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)
print('level', level)
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 = mincnf.min_energy_conformer_locators(
cnf_save_fs, levelp)
cnf_run_fs[-1].create(min_rngs_locs)
else:
min_rngs_locs, min_rngs_path = mincnf.conformer_locators(
cnf_save_fs, levelp, cnf_range='r100')
for min_locs in min_rngs_locs:
cnf_run_fs[-1].create(min_locs)
print('model filesys', min_rngs_locs, min_rngs_path)
# 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,
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 get_spc_locs_lst(spc_dct_i,
spc_model_dct_i,
run_prefix,
save_prefix,
saddle,
cnf_range='min',
sort_info_lst=None,
name=None,
nprocs=1):
""" return the locations for a pf level
"""
# Use the locs from the dict
user_conf_ids = spc_dct_i.get('conf_id')
if user_conf_ids is None:
# Set the spc_info
cnf_run_fs, cnf_save_fs, levelp, mod_info_lst = _get_prop_fs(
spc_model_dct_i,
spc_dct_i,
'vib',
sort_info_lst,
run_prefix,
save_prefix,
saddle=saddle,
name=name)
hbond_cutoffs = spc_dct_i['hbond_cutoffs']
min_locs_lst, _ = conformer_locators(cnf_save_fs,
levelp,
cnf_range=cnf_range,
sort_info_lst=mod_info_lst,
print_enes=True,
hbond_cutoffs=hbond_cutoffs,
nprocs=nprocs)
for min_locs in min_locs_lst:
cnf_run_fs[-1].create(min_locs)
else:
print('Using user specified conformer IDs')
min_locs_lst = (user_conf_ids, )
return min_locs_lst
def get_all_tors_locs_lst(spc_dct_i,
spc_model_dct_i,
run_prefix,
save_prefix,
saddle,
nprocs=1):
"""get all conformer locations for the torsion method
"""
tors_run_fs, tors_save_fs, levelp, _ = _get_prop_fs(spc_model_dct_i,
spc_dct_i,
'tors',
None,
run_prefix,
save_prefix,
saddle=saddle)
hbond_cutoffs = spc_dct_i['hbond_cutoffs']
tors_locs_lst, _ = conformer_locators(tors_save_fs,
levelp,
cnf_range='all',
hbond_cutoffs=hbond_cutoffs,
nprocs=nprocs)
return tors_run_fs, tors_save_fs, tors_locs_lst