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'))
def load_old(self, path):
"""
Load an old-style RMG kinetics library from the location `path`.
"""
path = os.path.abspath(path)
self.load_old_dictionary(os.path.join(path, 'species.txt'),
pattern=False)
species = dict([(label, Species(label=label, molecule=[entry.item]))
for label, entry in self.entries.items()])
# Add common bath gases (Ar, Ne, He, N2) if not already present
for label, smiles in [('Ar', '[Ar]'), ('He', '[He]'), ('Ne', '[Ne]'),
('N2', 'N#N')]:
if label not in species:
molecule = Molecule().from_smiles(smiles)
spec = Species(label=label, molecule=[molecule])
species[label] = spec
reactions = []
reactions.extend(
self._load_old_reactions(os.path.join(path, 'reactions.txt'),
species))
if os.path.exists(os.path.join(path, 'pdepreactions.txt')):
pdep_reactions = self._load_old_reactions(
os.path.join(path, 'pdepreactions.txt'), species)
# RMG-Py likes otherwise equivalent PDep and non-pdep reactions to be marked as duplicates
self.mark_valid_duplicates(reactions, pdep_reactions)
reactions.extend(pdep_reactions)
self.entries = {}
for index, reaction in enumerate(reactions):
entry = Entry(index=index + 1,
item=reaction,
data=reaction.kinetics,
label=str(reaction))
entry.long_desc = reaction.kinetics.comment
reaction.kinetics.comment = ''
self.entries[index + 1] = entry
reaction.kinetics = None
self.check_for_duplicates()
self.convert_duplicates_to_multi()
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
"""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
# Even though CHEMKIN does not require a duplicate flag, RMG needs it.
# Using flag mark_duplicates = True
kinetics_library.check_for_duplicates(mark_duplicates=True)
kinetics_library.convert_duplicates_to_multi()
# Save in Py format
database_directory = settings['database.directory']
try:
os.makedirs(
os.path.join(database_directory, 'kinetics', 'libraries', name))
