def chemkin_to_kinetic_lib(chem_path,
dict_path,
name,
save_path='',
use_chemkin_names=True):
"""
Convert a CHEMKIN file into a RMG kinetic library given species dictionary
and the library name.
Args:
chem_path (str): The path to the CHEMKIN file
dict_path (str): The path to a species dictionary
name (str): The name of the new library
save_path (str): The path to the saving directory. By default, the library
will be saved to RMG-database repository
use_chemkin_names (bool): Use the original CHEMKIN species name
"""
# Load the reactions from the CHEMKIN FILE
logging.info('Loading CHEMKIN file %s with species dictionary %s' %
(chem_path, dict_path))
_, rxns = load_chemkin_file(chem_path,
dict_path,
use_chemkin_names=use_chemkin_names)
kinetic_lib = KineticsLibrary(name=name)
kinetic_lib.entries = {}
# Create new entries
for i in range(len(rxns)):
rxn = rxns[i]
entry = Entry(
index=i + 1,
label=str(rxn),
item=rxn,
data=rxn.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + \
rxn.library + "\n" + rxn.kinetics.comment
except AttributeError:
entry.long_desc = rxn.kinetics.comment
kinetic_lib.entries[i + 1] = entry
logging.info('Adding reaction %s in to the kinetic library %s' %
(entry.label, name))
# Check for duplicates and convert them to multiArrhenius / multiPdepArrehenius
kinetic_lib.check_for_duplicates(mark_duplicates=True)
kinetic_lib.convert_duplicates_to_multi()
# Save the library
if not save_path:
save_path = os.path.join(settings['database.directory'], 'kinetics',
'libraries')
try:
os.makedirs(os.path.join(save_path, name))
except:
pass
logging.info('Saving the kinetic library to %s' %
(os.path.join(save_path, name)))
kinetic_lib.save(os.path.join(save_path, name, 'reactions.py'))
kinetic_lib.save_dictionary(os.path.join(save_path, name,
'dictionary.txt'))
rdkitmol = species.molecule[0].toRDKitMol(removeHs=False)
species.molecule = [Molecule().fromRDKitMol(rdkitmol)]#[0].toAdjacencyList(removeH=False)
print species.molecule[0].toAdjacencyList(removeH = removeH)
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(removeH = removeH),
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
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
user = getUsername() # Pulls username from current git repository
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),
item=reaction,
data=reaction.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.long_desc = reaction.kinetics.comment
kinetics_library.entries[i + 1] = entry
# Mark as duplicates where there are mixed pressure dependent and non-pressure dependent duplicate kinetics
thermoLibrary = ThermoLibrary(name=name)
for i in range(len(speciesList)):
species = speciesList[i]
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
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
kineticsLibrary = KineticsLibrary(name=name)
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
try:
entry.longDesc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
# Mark as duplicates where there are mixed pressure dependent and non-pressure dependent duplicate kinetics