() + section_length]

lines = section_pair.split('\n')

for line in lines[4:]:
if r'-'*40 in line:
break

pair_dict = {}
state_a = int(line.split()[0])
state_b = int(line.split()[1])

pair_dict['angular_momentum'] = [float(j) for j in line.split()[2:-1]]
pair_dict['length'] = float(line.split()[-1])

interstate_dict[(state_a, state_b)] = pair_dict

data_dict['interstate_angmom'] = interstate_dict

# diabatization
initial = output.find('Localization Code for CIS excited states')
Expand Down
13 changes: 12 additions & 1 deletion pyqchem/parsers/parser_rasci.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,10 @@ def parser_rasci(output):
end_section = search_bars(output, from_position=ini_section, bar_type=r'\*\*\*')[0]
dimension_section = output[ini_section: end_section]

enum = dimension_section.find('Active Elec')
active_elec = int(dimension_section[enum: enum+50].split()[2])
enum = dimension_section.find('Active Orb')
active_orb = int(dimension_section[enum: enum+50].split()[2])
enum = dimension_section.find('Doubly Occ')
doubly_occ = int(dimension_section[enum: enum+50].split()[3])
enum = dimension_section.find('Doubly Vir')
Expand All @@ -124,7 +128,9 @@ def parser_rasci(output):
enum = dimension_section.find('Particle configurations')
particle_conf = int(dimension_section[enum: enum+50].split()[2])

rasci_dimensions = {'doubly_occupied': doubly_occ,
rasci_dimensions = {'active_elec': active_elec,
'active_orb': active_orb,
'doubly_occupied': doubly_occ,
'doubly_virtual': doubly_vir,
'frozen_occupied': frozen_occ,
'frozen_virtual': frozen_vir,
Expand Down Expand Up @@ -205,6 +211,10 @@ def parser_rasci(output):
exc_energy_units = section_state[enum: enum + 30].split()[2].strip('(').strip(')')
exc_energy = float(section_state[enum: enum + 80].split()[4])

# symmetry
enum = section_state.find('State symmetry')
state_symmetry = section_state[enum: enum + 30].split()[2]

# multiplicity
n_multi = section_state.find('<S^2>')
multi_data = section_state[n_multi:n_multi + 30].split(':')[1]
Expand Down Expand Up @@ -287,6 +297,7 @@ def parser_rasci(output):
'total_energy_units': tot_energy_units,
'excitation_energy': exc_energy,
'excitation_energy_units': exc_energy_units,
'symmetry': state_symmetry,
'multiplicity': state_multiplicity,
'dipole_moment': dipole_mom,
'transition_moment': trans_mom,
Expand Down
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