# Print PES form and SUB PES Channels
print('\nCalculating Rates for PES {}: {}, SUB PES {}'.format(
pes_idx, formula, sub_pes_idx))
for chn_idx, rxn in enumerate(rxn_lst):
print(' Including Channel {}: {} = {}'.format(
rxn['chn_idx'],
'+'.join(rxn['reacs']),
'+'.join(rxn['prods'])))
ktpdriver.run(
formula, pes_idx, sub_pes_idx,
SPC_DCT,
CLA_DCT,
THY_DCT,
rxn_lst,
PES_MODEL_DCT, SPC_MODEL_DCT,
RUN_INP_DCT,
write_messrate=WRITE_MESSRATE,
run_messrate=RUN_MESSRATE,
run_fits=RUN_FITS
)
else:
print("Can't run kTPDriver without a PES being specified")
printer.program_exit('ktp')
# Exit Program
print('\n\n')
printer.program_exit('amech')
transdriver.run(
PES_RLST, SPC_RLST,
TRANS_TSKS,
SMOD_DCT,
SPC_DCT, THY_DCT,
INP_KEY_DCT['run_prefix'], INP_KEY_DCT['save_prefix']
)
ioprinter.program_exit('trans')
KTP_TSKS = TSK_LST_DCT.get('ktp')
if KTP_TSKS is not None:
ioprinter.program_header('ktp')
ktpdriver.run(
PES_RLST,
KTP_TSKS,
SPC_DCT, GLOB_DCT,
KMOD_DCT, SMOD_DCT,
INP_KEY_DCT['run_prefix'], INP_KEY_DCT['save_prefix']
)
ioprinter.program_exit('ktp')
PROC_TSKS = TSK_LST_DCT.get('proc')
if PROC_TSKS is not None:
ioprinter.program_header('proc')
PES_IDX = None
procdriver.run(
PES_RLST, SPC_RLST,
PROC_TSKS,
SPC_DCT,
KMOD_DCT, SMOD_DCT, THY_DCT,
INP_KEY_DCT['run_prefix'], INP_KEY_DCT['save_prefix']
THY_DCT,
INP_KEY_DCT['run_prefix'],
INP_KEY_DCT['save_prefix'],
)
ioprinter.program_exit('trans')
KTP_TSKS = TSK_LST_DCT.get('ktp')
if KTP_TSKS is not None:
ioprinter.program_header('ktp')
ktpdriver.run(
PES_RLST,
INPUT['pesgrp'],
KTP_TSKS,
SPC_DCT,
GLOB_DCT,
THY_DCT,
KMOD_DCT,
SMOD_DCT,
INP_KEY_DCT['run_prefix'],
INP_KEY_DCT['save_prefix'],
JOB_PATH,
)
ioprinter.program_exit('ktp')
PROC_TSKS = TSK_LST_DCT.get('proc')
if PROC_TSKS is not None:
ioprinter.program_header('proc')
procdriver.run(PES_RLST, SPC_RLST, PROC_TSKS, SPC_DCT, THY_DCT, KMOD_DCT,
SMOD_DCT, INP_KEY_DCT['run_prefix'],
INP_KEY_DCT['save_prefix'], JOB_PATH)
ioprinter.program_exit('proc')
def _mechdriver_main(tmp_dir):
""" Copy of MechDriver bin
"""
# print header message and host name (probably combine into one function)
ioprinter.program_header('amech')
ioprinter.random_cute_animal()
ioprinter.host_name()
# parse all of the input
ioprinter.program_header('inp')
inp_strs = ioparser.read_amech_input(tmp_dir)
thy_dct = ioparser.thy.theory_dictionary(inp_strs['thy'])
kmod_dct, smod_dct = ioparser.models.models_dictionary(
inp_strs['mod'], thy_dct)
inp_key_dct = ioparser.run.input_dictionary(inp_strs['run'])
pes_idx_dct, spc_idx_dct = ioparser.run.chem_idxs(inp_strs['run'])
tsk_lst_dct = ioparser.run.tasks(
inp_strs['run'], inp_strs['mech'], thy_dct)
spc_dct, glob_dct = ioparser.spc.species_dictionary(
inp_strs['spc'], inp_strs['dat'], inp_strs['geo'], 'csv')
pes_dct = ioparser.mech.pes_dictionary(
inp_strs['mech'], 'chemkin', spc_dct)
pes_rlst, spc_rlst = ioparser.rlst.run_lst(
pes_dct, spc_dct, pes_idx_dct, spc_idx_dct)
# build the run-save filesystem directories
prefix_fs(inp_key_dct['run_prefix'], inp_key_dct['save_prefix'])
# run drivers requested by user
es_tsks = tsk_lst_dct.get('es')
if es_tsks is not None:
ioprinter.program_header('es')
esdriver.run(
pes_rlst, spc_rlst,
es_tsks,
spc_dct, glob_dct, thy_dct,
inp_key_dct['run_prefix'], inp_key_dct['save_prefix']
)
ioprinter.program_exit('es')
therm_tsks = tsk_lst_dct.get('thermo')
if therm_tsks is not None:
ioprinter.program_header('thermo')
thermodriver.run(
pes_rlst, spc_rlst,
therm_tsks,
kmod_dct, smod_dct,
spc_dct, thy_dct,
inp_key_dct['run_prefix'], inp_key_dct['save_prefix'], tmp_dir
)
ioprinter.program_exit('thermo')
trans_tsks = tsk_lst_dct.get('trans')
if trans_tsks is not None:
ioprinter.program_header('trans')
if pes_dct:
transdriver.run(
pes_rlst, spc_rlst,
trans_tsks,
smod_dct,
spc_dct, thy_dct,
inp_key_dct['run_prefix'], inp_key_dct['save_prefix']
)
ioprinter.program_exit('trans')
ktp_tsks = tsk_lst_dct.get('ktp')
if ktp_tsks is not None:
ioprinter.program_header('ktp')
ktpdriver.run(
pes_rlst,
ktp_tsks,
spc_dct, glob_dct,
kmod_dct, smod_dct,
inp_key_dct['run_prefix'], inp_key_dct['save_prefix'], tmp_dir
)
ioprinter.program_exit('ktp')
proc_tsks = tsk_lst_dct.get('proc')
if proc_tsks is not None:
ioprinter.program_header('proc')
procdriver.run(
pes_rlst, spc_rlst,
proc_tsks,
spc_dct, thy_dct,
kmod_dct, smod_dct,
inp_key_dct['run_prefix'], inp_key_dct['save_prefix'], tmp_dir
)
ioprinter.program_exit('proc')
# exit program
ioprinter.obj('vspace')
ioprinter.program_exit('amech')
THY_DCT,
RUN_SPC_LST_DCT,
RUN_INP_DCT,
ref_scheme='basic',
run_pf=bool('pf' in RUN_JOBS_LST),
run_thermo=bool('thermo' in RUN_JOBS_LST))
if 'rates' in RUN_JOBS_LST or 'params' in RUN_JOBS_LST:
if RUN_OBJ_DCT['pes']:
# Call kTPDriver for spc in each PES
for pes_formula, rxn_lst in RUN_PES_DCT.items():
# Get info for the transition states
ts_dct = loadspc.build_sadpt_dct(rxn_lst, MODEL_DCT, THY_DCT,
ES_TSK_STR, RUN_INP_DCT,
RUN_OPTIONS_DCT, SPC_DCT, {})
SPC_DCT.update(ts_dct)
# Run the driver
ktpdriver.run(pes_formula,
SPC_DCT,
THY_DCT,
rxn_lst,
MODEL_DCT,
RUN_INP_DCT,
run_rates=bool('rates' in RUN_JOBS_LST),
run_fits=bool('params' in RUN_JOBS_LST))
else:
print("Can't run kTPDriver without a PES being specified")
# Print the program exist message
print('AutoMech has completed. I hope you had fun!')