def _check_tsks(tsk_lsts, thy_dct):
""" Loop over all of the tasks, add default keywords and parameters
and assesses if all the input is valid
"""
if tsk_lsts is not None:
for tsk_lst in tsk_lsts:
# Unpack the task
_tsk = tsk_lst[:-1]
if len(_tsk) == 2:
# Case(1): spc task keywords (ESDriver)
obj, tsk = _tsk[0], _tsk[1]
else:
# Case(2): task keywords (ThermoDriver, kTPDriver)
obj, tsk = None, _tsk[0]
key_dct = tsk_lst[-1]
# Check if the obj is allowed
if obj is not None:
# Have to make lst to handle case where obj == 'all'
obj_lst = SUPP_OBJS if obj == 'all' else (obj, )
for _obj in obj_lst:
if _obj not in TSK_KEY_DCT[tsk][0]:
print('obj {}, not allowed for {}'.format(obj, tsk))
print('')
sys.exit()
# Check if keyword values are allowed
check_dct1(key_dct, TSK_VAL_DCT, (), 'Task')
# Check keywords with thylvls as values use lvls defined in thy dct
check_thy_lvls(key_dct, thy_dct)
def theory_dictionary(thy_str):
""" Parse the theory.dat input for all of the user-defined level blocks.
These blocks are formatted into several keyword-value dictionaries
consisting of user-defined keywords as well as defaults:
{'user-defined level name': {keyword-value dictionary for level}}
These indiviual level dicts are packaged into an overall `thy_dct`.
:param thy_str: theory.dat input file string
:type thy_str: str
:rtype: dict[str: dict[str:obj]]
"""
# Format input to keyword-value theory dcts
thy_blocks = ioformat.ptt.named_end_blocks(
thy_str, 'level', footer='level')
thy_dct = ioformat.ptt.keyword_dcts_from_blocks(thy_blocks)
# Add defaults to each thy dictionary
full_thy_dct = {}
for lvl, dct in thy_dct.items():
full_thy_dct[lvl] = automol.util.dict_.right_update(
defaults_from_val_dct(THY_VAL_DCT), dct)
# Check each dictionary
for lvl, dct in full_thy_dct.items():
check_dct1(dct, THY_VAL_DCT, THY_REQ, 'Thy-{}'.format(lvl))
return full_thy_dct
def species_dictionary(spc_str, dat_str, geo_dct, spc_type):
""" Read each of the species input files:
(1) species.csv: CSV file with basic info like names,inchis,mults
(2) species.dat:
(3) *.xyz: XYZ-files with geometries
:param job_path: directory path where the input file(s) exist
:type job_path: str
:rtype dict[str: dict]
"""
# Parse out the dcts from the strings
spc_dct = mechanalyzer.parser.spc.build_spc_dct(spc_str, spc_type)
dat_blocks = ioformat.ptt.named_end_blocks(dat_str, 'spc', footer='spc')
dat_dct = ioformat.ptt.keyword_dcts_from_blocks(dat_blocks)
# Merge all of the species inputs into a dictionary
mod_spc_dct, glob_dct = modify_spc_dct(spc_dct, dat_dct, geo_dct)
# Assess if the species.dat information is valid
for name, dct in mod_spc_dct.items():
# last comment breaks since TS only partially built at this stage
# i.e. there is not a mult, that comes from the build later
# prolly fine, since we add required stuff for TS ourselves
# probably just check if stuff provided that is not supported
# req_lst = SPC_REQ if 'ts' not in name else SPC_REQ+TS_REQ
req_lst = SPC_REQ if 'ts' not in name else ()
val_dct = SPC_VAL_DCT if 'ts' not in name else TS_VAL_DCT
check_dct1(dct, val_dct, req_lst, 'Spc-{}'.format(name))
return mod_spc_dct, glob_dct
def input_dictionary(run_str):
""" Parses the `input` block and builds a
dictionary of keywords and their corresponding values.
:param run_str: input string of the run.dat block
:type run_str: str
:rtype: dict[str: obj]
"""
# Read the input block
inp_block = ioformat.ptt.end_block(run_str, 'input', footer='input')
inp_dct = ioformat.ptt.keyword_dct_from_block(inp_block)
# Add defaults to the dictionary
inp_dct = automol.util.dict_.right_update(
defaults_from_val_dct(RUN_INP_VAL_DCT), inp_dct)
# Check the dictionary
check_dct1(inp_dct, RUN_INP_VAL_DCT, RUN_INP_REQ, 'Run-Input')
return inp_dct
def theory_dictionary(thy_str):
""" Parse the theory.dat file
"""
# Format input to keyword-value theory dcts
thy_blocks = ioformat.ptt.named_end_blocks(thy_str,
'level',
footer='level')
thy_dct = ioformat.ptt.keyword_dcts_from_blocks(thy_blocks)
# Add defaults to each thy dictionary
full_thy_dct = {}
for lvl, dct in thy_dct.items():
full_thy_dct[lvl] = automol.util.dict_.right_update(
defaults_from_val_dct(THY_VAL_DCT), dct)
# Check each dictionary
for lvl, dct in full_thy_dct.items():
check_dct1(dct, THY_VAL_DCT, THY_REQ, 'Thy-{}'.format(lvl))
return full_thy_dct