def test_rotor_symmetry(self):
"""Test that ARC automatically determines a correct rotor symmetry"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'OOC1CCOCO1.out') # symmetry = 1; min at -10 o
path2 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'H2O2.out') # symmetry = 1
path3 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'N2O3.out') # symmetry = 2
path4 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'sBuOH.out') # symmetry = 3
path5 = os.path.join(arc_path, 'arc', 'testing', 'rotor_scans',
'CH3C(O)O_FreeRotor.out') # symmetry = 6
symmetry1, _ = determine_rotor_symmetry(rotor_path=path1,
label='label',
pivots=[3, 4])
symmetry2, _ = determine_rotor_symmetry(rotor_path=path2,
label='label',
pivots=[3, 4])
symmetry3, _ = determine_rotor_symmetry(rotor_path=path3,
label='label',
pivots=[3, 4])
symmetry4, _ = determine_rotor_symmetry(rotor_path=path4,
label='label',
pivots=[3, 4])
symmetry5, _ = determine_rotor_symmetry(rotor_path=path5,
label='label',
pivots=[3, 4])
self.assertEqual(symmetry1, 1)
self.assertEqual(symmetry2, 1)
self.assertEqual(symmetry3, 2)
self.assertEqual(symmetry4, 3)
self.assertEqual(symmetry5, 6)
def check_scan_quality(spc):
"""
A helper function used to get the status of rotor scans
"""
for rotor in spc['rotors_dict'].values():
path = rotor['scan_path']
if path:
scan_args = parse_scan_args(path)
energies, _ = parse_1d_scan_energies(path)
invalid, reason, _, actions = scan_quality_check(
spc['label'],
pivots=rotor['scan'][1:-1],
energies=energies,
scan_res=scan_args['step_size'],
log_file=path)
else:
rotor['success'] = False
rotor['invalidation_reason'] = 'Unknown'
continue
if not invalid:
rotor['success'] = True
rotor['symmetry'] = determine_rotor_symmetry(
label=spc['label'],
pivots=rotor['scan'][1:3],
energies=energies)[0]
continue
if 'change conformer' in actions:
print(spc['label'] +
': has a bad conformer orientation according to ' +
str(rotor['scan']))
xyz = xyz_to_xyz_file_format(actions['change conformer'])
return {'label': spc['label'], 'change conformer': xyz}
if 'barrier' in reason:
rotor['success'] = False
rotor['invalidation_reason'] = reason
continue
# Otherwise need to come up with troubleshooting methods
species_scan_lists = [rotor['scan']]
scan_trsh, scan_res = trsh_scan_job(spc['label'],
scan_args['step_size'],
rotor['scan'], species_scan_lists,
actions, path)
rotor['trsh_methods'] = [{
'scan_trsh': scan_trsh,
'scan_res': scan_res
}]
rotor['archived'].append(rotor['scan_path'])
spc['scan'].remove(rotor['scan_path'])
return spc
def _generate_arkane_species_file(self, species):
"""
A helper function for generating the Arkane species file.
Assigns the input file path to species.arkane_file.
Args:
species (ARCSpecies): The species to process.
Returns:
str: The Arkane output path.
"""
folder_name = 'rxns' if species.is_ts else 'Species'
output_path = os.path.join(self.project_directory, 'output', folder_name, species.label, 'arkane')
if not os.path.isdir(output_path):
os.makedirs(output_path)
if species.yml_path is not None:
species.arkane_file = species.yml_path
return output_path
species.determine_symmetry()
try:
sp_path = self.output[species.label]['composite']
except KeyError:
try:
sp_path = self.output[species.label]['sp']
except KeyError:
raise SchedulerError('Could not find path to sp calculation for species {0}'.format(
species.label))
if species.number_of_atoms == 1:
freq_path = sp_path
opt_path = sp_path
else:
freq_path = self.output[species.label]['freq']
opt_path = self.output[species.label]['freq']
rotors, rotors_description = '', ''
if any([i_r_dict['success'] for i_r_dict in species.rotors_dict.values()]):
rotors = '\n\nrotors = ['
rotors_description = '1D rotors:\n'
for i in range(species.number_of_rotors):
pivots = str(species.rotors_dict[i]['pivots'])
scan = str(species.rotors_dict[i]['scan'])
if species.rotors_dict[i]['success']:
rotor_path = species.rotors_dict[i]['scan_path']
rotor_type = determine_rotor_type(rotor_path)
top = str(species.rotors_dict[i]['top'])
try:
rotor_symmetry, max_e = determine_rotor_symmetry(rotor_path, species.label, pivots)
except RotorError:
logger.error('Could not determine rotor symmetry for species {0} between pivots {1}.'
' Setting the rotor symmetry to 1, which is probably WRONG.'.format(
species.label, pivots))
rotor_symmetry = 1
max_e = None
max_e = ', max scan energy: {0:.2f} kJ/mol'.format(max_e) if max_e is not None else ''
free = ' (set as a FreeRotor)' if rotor_type == 'FreeRotor' else ''
rotors_description += 'pivots: ' + str(pivots) + ', dihedral: ' + str(scan) +\
', rotor symmetry: ' + str(rotor_symmetry) + max_e + free + '\n'
if rotor_type == 'HinderedRotor':
rotors += input_files['arkane_hindered_rotor'].format(rotor_path=rotor_path, pivots=pivots,
top=top, symmetry=rotor_symmetry)
elif rotor_type == 'FreeRotor':
rotors += input_files['arkane_free_rotor'].format(rotor_path=rotor_path, pivots=pivots,
top=top, symmetry=rotor_symmetry)
if i < species.number_of_rotors - 1:
rotors += ',\n '
else:
rotors_description += '* Invalidated! pivots: ' + str(pivots) + ', dihedral: ' + str(scan) +\
', invalidation reason: ' + species.rotors_dict[i]['invalidation_reason'] +\
'\n'
rotors += ']'
species.long_thermo_description += rotors_description + '\n'
# write the Arkane species input file
input_file_path = os.path.join(self.project_directory, 'output', folder_name, species.label,
'{0}_arkane_input.py'.format(species.label))
input_file = input_files['arkane_input_species']
if self.use_bac and not species.is_ts:
logger.info('Using the following BAC for {0}: {1}'.format(species.label, species.bond_corrections))
bonds = 'bonds = {0}\n\n'.format(species.bond_corrections)
else:
logger.debug('NOT using BAC for {0}'.format(species.label))
bonds = ''
input_file = input_file.format(bonds=bonds, symmetry=species.external_symmetry,
multiplicity=species.multiplicity, optical=species.optical_isomers,
sp_level=self.sp_level, sp_path=sp_path, opt_path=opt_path,
freq_path=freq_path, rotors=rotors)
with open(input_file_path, 'wb') as f:
f.write(input_file)
species.arkane_file = input_file_path
return output_path
def generate_arkane_species_file(self,
species: Type[ARCSpecies],
bac_type: Optional[str],
) -> Optional[str]:
"""
A helper function for generating an Arkane Python species file.
Assigns the path of the generated file to the species.arkane_file attribute.
Args:
species (ARCSpecies): The species to process.
bac_type (str): The bond additivity correction type. 'p' for Petersson- or 'm' for Melius-type BAC.
``None`` to not use BAC.
Returns:
str: The path to the species arkane folder (Arkane's default output folder).
"""
folder_name = 'rxns' if species.is_ts else 'Species'
species_folder_path = os.path.join(self.output_directory, folder_name, species.label)
arkane_output_path = os.path.join(species_folder_path, 'arkane')
if not os.path.isdir(arkane_output_path):
os.makedirs(arkane_output_path)
if species.yml_path is not None:
species.arkane_file = species.yml_path
return arkane_output_path
species.determine_symmetry()
sp_path = self.output_dict[species.label]['paths']['composite'] \
or self.output_dict[species.label]['paths']['sp']
if species.number_of_atoms == 1:
freq_path = sp_path
opt_path = sp_path
else:
freq_path = self.output_dict[species.label]['paths']['freq']
opt_path = self.output_dict[species.label]['paths']['freq']
return_none_text = None
if not sp_path:
return_none_text = 'path to the sp calculation'
if not freq_path:
return_none_text = 'path to the freq calculation'
if not os.path.isfile(freq_path):
return_none_text = f'the freq file in path {freq_path}'
if not os.path.isfile(sp_path):
return_none_text = f'the freq file in path {sp_path}'
if return_none_text is not None:
logger.error(f'Could not find {return_none_text} for species {species.label}. Not calculating properties.')
return None
rotors, rotors_description = '', ''
if species.rotors_dict is not None and any([i_r_dict['pivots'] for i_r_dict in species.rotors_dict.values()]):
rotors = '\n\nrotors = ['
rotors_description = '1D rotors:\n'
for i in range(species.number_of_rotors):
pivots = str(species.rotors_dict[i]['pivots'])
scan = str(species.rotors_dict[i]['scan'])
if species.rotors_dict[i]['success']:
rotor_path = species.rotors_dict[i]['scan_path']
rotor_type = determine_rotor_type(rotor_path)
top = str(species.rotors_dict[i]['top'])
try:
rotor_symmetry, max_e, _ = determine_rotor_symmetry(species.label, pivots, rotor_path)
except RotorError:
logger.error(f'Could not determine rotor symmetry for species {species.label} between '
f'pivots {pivots}. Setting the rotor symmetry to 1, '
f'this could very well be WRONG.')
rotor_symmetry = 1
max_e = None
scan_trsh = ''
if 'trsh_methods' in species.rotors_dict[i]:
scan_res = 360
for scan_trsh_method in species.rotors_dict[i]['trsh_methods']:
if 'scan_trsh' in scan_trsh_method and len(scan_trsh) < len(scan_trsh_method['scan_trsh']):
scan_trsh = scan_trsh_method['scan_trsh']
if 'scan_res' in scan_trsh_method and scan_res > scan_trsh_method['scan_res']:
scan_res = scan_trsh_method['scan_res']
scan_trsh = f'Troubleshot with the following constraints and {scan_res} degrees ' \
f'resolution:\n{scan_trsh}' if scan_trsh else ''
max_e = f', max scan energy: {max_e:.2f} kJ/mol' if max_e is not None else ''
free = ' (set as a FreeRotor)' if rotor_type == 'FreeRotor' else ''
rotors_description += f'pivots: {pivots}, dihedral: {scan}, ' \
f'rotor symmetry: {rotor_symmetry}{max_e}{free}\n{scan_trsh}'
if rotor_type == 'HinderedRotor':
rotors += input_files['arkane_hindered_rotor'].format(rotor_path=rotor_path,
pivots=pivots,
top=top,
symmetry=rotor_symmetry)
elif rotor_type == 'FreeRotor':
rotors += input_files['arkane_free_rotor'].format(rotor_path=rotor_path,
pivots=pivots,
top=top,
symmetry=rotor_symmetry)
if i < species.number_of_rotors - 1:
rotors += ',\n '
else:
rotors_description += f'* Invalidated! pivots: {pivots}, dihedral: {scan}, ' \
f'invalidation reason: {species.rotors_dict[i]["invalidation_reason"]}\n'
rotors += ']'
if 'rotors' not in species.long_thermo_description:
species.long_thermo_description += rotors_description + '\n'
# write the Arkane species input file
bac_txt = '' if bac_type is not None else '_no_BAC'
input_file_path = os.path.join(species_folder_path, f'{species.label}_arkane_input{bac_txt}.py')
input_file = input_files['arkane_input_species'] if 'sp_sol' not in self.output_dict[species.label]['paths'] \
else input_files['arkane_input_species_explicit_e']
if bac_type is not None and not species.is_ts:
logger.info(f'Using the following BAC (type {bac_type}) for {species.label}: {species.bond_corrections}')
bonds = f'bonds = {species.bond_corrections}\n\n'
else:
logger.debug(f'NOT using BAC for {species.label}')
bonds = ''
if 'sp_sol' not in self.output_dict[species.label]['paths']:
input_file = input_file.format(bonds=bonds,
symmetry=species.external_symmetry,
multiplicity=species.multiplicity,
optical=species.optical_isomers,
sp_path=sp_path,
opt_path=opt_path,
freq_path=freq_path,
rotors=rotors)
else:
# e_elect = e_original + sp_e_sol_corrected - sp_e_uncorrected
original_log = ess_factory(self.output_dict[species.label]['paths']['sp'])
e_original = original_log.load_energy()
e_sol_log = ess_factory(self.output_dict[species.label]['paths']['sp_sol'])
e_sol = e_sol_log.load_energy()
e_no_sol_log = ess_factory(self.output_dict[species.label]['paths']['sp_no_sol'])
e_no_sol = e_no_sol_log.load_energy()
e_elect = (e_original + e_sol - e_no_sol) / (constants.E_h * constants.Na) # convert J/mol to Hartree
logger.info(f'\nSolvation correction scheme for {species.label}:\n'
f'Original electronic energy: {e_original * 0.001} kJ/mol\n'
f'Solvation correction: {(e_sol - e_no_sol) * 0.001} kJ/mol\n'
f'New electronic energy: {(e_original + e_sol - e_no_sol) * 0.001} kJ/mol\n\n')
print(f'e_elect final: {(e_original + e_sol - e_no_sol) * 0.001} kJ/mol\n\n')
input_file = input_files['arkane_input_species_explicit_e']
input_file = input_file.format(bonds=bonds,
symmetry=species.external_symmetry,
multiplicity=species.multiplicity,
optical=species.optical_isomers,
sp_level=self.sp_level,
e_elect=e_elect,
opt_path=opt_path,
freq_path=freq_path,
rotors=rotors)
if freq_path:
with open(input_file_path, 'w') as f:
f.write(input_file)
species.arkane_file = input_file_path
else:
species.arkane_file = None
return arkane_output_path