def _mod_class(class_typ, rxn_info):
""" Create the object containing the full description of the
reaction class, including its type, spin state, and whether
it is a radical-radical combination.
:param class_typ: reaction class type
:type class_typ: str
:param rxn_info: ???
:tpye rxn_info: ???
"""
# Set the spin of the reaction to high/low
_fake_class = (class_typ, '', '', False)
if automol.par.need_spin_designation(_fake_class):
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
_spin = 'high-spin' if ts_mul == high_mul else 'low-spin'
else:
_spin = ''
# Determine if it iss intersystem crossing
# rxn_muls = rinfo.value(rxn_info, 'mult')
# is_isc = automol.reac.intersystem_crossing(rxn_muls)
return automol.par.reaction_class_from_data(
class_typ, _spin, rinfo.radrad(rxn_info), False)
def skip_task(tsk, spc_dct, spc_name, thy_dct, es_keyword_dct, save_prefix):
""" Determine if an electronic structure task should be skipped based on
various parameters.
:param spc_dct: species dictionary
:type spc_dct: dictionary
:param spc_name: name of species
:type spc_name: string
:rtype: bool
"""
# Initialize skip to be false
skip = False
# Set theory info needed to find information
ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
ini_thy_info = tinfo.from_dct(ini_method_dct)
# Perform checks
if 'ts' in spc_name:
# Skip all tasks except find_ts
# if rad-rad TS
if tsk not in ('find_ts', 'rpath_scan'): # generalize to other rpath
rxn_info = spc_dct[spc_name]['rxn_info']
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_ts_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
if rinfo.radrad(rxn_info) and ts_mul != high_ts_mul:
skip = True
ioprinter.info_message(
f'Skipping task because {spc_name}',
'is a low-spin radical radical reaction')
else:
spc_natoms = len(automol.inchi.geometry(spc_dct[spc_name]['inchi']))
if spc_natoms == 1:
# Skip all tasks except init_geom and conf_energy
# if species is an atom
if tsk not in ('init_geom', 'conf_energy'):
skip = True
ioprinter.info_message('Skipping task for an atom...',
newline=1)
else:
# Skip all tasks except ini_geom
# if (non-TS) species is unstable (zrxn found (i.e. is not None))
if tsk != 'init_geom':
instab, path = filesys.read.instability_transformation(
spc_dct, spc_name, ini_thy_info, save_prefix)
skip = (instab is not None)
if skip:
ioprinter.info_message(
f'Found instability file at path {path}', newline=1)
ioprinter.info_message(
'Skipping task for unstable species...', newline=1)
return skip
def _mod_class(class_typ, rxn_info):
""" Create the object containing the full description of the
reaction class, including its type, spin state, and whether
it is a radical-radical combination.
:param class_typ: reaction class type
:type class_typ: str
:param rxn_info: ???
:tpye rxn_info: ???
"""
# Set the spin of the reaction to high/low
if automol.par.need_spin_designation(class_typ):
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
_spin = 'high-spin' if ts_mul == high_mul else 'low-spin'
else:
_spin = ''
return automol.par.reaction_class_from_data(class_typ, _spin,
rinfo.radrad(rxn_info))
def remove_radrad_ts(obj_queue, spc_dct):
""" Remove TSs who have no information from the queue and
include them in the missing data lists
"""
ioprinter.info_message(
'Removing low-spin radical-radical TS from queue...\n')
new_queue = ()
for obj in obj_queue:
if 'ts_' in obj:
rxn_info = spc_dct[obj]['rxn_info']
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_ts_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
if rinfo.radrad(rxn_info) and ts_mul != high_ts_mul:
ioprinter.info_message(f'Removing {obj} from queue.')
else:
new_queue += (obj, )
else:
new_queue += (obj, )
return new_queue
def skip_task(spc_dct, spc_name):
""" Should this task be skipped?
:param spc_dct: species dictionary
:type spc_dct: dictionary
:param spc_name: name of species
:type spc_name: string
:rtype skip: boolean
"""
skip = False
# It should be skipped if its radical radical
if 'ts' in spc_name:
rxn_info = spc_dct[spc_name]['rxn_info']
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_ts_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
if rinfo.radrad(rxn_info) and ts_mul != high_ts_mul:
skip = True
ioprinter.info_message(
'Skipping task because {} is a low-spin radical radical reaction'
.format(spc_name))
return skip
def _mod_class(cls, rxn_info):
""" append additional info to the class
"""
full_cls_str = ''
# Determine the string for radical radical reactions
radrad = rinfo.radrad(rxn_info)
radrad_str = 'radical-radical' if radrad else ''
full_cls_str += radrad_str
# Set the spin of the reaction to high/low
if 'addition' in cls or 'absraction' in cls:
ts_mul = rinfo.value(rxn_info, 'tsmult')
high_mul = rinfo.ts_mult(rxn_info, rxn_mul='high')
spin_str = 'high-spin' if ts_mul == high_mul else 'low-spin'
full_cls_str += ' ' + spin_str
else:
spin_str = ''
# Add the class label
full_cls_str += ' ' + cls
return full_cls_str