def objects_dct(job_path):
""" Get the sections for the run block
"""
# Read the obj section
run_str = ptt.read_inp_str(job_path, RUN_INP, remove_comments='#')
obj_str = object_block(run_str)
# Read the sections of the obj section
pes_block_str = apf.first_capture(ptt.paren_section('pes'), obj_str)
spc_block_str = apf.first_capture(ptt.paren_section('spc'), obj_str)
# Check if the obj section has been specified
check_obj_spec(obj_str, pes_block_str, spc_block_str)
# Build the run dictionary
run_dct = {}
if pes_block_str is not None:
run_dct['pes'] = get_pes_idxs(
ioformat.remove_whitespace(pes_block_str))
else:
run_dct['pes'] = []
if spc_block_str is not None:
run_dct['spc'] = get_spc_idxs(
ioformat.remove_whitespace(spc_block_str))
else:
run_dct['spc'] = []
return run_dct
def build_pes_dct(job_path, mech_type, spc_dct, run_obj_dct, sort_rxns=True):
"""Build the PES dct
"""
# Read the string
mech_str = ptt.read_inp_str(job_path, MECH_INP, remove_comments='!')
# Build the total PES dct
mech_info = mechanalyzer.parser.pes.read_mechanism_file(
mech_str, mech_type, spc_dct, sort_rxns=sort_rxns)
pes_dct = mechanalyzer.parser.pes.build_pes_dct(*mech_info)
# Build an index dct relating idx to formula
idx_dct, form_dct = build_pes_idx_dct(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 with the PESs to run
conn_chnls_dct = mechanalyzer.parser.pes.connected_channels_dct(
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(reduced_pes_dct, idx_dct, form_dct,
conn_chnls_dct, run_obj_dct)
# Print the channels for the whole mechanism file
print_pes_channels(pes_dct)
return run_pes_dct
def read_spc_amech(job_path):
""" Read an amech style input file for the species
"""
# Read the AMech species string
if os.path.exists(os.path.join(job_path, DAT_INP)):
spc_amech_str = ptt.read_inp_str(
job_path, DAT_INP, remove_comments='#')
print('Found species.dat. Reading file...')
else:
spc_amech_str = ''
print('No species.dat file...')
# Build the keyword dcts
amech_dct = {}
if spc_amech_str:
# Read each of the species sections and build the dcts
spc_sections = apf.all_captures(
ptt.end_section_wname2('spc'), spc_amech_str)
if spc_sections:
# Get the global species section
for section in spc_sections:
if section[0] == 'global':
# Build the global species section
keyword_dct = ptt.build_keyword_dct(section[1])
amech_dct['global'] = keyword_dct
else:
# Build each species dct to overwrite global dct
name = section[0]
keyword_dct = ptt.build_keyword_dct(section[1])
amech_dct[name] = keyword_dct
return amech_dct
def build_spc_dct(job_path, spc_type):
""" Build the species dct
"""
spc_str = ptt.read_inp_str(job_path, CSV_INP)
spc_dct = mechanalyzer.parser.spc.build_spc_dct(spc_str, spc_type)
# Modify spc dct with params from the AMech file
mod_spc_dct = modify_spc_dct(job_path, spc_dct)
return mod_spc_dct
def build_run_jobs_lst(job_path):
""" Build a dictionary for all the theory keywords
"""
# Read the jobs section
job_str = ptt.read_inp_str(job_path, RUN_INP, remove_comments='#')
keyword_lst = ptt.build_keyword_lst(jobs_block(job_str))
# Check the jobs sectuib
check_run_jobs_section(job_str, keyword_lst)
return keyword_lst
def parse_rxn_class_file(job_path):
""" Read the class dictionary
"""
if os.path.exists(os.path.join(job_path, CLA_INP)):
print(' class.dat found. Reading contents...')
cla_str = ptt.read_inp_str(job_path, CLA_INP, remove_comments='#')
cla_dct = _build_cla_dct(cla_str)
else:
print(' No class.dat found.')
cla_dct = {}
return cla_dct
def read_es_tsks(job_path):
""" Build a dictionary for all the theory keywords
"""
# Read the electronic structure tasks section
run_str = ptt.read_inp_str(job_path, RUN_INP, remove_comments='#')
es_tsks_str = es_tsks_block(run_str)
# Check if section is there
if es_tsks_str is None:
print('*ERROR: No "es_tsks" section defined in run.dat')
sys.exit()
return es_tsks_str
def read_models_sections(job_path):
""" species input
"""
mod_str = ptt.read_inp_str(job_path, MODEL_INP, remove_comments='#')
# Build a dictionary for the PES models
pes_model_sections = apf.all_captures(ptt.end_section_wname2('pes_model'),
mod_str)
assert pes_model_sections is not None
pes_model_methods = {}
glob_pes_model_methods = {}
for section in pes_model_sections:
if section[0] == 'global':
name = section[0]
keyword_dct = build_pes_model_keyword_dct(section[1])
glob_pes_model_methods = keyword_dct
break
pes_model_methods['global'] = glob_pes_model_methods
for section in pes_model_sections:
if section[0] != 'global':
name = section[0]
keyword_dct = build_pes_model_keyword_dct(section[1])
pes_model_methods[name] = combine_glob_and_spc_dct(
glob_pes_model_methods, keyword_dct)
# Build a dictionary for the spc models
spc_model_sections = apf.all_captures(ptt.end_section_wname2('spc_model'),
mod_str)
assert spc_model_sections is not None
spc_model_methods = {}
glob_spc_model_methods = {}
for section in spc_model_sections:
if section[0] == 'global':
name = section[0]
keyword_dct = build_spc_model_keyword_dct(section[1])
glob_spc_model_methods = keyword_dct
break
spc_model_methods['global'] = glob_spc_model_methods
for section in spc_model_sections:
if section[0] != 'global':
name = section[0]
keyword_dct = build_spc_model_keyword_dct(section[1])
spc_model_methods[name] = combine_glob_and_spc_dct(
glob_spc_model_methods, keyword_dct)
return pes_model_methods, spc_model_methods
def build_thy_dct(job_path):
""" species input
"""
# Obtain the species string
thy_str = ptt.read_inp_str(job_path, THY_INP, remove_comments='#')
# Obtain any thy_sections
thy_sections = apf.all_captures(
ptt.end_section_wname2('level'), thy_str)
check_thy_sections_nonempty(thy_sections)
# Build dictionary of theory methods
thy_methods = {}
for section in thy_sections:
name = section[0]
keyword_dct = build_thy_keyword_dct(name, section[1])
thy_methods[name] = keyword_dct
return thy_methods
def build_run_inp_dct(job_path):
""" Build a dictionary for all the theory keywords
"""
# Read the input section
run_str = ptt.read_inp_str(job_path, RUN_INP, remove_comments='#')
keyword_dct = ptt.build_keyword_dct(inp_block(run_str))
# Add defaults
if 'mech' not in keyword_dct:
keyword_dct['mech'] = 'chemkin'
if 'spc' not in keyword_dct:
keyword_dct['spc'] = 'csv'
if 'print_mech' not in keyword_dct:
keyword_dct['print_mech'] = False
# Check if section specified fully and supported
check_run_keyword_dct(keyword_dct)
return keyword_dct
def modify_spc_dct(job_path, spc_dct):
""" Modify the species dct using input from the additional AMech file
"""
# Read in other dcts
amech_dct = read_spc_amech(job_path)
geom_dct = geometry_dictionary(job_path)
mod_spc_dct = {}
for spc in spc_dct:
# Set the ich and mult
ich = spc_dct[spc]['inchi']
mul = spc_dct[spc]['mult']
chg = spc_dct[spc]['charge']
mod_spc_dct[spc] = {}
mod_spc_dct[spc]['inchi'] = ich
mod_spc_dct[spc]['mult'] = mul
mod_spc_dct[spc]['charge'] = chg
# Add params from global dct in amech dct
if 'global' in amech_dct:
for key, val in amech_dct['global'].items():
mod_spc_dct[spc][key] = val
# Add/Reset the parameters from the species specific dct
if spc in amech_dct:
for key, val in amech_dct[spc].items():
mod_spc_dct[spc][key] = val
# Second loop for transtion states defined in species.dat
for spc in amech_dct:
if 'ts' in spc:
mod_spc_dct[spc] = {}
# Add params from global dct in amech dct
if 'global' in amech_dct:
for key, val in amech_dct['global'].items():
mod_spc_dct[spc][key] = val
# Add the ts stuff
mod_spc_dct[spc] = amech_dct[spc]
# Add global to mod_spc_dct for other TS stuff later
if 'global' in amech_dct:
mod_spc_dct['global'] = amech_dct['global']
# Final loop to add in things that are needed but could be missing
for spc in mod_spc_dct:
if spc != 'global' and 'ts_' not in spc:
ich, mul = mod_spc_dct[spc]['inchi'], mod_spc_dct[spc]['mult']
if 'elec_levels' not in mod_spc_dct[spc]:
if (ich, mul) in eleclvl.DCT:
mod_spc_dct[spc]['elec_levels'] = eleclvl.DCT[(ich, mul)]
else:
mod_spc_dct[spc]['elec_levels'] = [[0.0, mul]]
if 'sym_factor' not in mod_spc_dct[spc]:
if (ich, mul) in symm.DCT:
mod_spc_dct[spc]['sym_factor'] = symm.DCT[(ich, mul)]
# Add defaults here for now
if 'hind_inc' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['hind_inc'] = 30.0
if 'kickoff' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['kickoff'] = [0.1, False]
if 'tau_nsamp' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['tau_nsamp'] = [True, 12, 1, 3, 100, 25]
if 'mc_nsamp' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['mc_nsamp'] = [True, 12, 1, 3, 100, 25]
if 'pst_params' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['pst_params'] = [1.0, 6]
# Set active space stuff
if 'active' not in mod_spc_dct[spc]:
mod_spc_dct[spc]['active_space'] = None
else:
aspace = mod_spc_dct[spc].get('active')
assert len(aspace) == 4, (
'active must be length 4: {}'.format(aspace)
)
wfn_file = aspace[3]
wfn_inp = os.path.join(os.path.join(job_path, 'inp/'+wfn_file))
if os.path.exists(wfn_inp):
wfn_str = ptt.read_inp_str(job_path, wfn_inp)
print('Found file: {}. Reading file...'.format(wfn_file))
else:
wfn_str = None
print('No file: {}. Reading file...'.format(wfn_file))
mod_spc_dct[spc]['active_space'] = (
aspace[0], aspace[1], aspace[2], wfn_str)
# Perform conversions as needed
mod_spc_dct[spc]['hind_inc'] *= phycon.DEG2RAD
# if 'ts' in spc:
# print(mod_spc_dct[spc]['hind_inc'])
# Add geoms from geo dct (prob switch to amech file)
if ich in geom_dct:
mod_spc_dct[spc]['geo_inp'] = geom_dct[ich]
return mod_spc_dct
