def read_class_dct(job_path):
""" Read the class dictionary
"""
cla_str = ptt.read_inp_str(job_path, CLA_INP)
cla_str = cla_str if cla_str else 'REACTION,RCLASS\nEND'
cla_dct = chemkin_io.parser.mechanism.reac_class_dct(cla_str, 'class')
return cla_dct
def read_es_tsks(job_path):
""" Build a dictionary for all the theory keywords
"""
run_str = ptt.read_inp_str(job_path, RUN_INP)
es_tsks_str = es_tsks_block(run_str)
assert es_tsks_str
return es_tsks_str
def build_run_jobs_lst(job_path):
""" Build a dictionary for all the theory keywords
"""
job_str = ptt.read_inp_str(job_path, RUN_INP)
keyword_lst = ptt.build_keyword_lst(jobs_block(job_str))
assert keyword_lst
# assert check_run_keyword_dct(keyword_dct)
return keyword_lst
def build_spc_dct(job_path, spc_type):
""" Get a dictionary of all the input species
indexed by InChi string
"""
spc_csv_str = ptt.read_inp_str(job_path, CSV_INP)
if spc_type == 'csv':
spc_dct = csv_dct(spc_csv_str, check_stereo=False)
else:
raise NotImplementedError
# Modify spc dct with params from the AMech file
mod_spc_dct = modify_spc_dct(job_path, spc_dct)
return mod_spc_dct
def read_spc_amech(job_path):
""" Read an amech style input file for the species
"""
spc_amech_str = ptt.read_inp_str(job_path, DAT_INP)
spc_dct = {}
if spc_amech_str:
spc_sections = apf.all_captures(ptt.end_section_wname2('spc'),
spc_amech_str)
if spc_sections:
for section in spc_sections:
name = section[0]
keyword_dct = ptt.build_keyword_dct(section[1])
spc_dct[name] = keyword_dct
return spc_dct
def read_models_sections(job_path):
""" species input
"""
mod_str = ptt.read_inp_str(job_path, MODEL_INP)
# Obtain the species string
model_sections = apf.all_captures(ptt.end_section_wname2('model'), mod_str)
# Make sure some section has been defined
assert model_sections is not None
# Build dictionary of models methods
model_methods = {}
for section in model_sections:
name = section[0]
keyword_dct = build_model_keyword_dct(section[1])
model_methods[name] = keyword_dct
return model_methods
def build_thy_dct(job_path):
""" species input
"""
# Obtain the species string
thy_str = ptt.read_inp_str(job_path, THY_INP)
if thy_str:
thy_sections = apf.all_captures(ptt.end_section_wname2('level'),
thy_str)
# Make sure some section has been defined
assert thy_sections is not None
# Build dictionary of theory methods
thy_methods = {}
for section in thy_sections:
name = section[0]
keyword_dct = build_thy_keyword_dct(section[1])
thy_methods[name] = keyword_dct
return thy_methods
def parse_mechanism_file(job_path,
mech_type,
spc_dct,
run_obj_dct,
sort_rxns=False):
""" Get the reactions and species from the mechanism input
"""
# parsing moved to the input parsing module I am writing
mech_str = ptt.read_inp_str(job_path, MECH_INP)
if mech_type.lower() == 'chemkin':
formulas, rct_names, prd_names, rxn_names = _parse_chemkin(
mech_str, spc_dct, sort_rxns)
# elif mech_type.lower() == 'json':
# spc_dct, rct_names, prd_names, rxn_name, form_strs = _parse_json(
# mech_path, mech_file, check_stereo, rad_rad_sort)
else:
raise NotImplementedError
# Build the total PES dct
pes_dct = build_pes_dct(formulas, rct_names, prd_names, rxn_names)
# Print the channels
print_pes_channels(pes_dct)
# Reduce the PES dct to only what the user requests
if run_obj_dct:
pesnums = [idx_pair[0] for idx_pair in run_obj_dct]
else:
pesnums = [idx_pair[0] for idx_pair in run_obj_dct]
reduced_pes_dct = reduce_pes_dct_to_user_inp(pes_dct, pesnums)
# Get a dct for all of the connected channels
conn_chnls_dct = determine_connected_pes_channels(reduced_pes_dct)
# Form the pes dct that has info formatted to run
# Get the models in here
run_pes_dct = pes_dct_w_rxn_lsts(pes_dct, conn_chnls_dct, run_obj_dct)
return run_pes_dct
def objects_dct(job_path):
""" Get the sections for the run block
"""
run_str = ptt.read_inp_str(job_path, RUN_INP)
obj_str = object_block(run_str)
# Read one of a set of objects to run calcs on (only one supported)
pes_block_str = apf.first_capture(ptt.paren_section('pes'), obj_str)
pspc_block_str = apf.first_capture(ptt.paren_section('pspc'), obj_str)
spc_block_str = apf.first_capture(ptt.paren_section('spc'), obj_str)
# ts_block_str = apf.first_capture(paren_section('ts'), section_str)
# wells_block_str = apf.first_capture(paren_section('wells'), section_str)
# Build the run dictionary
run_dct = {}
if pes_block_str is not None:
run_dct['pes'] = get_pes_idxs(ptt.remove_empty_lines(pes_block_str))
else:
run_dct['pes'] = []
if pspc_block_str is not None:
run_dct['pspc'] = get_pspc_idxs(ptt.remove_empty_lines(pspc_block_str))
else:
run_dct['pspc'] = []
if spc_block_str is not None:
run_dct['spc'] = get_spc_idxs(ptt.remove_empty_lines(spc_block_str))
else:
run_dct['spc'] = []
# elif ts_block_str is not None:
# obj_str = ts_block_str
# elif ts_block_str is not None:
# obj_str = ts_block_str
# elif wells_block_str is not None:
# obj_str = wells_block_str
# else:
# raise ValueError
return run_dct