def save_kinetics_lib(rxn_list, path, name, lib_long_desc):
"""
Save an RMG kinetics library.
Args:
rxn_list (list): Entries are Reaction object instances for which kinetics will be saved.
path (str): The base folder in which the kinetic library will be saved.
name (str): The library name.
lib_long_desc (str): A multiline string with relevant description.
"""
entries = dict()
if rxn_list:
for i, rxn in enumerate(rxn_list):
if rxn.kinetics is not None:
entry = Entry(index=i,
item=rxn,
data=rxn.kinetics,
label=rxn.label)
entries[i + 1] = entry
else:
logging.warning(
f'Reaction {rxn.label} did not contain any kinetic data and was omitted from the '
f'kinetics library.')
kinetics_library = KineticsLibrary(name=name,
long_desc=lib_long_desc,
auto_generated=True)
kinetics_library.entries = entries
if os.path.exists(path):
shutil.rmtree(path)
try:
os.makedirs(path)
except OSError:
pass
kinetics_library.save(os.path.join(path, 'reactions.py'))
kinetics_library.save_dictionary(os.path.join(path, 'dictionary.txt'))
def save_kinetics_lib(rxn_list, path, name, lib_long_desc):
"""
Save an RMG kinetics library of all reactions in `rxn_list` in the supplied `path`
`rxn_list` is a list of ARCReaction objects
`name` is the library's name (or project's name)
`long_desc` is a multiline string with level of theory description
"""
entries = dict()
if rxn_list:
for i, rxn in enumerate(rxn_list):
if rxn.kinetics is not None:
if len(rxn.rmg_reaction.reactants):
reactants = rxn.rmg_reaction.reactants
products = rxn.rmg_reaction.products
elif rxn.r_species.mol_list is not None:
reactants = [Species(molecule=arc_spc.mol_list) for arc_spc in rxn.r_species]
products = [Species(molecule=arc_spc.mol_list) for arc_spc in rxn.p_species]
elif rxn.r_species.mol is not None:
reactants = [Species(molecule=[arc_spc.mol]) for arc_spc in rxn.r_species]
products = [Species(molecule=[arc_spc.mol]) for arc_spc in rxn.p_species]
else:
reactants = [Species(molecule=[arc_spc.xyz_mol]) for arc_spc in rxn.r_species]
products = [Species(molecule=[arc_spc.xyz_mol]) for arc_spc in rxn.p_species]
rxn.rmg_reaction.reactants = reactants
rxn.rmg_reaction.products = products
entry = Entry(
index=i,
item=rxn.rmg_reaction,
data=rxn.kinetics,
label=rxn.label)
rxn.ts_species.make_ts_report()
entry.longDesc = rxn.ts_species.ts_report + '\n\nOptimized TS geometry:\n' + rxn.ts_species.final_xyz
rxn.rmg_reaction.kinetics = rxn.kinetics
rxn.rmg_reaction.kinetics.comment = str('')
entries[i+1] = entry
else:
logging.warning('Reaction {0} did not contain any kinetic data and was omitted from the kinetics'
' library.'.format(rxn.label))
kinetics_library = KineticsLibrary(name=name, longDesc=lib_long_desc, autoGenerated=True)
kinetics_library.entries = entries
lib_path = os.path.join(path, 'kinetics', '')
if os.path.exists(lib_path):
shutil.rmtree(lib_path)
try:
os.makedirs(lib_path)
except OSError:
pass
kinetics_library.save(os.path.join(lib_path, 'reactions.py'))
kinetics_library.saveDictionary(os.path.join(lib_path, 'dictionary.txt'))