def rcts_cnf_fs(rct_infos, thy_dct, es_keyword_dct, run_prefix, save_prefix):
""" set reactant filesystem stuff
"""
ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
ini_thy_info = tinfo.from_dct(ini_method_dct)
rct_cnf_fs = ()
for rct_info in rct_infos:
mod_ini_thy_info = tinfo.modify_orb_label(ini_thy_info, rct_info)
# Build filesys for ini thy info
ini_cnf_run_fs, ini_cnf_save_fs = build_fs(
run_prefix,
save_prefix,
'CONFORMER',
spc_locs=rct_info,
thy_locs=mod_ini_thy_info[1:])
ini_loc_info = min_energy_conformer_locators(ini_cnf_save_fs,
mod_ini_thy_info)
ini_min_cnf_locs, ini_min_cnf_path = ini_loc_info
# Create run fs if that directory has been deleted to run the jobs
ini_cnf_run_fs[-1].create(ini_min_cnf_locs)
rct_cnf_fs += ((ini_cnf_run_fs, ini_cnf_save_fs, ini_min_cnf_locs,
ini_min_cnf_path), )
return rct_cnf_fs
def instability_transformation(spc_dct,
spc_name,
thy_info,
save_prefix,
zma_locs=(0, )):
""" see if a species and unstable and handle task management
"""
spc_info = sinfo.from_dct(spc_dct[spc_name])
mod_thy_info = tinfo.modify_orb_label(thy_info, spc_info)
_, cnf_save_fs = build_fs('',
save_prefix,
'CONFORMER',
spc_locs=spc_info,
thy_locs=mod_thy_info[1:])
# Check if any locs exist first?
ini_loc_info = min_energy_conformer_locators(cnf_save_fs, mod_thy_info)
_, min_cnf_path = ini_loc_info
zma_save_fs = autofile.fs.zmatrix(min_cnf_path)
# Check if the instability files exist
if zma_save_fs[-1].file.instability.exists(zma_locs):
instab_trans = zma_save_fs[-1].file.instability.read(zma_locs)
zma = zma_save_fs[-1].file.zmatrix.read(zma_locs)
_instab = (instab_trans, zma)
path = zma_save_fs[-1].file.zmatrix.path(zma_locs)
else:
_instab = None
path = None
return _instab, path
def reactions(rxn_info, ini_thy_info, zma_locs, save_prefix):
""" Check if reaction exists in the filesystem and has been identified
"""
zrxns, zmas = (), ()
sort_rxn_info = rinfo.sort(rxn_info, scheme='autofile')
ts_info = rinfo.ts_info(rxn_info)
mod_ini_thy_info = tinfo.modify_orb_label(ini_thy_info, ts_info)
rxn_fs = autofile.fs.reaction(save_prefix)
if rxn_fs[-1].exists(sort_rxn_info):
_, ts_save_fs = build_fs(save_prefix,
save_prefix,
'TRANSITION STATE',
rxn_locs=sort_rxn_info,
thy_locs=mod_ini_thy_info[1:])
for ts_locs in ts_save_fs[-1].existing():
zrxn, zma = reaction(rxn_info,
ini_thy_info,
zma_locs,
save_prefix,
ts_locs=ts_locs)
if zrxn is not None:
zrxns += (zrxn, )
zmas += (zma, )
if not zrxns:
zrxns, zmas = None, None
return zrxns, zmas
def reaction(rxn_info,
ini_thy_info,
zma_locs,
save_prefix,
ts_locs=(0, ),
hbond_cutoffs=None):
""" Check if reaction exists in the filesystem and has been identified
"""
zrxn, zma = None, None
sort_rxn_info = rinfo.sort(rxn_info, scheme='autofile')
ts_info = rinfo.ts_info(rxn_info)
mod_ini_thy_info = tinfo.modify_orb_label(ini_thy_info, ts_info)
rxn_fs = autofile.fs.reaction(save_prefix)
if rxn_fs[-1].exists(sort_rxn_info):
_, cnf_save_fs = build_fs(save_prefix,
save_prefix,
'CONFORMER',
rxn_locs=sort_rxn_info,
thy_locs=mod_ini_thy_info[1:],
ts_locs=ts_locs)
_, ini_min_cnf_path = min_energy_conformer_locators(
cnf_save_fs, mod_ini_thy_info, hbond_cutoffs=hbond_cutoffs)
if ini_min_cnf_path:
zma_fs = autofile.fs.zmatrix(ini_min_cnf_path)
if zma_fs[-1].file.reaction.exists(zma_locs):
zrxn = zma_fs[-1].file.reaction.read(zma_locs)
zma = zma_fs[-1].file.zmatrix.read(zma_locs)
# For barrierless reactions with no conformer
if zrxn is None:
_, zma_fs = build_fs(save_prefix,
save_prefix,
'ZMATRIX',
rxn_locs=sort_rxn_info,
ts_locs=ts_locs,
thy_locs=mod_ini_thy_info[1:])
if zma_fs[-1].file.reaction.exists(zma_locs):
zrxn = zma_fs[-1].file.reaction.read(zma_locs)
zma = zma_fs[-1].file.zmatrix.read(zma_locs)
return zrxn, zma
def set_model_filesys(spc_dct_i,
level,
run_prefix,
save_prefix,
saddle,
name=None,
cnf_range='min',
spc_locs=None,
nprocs=1):
""" Gets filesystem objects for reading many calculations
"""
# Set the spc_info
if saddle:
rxn_info = spc_dct_i['rxn_info']
spc_info = rinfo.ts_info(rxn_info)
else:
spc_info = sinfo.from_dct(spc_dct_i)
levelp = tinfo.modify_orb_label(level, spc_info)
_root = root_locs(spc_dct_i, saddle=saddle, name=name)
cnf_run_fs, cnf_save_fs = build_fs(run_prefix,
save_prefix,
'CONFORMER',
thy_locs=levelp[1:],
**_root)
hbond_cutoffs = spc_dct_i['hbond_cutoffs']
if cnf_range == 'specified':
min_rngs_locs = spc_locs
min_rngs_path = cnf_save_fs[-1].path(min_rngs_locs)
cnf_run_fs[-1].create(min_rngs_locs)
elif cnf_range == 'min':
min_rngs_locs, min_rngs_path = min_energy_conformer_locators(
cnf_save_fs, levelp, hbond_cutoffs=hbond_cutoffs)
cnf_run_fs[-1].create(min_rngs_locs)
else:
min_rngs_locs_lst, min_rngs_path_lst = conformer_locators(
cnf_save_fs,
levelp,
cnf_range=cnf_range,
hbond_cutoffs=hbond_cutoffs,
nprocs=nprocs)
for min_locs in min_rngs_locs_lst:
cnf_run_fs[-1].create(min_locs)
min_rngs_locs = min_rngs_locs_lst[0]
min_rngs_path = min_rngs_path_lst[0]
ioprinter.warning_message('Only returning first location in this list')
# Create run fs if that directory has been deleted to run the jobs
return [cnf_save_fs, min_rngs_path, min_rngs_locs, '', cnf_run_fs]
def set_model_filesys(spc_dct_i,
level,
run_prefix,
save_prefix,
saddle,
name=None,
rings='all'):
""" Gets filesystem objects for reading many calculations
"""
# Set the spc_info
if saddle:
rxn_info = spc_dct_i['rxn_info']
spc_info = rinfo.ts_info(rxn_info)
else:
spc_info = sinfo.from_dct(spc_dct_i)
levelp = tinfo.modify_orb_label(level, spc_info)
_root = root_locs(spc_dct_i, saddle=saddle, name=name)
cnf_run_fs, cnf_save_fs = build_fs(run_prefix,
save_prefix,
'CONFORMER',
thy_locs=levelp[1:],
**_root)
if rings == 'min':
min_rngs_locs, min_rngs_path = min_energy_conformer_locators(
cnf_save_fs, levelp)
cnf_run_fs[-1].create(min_rngs_locs)
else:
min_rngs_locs, min_rngs_path = conformer_locators(cnf_save_fs,
levelp,
cnf_range='r100')
for min_locs in min_rngs_locs:
cnf_run_fs[-1].create(min_locs)
# Create run fs if that directory has been deleted to run the jobs
return [cnf_save_fs, min_rngs_path, min_rngs_locs, '', cnf_run_fs]
def _get_prop_fs(spc_model_dct_i,
spc_dct_i,
prop,
sort_info_lst,
run_prefix,
save_prefix,
saddle=False,
name=None):
""" Get filesystem info for a property in the spc model dct
"""
if saddle:
rxn_info = spc_dct_i['rxn_info']
spc_info = rinfo.ts_info(rxn_info)
else:
spc_info = sinfo.from_dct(spc_dct_i)
level = spc_model_dct_i[prop]['geolvl'][1][1]
levelp = tinfo.modify_orb_label(level, spc_info)
mod_info_lst = []
if sort_info_lst is not None:
for info in sort_info_lst[:2]:
if info is not None:
mod_info_lst.append(tinfo.modify_orb_label(info, spc_info))
else:
mod_info_lst.append(info)
for info in sort_info_lst[2:]:
mod_info_lst.append(info)
_root = root_locs(spc_dct_i, saddle=saddle, name=name)
cnf_run_fs, cnf_save_fs = build_fs(run_prefix,
save_prefix,
'CONFORMER',
thy_locs=levelp[1:],
**_root)
return cnf_run_fs, cnf_save_fs, levelp, mod_info_lst