def make_pes_mess_str(spc_dct, rxn_lst, pes_idx,
run_prefix, save_prefix, label_dct,
pes_model_dct_i, spc_model_dct_i,
spc_model, thy_dct):
""" Write all the MESS input file strings for the reaction channels
"""
ioprinter.messpf('channel_section')
# Initialize empty MESS strings
full_well_str, full_bi_str, full_ts_str = '', '', ''
full_dat_str_dct = {}
pes_ene_dct = {}
conn_lst = tuple()
# Set the energy and model for the first reference species
ioprinter.info_message('\nCalculating reference energy for PES')
ref_ene = set_reference_ene(
rxn_lst, spc_dct, thy_dct,
pes_model_dct_i, spc_model_dct_i,
run_prefix, save_prefix, ref_idx=0)
# Loop over all the channels and write the MESS strings
written_labels = []
basis_energy_dct = {}
for rxn in rxn_lst:
chnl_idx, (reacs, prods) = rxn
ioprinter.obj('vspace')
ioprinter.reading('PES electrion structure data')
ioprinter.channel(chnl_idx, reacs, prods)
# Set the TS name and channel model
tsname = 'ts_{:g}_{:g}'.format(pes_idx+1, chnl_idx+1)
# Obtain all of the species data
if spc_model not in basis_energy_dct:
basis_energy_dct[spc_model] = {}
# Pass in full ts class
chnl_infs, chn_basis_ene_dct = get_channel_data(
reacs, prods, tsname,
spc_dct, basis_energy_dct[spc_model],
pes_model_dct_i, spc_model_dct_i,
run_prefix, save_prefix)
basis_energy_dct[spc_model].update(chn_basis_ene_dct)
# Calculate the relative energies of all spc on the channel
chnl_enes = sum_channel_enes(chnl_infs, ref_ene)
# Write the mess strings for all spc on the channel
mess_strs, dat_str_dct, written_labels = _make_channel_mess_strs(
tsname, reacs, prods, spc_dct, label_dct, written_labels,
chnl_infs, chnl_enes, spc_model_dct_i)
# Append to full MESS strings
[well_str, bi_str, ts_str] = mess_strs
full_well_str += well_str
full_bi_str += bi_str
full_ts_str += ts_str
full_dat_str_dct.update(dat_str_dct)
ioprinter.debug_message('rxn', rxn)
ioprinter.debug_message('enes', chnl_enes)
ioprinter.debug_message('label dct', label_dct)
ioprinter.debug_message('written labels', written_labels)
# Combine all the reaction channel strings
rxn_chan_str = '\n'.join([full_well_str, full_bi_str, full_ts_str])
return rxn_chan_str, full_dat_str_dct, pes_ene_dct, conn_lst
def make_pes_mess_str(spc_dct, rxn_lst, pes_idx, pesgrp_num, unstable_chnls,
run_prefix, save_prefix, label_dct, tsk_key_dct,
pes_param_dct, thy_dct, pes_model_dct_i, spc_model_dct_i,
spc_model):
""" Write all the MESS input file strings for the reaction channels
"""
ioprinter.messpf('channel_section')
# Initialize data carrying objects and empty MESS strings
basis_energy_dct = {}
basis_energy_dct[spc_model] = {}
full_well_str, full_bi_str, full_ts_str = '', '', ''
full_dat_str_dct = {}
# Set the energy and model for the first reference species
ioprinter.info_message('\nCalculating reference energy for PES')
ref_ene, model_basis_energy_dct = set_reference_ene(
rxn_lst,
spc_dct,
tsk_key_dct,
basis_energy_dct[spc_model],
thy_dct,
pes_model_dct_i,
spc_model_dct_i,
run_prefix,
save_prefix,
ref_idx=0)
basis_energy_dct[spc_model].update(model_basis_energy_dct)
print('basis energy dct')
print(basis_energy_dct)
# Loop over all the channels and write the MESS strings
written_labels = []
for rxn in rxn_lst:
chnl_idx, (reacs, prods) = rxn
ioprinter.obj('vspace')
ioprinter.reading('PES electronic structure data')
ioprinter.channel(chnl_idx + 1, reacs, prods)
# Get the names for all of the configurations of the TS
tsname = base_tsname(pes_idx, chnl_idx)
tsname_allconfigs = tsnames_in_dct(pes_idx, chnl_idx, spc_dct)
# Pass in full ts class
chnl_infs, chn_basis_ene_dct = get_channel_data(
reacs, prods, tsname_allconfigs, spc_dct, tsk_key_dct,
basis_energy_dct[spc_model], thy_dct, pes_model_dct_i,
spc_model_dct_i, run_prefix, save_prefix)
basis_energy_dct[spc_model].update(chn_basis_ene_dct)
# Calculate the relative energies of all spc on the channel
chnl_enes = sum_channel_enes(chnl_infs, ref_ene)
# Set the hot energies using the relative enes that will be
# written into the global key section of MESS input later
hot_enes_dct = set_hot_enes(pesgrp_num,
reacs,
prods,
chnl_enes,
pes_param_dct,
ene_range=None)
# Write the mess strings for all spc on the channel
mess_strs, dat_str_dct, written_labels = _make_channel_mess_strs(
tsname,
reacs,
prods,
pesgrp_num,
spc_dct,
label_dct,
written_labels,
pes_param_dct,
chnl_infs,
chnl_enes,
spc_model_dct_i,
unstable_chnl=(chnl_idx in unstable_chnls))
# Append to full MESS strings
[well_str, bi_str, ts_str] = mess_strs
full_well_str += well_str
full_bi_str += bi_str
full_ts_str += ts_str
full_dat_str_dct.update(dat_str_dct)
# Combine all the reaction channel strings; remove empty lines
rxn_chan_str = '\n'.join([full_well_str, full_bi_str, full_ts_str])
rxn_chan_str = ioformat.remove_empty_lines(rxn_chan_str)
return rxn_chan_str, full_dat_str_dct, hot_enes_dct
# ESDriver
if RUN_ES:
ioprinter.program_header('es')
# Build the elec struct tsk lst
ES_TSK_LST = parser.tsks.es_tsk_lst(ES_TSK_STR, THY_DCT)
# Call ESDriver for spc in each PES or SPC
if RUN_OBJ_DCT['pes']:
for (formula, pes_idx, sub_pes_idx), rxn_lst in RUN_PES_DCT.items():
# Print PES form and SUB PES Channels
ioprinter.pes(pes_idx, formula, sub_pes_idx)
for rxn in rxn_lst:
ioprinter.channel(rxn['chn_idx'], rxn['reacs'], rxn['prods'])
esdriver.run(
pes_idx,
rxn_lst,
SPC_DCT,
ES_TSK_LST,
THY_DCT,
RUN_INP_DCT
)
else:
PES_IDX = 0
esdriver.run(
PES_IDX,
RUN_SPC_LST_DCT,
SPC_DCT,