def save_thermo_lib(species_list, path, name, lib_long_desc):
"""
Save an RMG thermo library.
Args:
species_list (list): Entries are Species object instances for which thermo will be saved.
path (str): The base folder in which the thermo library will be saved.
name (str): The library name.
lib_long_desc (str): A multiline string with relevant description.
"""
if species_list:
lib_path = os.path.join(path, f'{name}.py')
thermo_library = ThermoLibrary(name=name, long_desc=lib_long_desc)
for i, spc in enumerate(species_list):
if spc.thermo is not None:
long_thermo_description = f'\nSpin multiplicity: {spc.conformer.spin_multiplicity}' \
f'\nExternal symmetry: {spc.molecule[0].symmetry_number}' \
f'\nOptical isomers: {spc.conformer.optical_isomers}\n'
xyz = get_str_xyz(spc)
if xyz is not None:
long_thermo_description += f'\nGeometry:\n{xyz}'
thermo_library.load_entry(
index=i,
label=spc.label,
molecule=spc.molecule[0].to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.thermo.comment,
longDesc=long_thermo_description)
else:
logging.warning(
f'Species {spc.label} did not contain any thermo data and was omitted from the thermo '
f'library {name}.')
thermo_library.save(lib_path)
def run_thermo_estimator(input_file, library_flag):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.load_thermo_input(input_file)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.load_thermo(os.path.join(path, 'thermo'),
rmg.thermo_libraries,
depository=False)
if rmg.solvent:
rmg.database.load_solvation(os.path.join(path, 'solvation'))
Species.solvent_data = rmg.database.solvation.get_solvent_data(
rmg.solvent)
Species.solvent_name = rmg.solvent
for species in rmg.initial_species:
submit(species)
if library_flag:
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initial_species:
library.load_entry(
index=len(library.entries) + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.get_thermo_data().to_thermo_data(),
shortDesc=species.get_thermo_data().comment,
)
library.save(os.path.join(rmg.output_directory, 'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
save_chemkin_file(os.path.join(rmg.output_directory, 'chem_annotated.inp'),
species=rmg.initial_species,
reactions=[])
save_species_dictionary(os.path.join(rmg.output_directory,
'species_dictionary.txt'),
species=rmg.initial_species)
def get_libraries(self):
"""Get RMG kinetics and thermo libraries"""
name = 'kineticsjobs'
species_list = list(self.species_dict.values())
reaction_list = list(self.reaction_dict.values())
# remove duplicate species
for rxn in reaction_list:
for i, rspc in enumerate(rxn.reactants):
for spc in species_list:
if spc.is_isomorphic(rspc):
rxn.reactants[i] = spc
break
for i, rspc in enumerate(rxn.products):
for spc in species_list:
if spc.is_isomorphic(rspc):
rxn.products[i] = spc
break
del_inds = []
for i, spc1 in enumerate(species_list):
for j, spc2 in enumerate(species_list):
if j > i and spc1.is_isomorphic(spc2):
del_inds.append(j)
for j in sorted(del_inds)[::-1]:
del species_list[j]
thermo_library = ThermoLibrary(name=name)
for i, species in enumerate(species_list):
if species.thermo:
thermo_library.load_entry(
index=i + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.thermo,
shortDesc=species.thermo.comment)
else:
logging.warning(
'Species {0} did not contain any thermo data and was omitted from the thermo library.'
.format(str(species)))
# load kinetics library entries
kinetics_library = KineticsLibrary(name=name, auto_generated=True)
kinetics_library.entries = {}
for i, reaction in enumerate(reaction_list):
entry = Entry(index=i + 1,
label=reaction.to_labeled_str(),
item=reaction,
data=reaction.kinetics)
if reaction.kinetics is not None:
if hasattr(reaction, 'library') and reaction.library:
entry.long_desc = 'Originally from reaction library: ' + \
reaction.library + "\n" + reaction.kinetics.comment
else:
entry.long_desc = reaction.kinetics.comment
kinetics_library.entries[i + 1] = entry
kinetics_library.label = name
return thermo_library, kinetics_library, species_list
args = parser.parse_args()
chemkin_path = args.chemkin_path[0]
dictionary_path = args.dictionary_path[0]
name = args.name[0]
species_list, reaction_list = load_chemkin_file(chemkin_path,
dictionary_path)
thermo_library = ThermoLibrary(name=name)
for i in range(len(species_list)):
species = species_list[i]
if species.thermo:
thermo_library.load_entry(
index=i + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.thermo,
)
else:
logging.warning(
"""Species {0} did not contain any thermo data and was omitted from the thermo
library.""".format(str(species)))
# load kinetics library entries
kinetics_library = KineticsLibrary(name=name)
kinetics_library.entries = {}
for i in range(len(reaction_list)):
reaction = reaction_list[i]
entry = Entry(
index=i + 1,
label=str(reaction),
