def load_libraries(self, path, libraries=None):
"""
Load the listed kinetics libraries from the given `path` on disk.
Loads them all if `libraries` list is not specified or `None`.
The `path` points to the folder of kinetics libraries in the database,
and the libraries should be in files like :file:`<path>/<library>.py`.
"""
if libraries is not None:
for library_name in libraries:
library_file = os.path.join(path, library_name, 'reactions.py')
if os.path.exists(library_file):
logging.info(
'Loading kinetics library {0} from {1}...'.format(
library_name, library_file))
library = KineticsLibrary(label=library_name)
library.load(library_file, self.local_context,
self.global_context)
self.libraries[library.label] = library
else:
if library_name == "KlippensteinH2O2":
logging.info(
"""\n** Note: The KlippensteinH2O2 library was replaced and is no longer available in RMG.
For H2 combustion chemistry consider using either the BurkeH2inN2 or BurkeH2inArHe
library instead, depending on the main bath gas (N2 or Ar/He, respectively)\n"""
)
raise IOError("Couldn't find kinetics library {0}".format(
library_file))
else:
# load all the libraries you can find
# this cannot be activated in a normal RMG job. Only activated when loading the database for other purposes
self.library_order = []
for (root, dirs, files) in os.walk(os.path.join(path)):
for f in files:
name, ext = os.path.splitext(f)
if ext.lower() == '.py':
library_file = os.path.join(root, f)
label = os.path.dirname(library_file)[len(path) + 1:]
logging.info(
'Loading kinetics library {0} from {1}...'.format(
label, library_file))
library = KineticsLibrary(label=label)
try:
library.load(library_file, self.local_context,
self.global_context)
except:
logging.error(
"Problem loading reaction library {0!r}".
format(library_file))
raise
self.libraries[library.label] = library
self.library_order.append(
(library.label, 'Reaction Library'))
def import_kinetics(kinetics_path, kinetic_model, models):
local_context = {
"KineticsData": kinetics.KineticsData,
"Arrhenius": kinetics.Arrhenius,
"ArrheniusEP": kinetics.ArrheniusEP,
"MultiArrhenius": kinetics.MultiArrhenius,
"MultiPDepArrhenius": kinetics.MultiPDepArrhenius,
"PDepArrhenius": kinetics.PDepArrhenius,
"Chebyshev": kinetics.Chebyshev,
"ThirdBody": kinetics.ThirdBody,
"Lindemann": kinetics.Lindemann,
"Troe": kinetics.Troe,
"R": constants.R,
}
library = KineticsLibrary(label=kinetic_model.model_name)
library.SKIP_DUPLICATES = True
library.load(kinetics_path, local_context=local_context)
for entry in library.entries.values():
try:
with transaction.atomic():
rmg_kinetics_data = entry.data
comment = entry.short_desc
rmg_reaction = entry.item
reaction = get_or_create_reaction(kinetic_model, rmg_reaction,
models)
kinetics_data = create_kinetics_data(kinetic_model,
rmg_kinetics_data, models)
base_fields = get_base_kinetics_data_fields(rmg_kinetics_data)
kinetics_instance, created = models.Kinetics.objects.get_or_create(
reaction=reaction,
raw_data=kinetics_data,
defaults=base_fields)
if created and kinetics_data.get("type") not in [
"arrhenius",
"arrhenius_ep",
"multi_arrhenius",
]:
create_and_save_efficiencies(kinetic_model,
kinetics_instance,
rmg_kinetics_data, models)
models.KineticsComment.objects.get_or_create(
kinetics=kinetics_instance,
kinetic_model=kinetic_model,
defaults={"comment": comment},
)
except Exception:
logger.exception(f"Failed to import reaction {entry.label}")