def loadKinetics(self,
path,
reactionLibraries=None,
seedMechanisms=None,
kineticsFamilies=None,
kineticsDepositories=None):
"""
Load the RMG kinetics database from the given `path` on disk, where
`path` points to the top-level folder of the RMG kinetics database.
"""
kineticsLibraries = []
libraryOrder = []
if seedMechanisms is None and reactionLibraries is None:
kineticsLibraries = None
if seedMechanisms is not None:
for library in seedMechanisms:
kineticsLibraries.append(library)
libraryOrder.append((library, 'Seed'))
if reactionLibraries is not None:
for library in reactionLibraries:
kineticsLibraries.append(library)
libraryOrder.append((library, 'Reaction Library'))
self.kinetics = KineticsDatabase()
self.kinetics.libraryOrder = libraryOrder
self.kinetics.load(path,
families=kineticsFamilies,
libraries=kineticsLibraries,
depositories=kineticsDepositories)
broadcast(self.kinetics, 'kinetics')
def setUpClass(cls):
"""A function run ONCE before all unit tests in this class."""
# Set up a dummy database
cls.database = RMGDatabase()
cls.database.load(
path=os.path.join(settings['test_data.directory'],
'testing_database'),
thermoLibraries=[],
reactionLibraries=[],
kineticsFamilies=[],
depository=False,
solvation=False,
testing=True,
)
cls.database.loadForbiddenStructures()
cls.thermoDatabase = ThermoDatabase() #the real full Thermo Database
cls.thermoDatabase.load(path=os.path.join(
settings['database.directory'], 'thermo'),
libraries=['primaryThermoLibrary'])
cls.kineticsDatabase = KineticsDatabase()
cls.kineticsDatabase.loadFamilies(
path=os.path.join(settings['test_data.directory'],
'testing_database/kinetics/families'),
families=[
'Singlet_Carbene_Intra_Disproportionation',
],
)
cls.family = cls.kineticsDatabase.families[
'Singlet_Carbene_Intra_Disproportionation']
def setUpClass(cls):
"""A function run ONCE before all unit tests in this class."""
# Set up a dummy database
cls.database = RMGDatabase()
cls.database.load(
path=os.path.join(settings['test_data.directory'], 'testing_database'),
thermo_libraries=[],
reaction_libraries=[],
kinetics_families=[],
depository=False,
solvation=False,
testing=True,
)
cls.database.load_forbidden_structures()
cls.thermoDatabase = ThermoDatabase() # the real full Thermo Database
cls.thermoDatabase.load(path=os.path.join(settings['database.directory'], 'thermo'),
libraries=['primaryThermoLibrary'])
cls.kineticsDatabase = KineticsDatabase()
cls.kineticsDatabase.load_families(
path=os.path.join(settings['test_data.directory'], 'testing_database/kinetics/families'),
families=[
'Singlet_Carbene_Intra_Disproportionation',
],
)
cls.family = cls.kineticsDatabase.families['Singlet_Carbene_Intra_Disproportionation']
cls.treerxns = cls.family.get_training_set(thermo_database=cls.thermoDatabase, remove_degeneracy=True,
estimate_thermo=True, fix_labels=True, get_reverse=True)
def setUpClass(cls):
"""
A function run ONCE before all unit tests in this class.
"""
# Set up a dummy database
cls.database = KineticsDatabase()
cls.database.loadLibraries(os.path.join(settings['test_data.directory'], 'testing_database','kinetics','libraries'),
libraries=None) #this loads all of them: ['GRI-Mech3.0', 'ethane-oxidation'])
cls.libraries = cls.database.libraries
def setUp(self):
"""
A function run before each unit test in this class.
"""
# Set up a dummy database
dir_path = os.path.dirname(os.path.realpath(__file__))
self.database = KineticsDatabase()
self.database.loadFamilies(os.path.join(dir_path, "family_test_data"),
families=['intra_H_migration'])
self.family = self.database.families['intra_H_migration']
def setUp(self):
"""
A function run before each unit test in this class.
"""
# Set up a dummy database
self.database = KineticsDatabase()
self.database.loadFamilies(os.path.join(
settings['test_data.directory'],
'testing_database/kinetics/families'),
families=['intra_H_migration'])
self.family = self.database.families['intra_H_migration']
def setUpClass(cls):
"""
A function run ONCE before all unit tests in this class.
"""
# Set up a dummy database
cls.database = KineticsDatabase()
cls.database.loadFamilies(
os.path.join(settings['test_data.directory'],
'testing_database/kinetics/families'),
families=['intra_H_migration', 'R_Addition_MultipleBond'])
cls.family = cls.database.families['intra_H_migration']
def test_load_families_correct(self):
"""Test valid methods for loading kinetics families."""
path = os.path.join(settings['test_data.directory'],
'testing_database', 'kinetics', 'families')
database = KineticsDatabase()
database.loadRecommendedFamiliesList(
os.path.join(path, 'recommended.py'))
try:
database.loadFamilies(path, families=[])
except DatabaseError:
self.fail("Unable to load families using list []")
try:
database.loadFamilies(path, families='none')
except DatabaseError:
self.fail("Unable to load families using keyword 'none'")
try:
database.loadFamilies(path, families='default')
except DatabaseError:
self.fail("Unable to load families using keyword 'default'")
try:
database.loadFamilies(path, families=['default', 'pah'])
except DatabaseError:
self.fail("Unable to load families using list ['default', 'pah']")
try:
database.loadFamilies(path, families=['R_Addition_MultipleBond'])
except DatabaseError:
self.fail(
"Unable to load families using list ['R_Addition_MultipleBond']"
)
try:
database.loadFamilies(
path, families=['!H_Abstraction', '!Disproportionation'])
except DatabaseError:
self.fail(
"Unable to load families using list ['!H_Abstraction', '!Disproportionation']"
)
try:
database.loadFamilies(path, families='!pah')
except DatabaseError:
self.fail("Unable to load families using keyword '!pah'")
try:
database.loadFamilies(path, families=['H_Abstraction', 'pah'])
except DatabaseError:
self.fail(
"Unable to load families using list ['H_Abstraction', 'pah']")
def test_load_families_incorrect(self):
"""Test invalid methods for loading kinetics families"""
path = os.path.join(settings['test_data.directory'], 'testing_database', 'kinetics', 'families')
database = KineticsDatabase()
database.loadRecommendedFamiliesList(os.path.join(path, 'recommended.py'))
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families='random')
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families=['!H_Abstraction','Disproportionation'])
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families=['fake_family'])
def read_kinetic_lib_from_path(lib_path,
kinetic_db,
overwrite=False,
create=False):
"""
Read RMG kinetic library given its file path. The species dictionary should
be included under the same directory.
Args:
lib_path (str): Path to thermo library file
kinetic_db (RMG KineticsDatabase): RMG database object
"""
if not os.path.exists(lib_path) and create:
create_kinetic_lib(os.path.dirname(lib_path))
lib = KineticsLibrary()
kinetic_db.libraries[lib_path] = lib
kinetic_db.library_order.append(lib_path)
logging.info(
'Created kinetics library {1} at {0} ...'.format(
os.path.split(lib_path)[0],
os.path.split(lib_path)[1]), )
elif lib_path not in kinetic_db.library_order or overwrite:
lib = KineticsLibrary()
try:
lib.load(lib_path,
KineticsDatabase().local_context,
KineticsDatabase().global_context)
except:
logging.error('The library file %s is not vaild.' % (lib_path))
else:
lib.label = lib_path
kinetic_db.libraries[lib.label] = lib
kinetic_db.library_order.append(lib.label)
logging.info(
'Loading kinetics library {1} from {0} ...'.format(
os.path.split(lib_path)[0],
os.path.split(lib_path)[1]), )
else:
logging.warning('The library %s has already been loaded' % (lib_path))
def testLoadFamilies(self):
"""
Test that the loadFamilies function raises the correct exceptions
"""
path = os.path.join(settings['database.directory'],'kinetics','families')
database = KineticsDatabase()
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families='random')
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families=['!H_Abstraction','Disproportionation'])
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families=['fake_family'])
with self.assertRaises(DatabaseError):
database.loadFamilies(path, families=[])
def loadOld(self, path):
"""
Load the old RMG database from the given `path` on disk, where `path`
points to the top-level folder of the old RMG database.
"""
self.thermo = ThermoDatabase()
self.thermo.loadOld(path)
self.transport = TransportDatabase()
#self.transport.loadOld(path) # Currently no loadOld import function available for transport groups
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.loadOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics = KineticsDatabase()
self.kinetics.loadOld(path)
self.statmech = StatmechDatabase()
self.statmech.loadOld(path)
self.solvation = SolvationDatabase()
def setUpClass(cls):
"""
A function run ONCE before all unit tests in this class.
"""
# Set up a dummy database
cls.database = KineticsDatabase()
cls.database.loadFamilies(
path=os.path.join(settings['test_data.directory'],
'testing_database/kinetics/families'),
families=[
'intra_H_migration', 'R_Addition_MultipleBond',
'H_Abstraction', 'Intra_ene_reaction',
'6_membered_central_C-C_shift', '1,2_shiftC',
'Intra_R_Add_Exo_scission',
'intra_substitutionS_isomerization', 'R_Addition_COm'
],
)
cls.family = cls.database.families['intra_H_migration']
