def active_space(info_obj, typ='ts'):
""" Determine the active space for the multireference MEP scan
"""
def _active_space(ich, mul):
""" Determine the active sapce for an InChI string
"""
if ich in act_space.DCT:
num_act_orb = act_space.DCT[ich][0]
num_act_elc = act_space.DCT[ich][1]
num_states = act_space.DCT[ich][2]
else:
num_act_orb = (mul - 1)
num_act_elc = (mul - 1)
num_states = 1
return num_act_orb, num_act_elc, num_states
if typ == 'spc':
ich = sinfo.value(info_obj, 'inchi')
mul = sinfo.value(info_obj, 'mult')
num_act_orb, num_act_elec, num_states = _active_space(ich, mul)
elif typ == 'ts':
rct_ichs = rinfo.value(info_obj, 'inchi')[0]
rct_muls = rinfo.value(info_obj, 'mult')[0]
num_act_orb, num_act_elec, num_states = 0, 0, 1
for ich, mul in zip(rct_ichs, rct_muls):
norb, nelec, nstat = _active_space(ich, mul)
num_act_orb += norb
num_act_elec += nelec
num_states *= nstat
return num_act_orb, num_act_elec, num_states
def ts_dct_sing_chnl(pes_idx,
reaction,
spc_dct,
run_prefix,
save_prefix,
thy_info=None,
ini_thy_info=None):
""" build dct for single reaction
"""
# Unpack the reaction object
chnl_idx, (reacs, prods) = reaction
rxn_info = rinfo.from_dct(reacs, prods, spc_dct)
print(' Preparing for reaction {} = {}'.format('+'.join(reacs),
'+'.join(prods)))
# Set the reacs and prods for the desired direction
reacs, prods = rxnid.set_reaction_direction(reacs,
prods,
rxn_info,
thy_info,
ini_thy_info,
save_prefix,
direction='forw')
# Obtain the reaction object for the reaction
zma_locs = (0, )
zrxns, zmas, rclasses = rxnid.build_reaction(rxn_info, ini_thy_info,
zma_locs, save_prefix)
# Could reverse the spc dct
if zrxns is not None:
ts_dct = {}
for idx, (zrxn, zma, cls) in enumerate(zip(zrxns, zmas, rclasses)):
tsname = 'ts_{:g}_{:g}_{:g}'.format(pes_idx + 1, chnl_idx + 1, idx)
ts_dct[tsname] = {
'zrxn': zrxn,
'zma': zma,
'reacs': reacs,
'prods': prods,
'rxn_info': rxn_info,
'inchi': '',
'charge': rinfo.value(rxn_info, 'charge'),
'mult': rinfo.value(rxn_info, 'tsmult'),
'elec_levels': ((0.0, rinfo.value(rxn_info, 'tsmult')), ),
'hind_inc': 30.0 * phycon.DEG2RAD,
# 'sym_factor': 1.0, # remove later
'class': cls,
'rxn_fs': reaction_fs(run_prefix, save_prefix, rxn_info)
}
else:
ts_dct = {}
print('Skipping reaction as class not given/identified')
# Add the ts dct to the spc dct here?
return ts_dct
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 _id_reaction(rxn_info):
""" Identify the reaction and build the object
:param rxn_info: reaction info object
:type rxn_info: mechanalyzer.inf.rxn object
:rtype: (tuple(automol.Reaction object), tuple(automol.zmat object))
"""
rxn_ichs = rinfo.value(rxn_info, 'inchi')
rct_ichs, prd_ichs = rxn_ichs[0], rxn_ichs[1]
zrxn_objs = automol.reac.rxn_objs_from_inchi(rct_ichs,
prd_ichs,
indexing='zma')
# zrxns = tuple(obj[0] for obj in zrxn_objs)
# zmas = tuple(obj[1] for obj in zrxn_objs)
zrxns, zmas = [], []
# for objs in zrxn_objs:
# zrxn, zma, _, _ = objs
# zrxns.append(zrxn)
# zmas.append(zma)
# print('zrxn, zma in id:', zrxn, automol.zmat.string(zma))
# for now just use first zma until we are properly producing extra zmas
if zrxn_objs:
zrxns.append(zrxn_objs[0][0])
zmas.append(zrxn_objs[0][1])
return zrxns, zmas
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 _id_reaction(rxn_info, thy_info, save_prefix):
""" Identify the reaction and build the object
:param rxn_info: reaction info object
:type rxn_info: mechanalyzer.inf.rxn object
:rtype: (tuple(automol.Reaction object), tuple(automol.zmat object))
"""
# Check the save filesystem for the reactant and product geometries
rct_geos, prd_geos, rct_paths, prd_paths = reagent_geometries(
rxn_info, thy_info, save_prefix)
# Identify reactants and products from geoms or InChIs, depending
# We automatically assess and add stereo to the reaction object, as needed
if any(rct_geos) and any(prd_geos):
print(' Reaction ID from geometries from SAVE filesys')
for i, path in enumerate(rct_paths):
print(f' - reactant {i+1}: {path}')
for i, path in enumerate(prd_paths):
print(f' - product {i+1}: {path}')
zrxn_objs = automol.reac.rxn_objs_from_geometry(
rct_geos, prd_geos, indexing='zma', stereo=False)
# rct_geos, prd_geos, indexing='zma', stereo=True)
else:
print(' Reaction ID from geometries from input InChIs')
rxn_ichs = rinfo.value(rxn_info, 'inchi')
rct_ichs, prd_ichs = rxn_ichs[0], rxn_ichs[1]
zrxn_objs = automol.reac.rxn_objs_from_inchi(
rct_ichs, prd_ichs, indexing='zma', stereo=False)
# rct_ichs, prd_ichs, indexing='zma', stereo=True)
# Loop over the found reaction objects
if zrxn_objs is not None:
zrxns, zmas = (), ()
for obj_set in zrxn_objs:
zrxn, zma, _, _ = obj_set
zrxns += (zrxn,)
zmas += (zma,)
else:
zrxns, zmas = None, None
return zrxns, zmas
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
def ts_dct_sing_chnl(pes_idx,
reaction,
spc_dct,
run_prefix,
save_prefix,
thy_info=None,
ini_thy_info=None,
id_missing=True,
re_id=False):
""" build dct for single reaction
"""
# Unpack the reaction object
chnl_idx, (reacs, prods) = reaction
rxn_info = rinfo.from_dct(reacs, prods, spc_dct)
rct_str, prd_str = '+'.join(reacs), '+'.join(prods)
print(f'\n Preparing for reaction {rct_str} = {prd_str}')
# Set the reacs and prods for the desired direction
reacs, prods = rxnid.set_reaction_direction(reacs,
prods,
rxn_info,
thy_info,
ini_thy_info,
save_prefix,
direction='forw')
# Obtain the reaction object for the reaction
zma_locs = (0, )
# is there a better way to get this hbond param out of spc_dct and does
# it matter in getting the mincofs to build the reaction if we bother
# to include it?
# hbond_cutoffs = spc_dct[reacs[0]]['hbond_cutoffs']
zrxns, zmas, rclasses, status = rxnid.build_reaction(rxn_info,
ini_thy_info,
zma_locs,
save_prefix,
id_missing=id_missing,
re_id=re_id)
# , hbond_cutoffs=hbond_cutoffs)
# Could reverse the spc dct
if status not in ('MISSING-SKIP', 'MISSING-ADD'):
ts_dct = {}
for idx, (zrxn, zma, cls) in enumerate(zip(zrxns, zmas, rclasses)):
tsname = f'ts_{pes_idx+1:d}_{chnl_idx+1:d}_{idx:d}'
ts_dct[tsname] = {
'zrxn': zrxn,
'zma': zma,
'reacs': reacs,
'prods': prods,
'rxn_info': rxn_info,
'inchi': '',
'charge': rinfo.ts_chg(rxn_info),
'mult': rinfo.value(rxn_info, 'tsmult'),
'elec_levels': ((0.0, rinfo.value(rxn_info, 'tsmult')), ),
'hind_inc': 30.0 * phycon.DEG2RAD,
'hbond_cutoffs': (4.55, 1.92),
'class': cls,
'rxn_fs': reaction_fs(run_prefix, save_prefix, rxn_info)
}
elif status == 'MISSING-ADD':
tsname = f'ts_{pes_idx+1:d}_{chnl_idx+1:d}_0'
ts_dct = {}
ts_dct[tsname] = {'missdata': ini_thy_info}
elif status == 'MISSING-SKIP':
ts_dct = {}
print('Skipping reaction as class not given/identified')
return ts_dct
