def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
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 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.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)
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)
class RMGDatabase:
"""
The primary class for working with the RMG database.
"""
def __init__(self):
self.thermo = None
self.transport = None
self.forbiddenStructures = None
self.kinetics = None
self.statmech = None
self.solvation = None
# Store the newly created database in the module.
global database
# assert database is None, "Should only make one instance of RMGDatabase because it's stored as a module-level variable."
if database is None:
database = self
else:
import logging
logging.warning("Should only make one instance of RMGDatabase because it's stored as a module-level variable!")
logging.warning("Unexpected behaviour may result!")
def load(self,
path,
thermoLibraries=None,
transportLibraries=None,
reactionLibraries=None,
seedMechanisms=None,
kineticsFamilies=None,
kineticsDepositories=None,
statmechLibraries=None,
depository=True,
solvation=True,
):
"""
Load the RMG database from the given `path` on disk, where `path`
points to the top-level folder of the RMG database. If none of the
optional arguments are provided, then the entire database will be
loaded. You can use the optional arguments to specify that only certain
components of the database be loaded.
"""
self.loadThermo(os.path.join(path, 'thermo'), thermoLibraries, depository)
self.loadTransport(os.path.join(path, 'transport'), transportLibraries)
self.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
self.loadKinetics(os.path.join(path, 'kinetics'),
reactionLibraries,
seedMechanisms,
kineticsFamilies,
kineticsDepositories
)
self.loadStatmech(os.path.join(path, 'statmech'), statmechLibraries, depository)
if solvation:
self.loadSolvation(os.path.join(path, 'solvation'))
def loadThermo(self, path, thermoLibraries=None, depository=True):
"""
Load the RMG thermo database from the given `path` on disk, where
`path` points to the top-level folder of the RMG thermo database.
"""
self.thermo = ThermoDatabase()
self.thermo.load(path, thermoLibraries, depository)
def loadTransport(self, path, transportLibraries=None):
"""
Load the RMG transport database from the given 'path' on disk, where
'path' points to the top-level folder of the RMG transport database.
"""
self.transport = TransportDatabase()
self.transport.load(path, transportLibraries)
def loadForbiddenStructures(self, path):
"""
Load the RMG forbidden structures from the given `path` on disk, where
`path` points to the forbidden structures file.
"""
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.load(path)
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
)
def loadSolvation(self, path):
"""
Load the RMG solvation database from the given `path` on disk, where
`path` points to the top-level folder of the RMG solvation database.
"""
self.solvation = SolvationDatabase()
self.solvation.load(path)
def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
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)
def save(self, path):
"""
Save the RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.forbiddenStructures.save(os.path.join(path, 'forbiddenStructures.py'))
self.thermo.save(os.path.join(path, 'thermo'))
# self.transport.save(os.path.join(path, 'transport')) #Currently no function for saving transport groups
self.kinetics.save(os.path.join(path, 'kinetics'))
self.statmech.save(os.path.join(path, 'statmech'))
def saveOld(self, path):
"""
Save the old RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.thermo.saveOld(path)
self.transport.saveOld(path)
self.forbiddenStructures.saveOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics.saveOld(path)
self.statmech.saveOld(path)
class RMGDatabase:
"""
The primary class for working with the RMG database.
"""
def __init__(self):
self.thermo = None
self.forbiddenStructures = None
self.kinetics = None
self.statmech = None
# Store the newly created database in the module.
global database
assert database is None, "Should only make one instance of RMGDatabase because it's stored as a module-level variable."
database = self
def load(self,
path,
thermoLibraries=None,
reactionLibraries=None,
seedMechanisms=None,
kineticsFamilies=None,
kineticsDepositories=None,
statmechLibraries=None,
depository=True
):
"""
Load the RMG database from the given `path` on disk, where `path`
points to the top-level folder of the RMG database. If none of the
optional arguments are provided, then the entire database will be
loaded. You can use the optional arguments to specify that only certain
components of the database be loaded.
"""
self.loadThermo(os.path.join(path, 'thermo'), thermoLibraries, depository)
self.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
self.loadKinetics(os.path.join(path, 'kinetics'),
reactionLibraries,
seedMechanisms,
kineticsFamilies,
kineticsDepositories
)
self.loadStatmech(os.path.join(path, 'statmech'), statmechLibraries, depository)
def loadThermo(self, path, thermoLibraries=None, depository=True):
"""
Load the RMG thermo database from the given `path` on disk, where
`path` points to the top-level folder of the RMG thermo database.
"""
self.thermo = ThermoDatabase()
self.thermo.load(path, thermoLibraries, depository)
def loadForbiddenStructures(self, path):
"""
Load the RMG forbidden structures from the given `path` on disk, where
`path` points to the forbidden structures file.
"""
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.load(path)
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 = []
if reactionLibraries is not None and seedMechanisms is not None:
kineticsLibraries.extend(seedMechanisms)
kineticsLibraries.extend(reactionLibraries)
elif reactionLibraries is not None and seedMechanisms is None:
kineticsLibraries.extend(reactionLibraries)
elif reactionLibraries is None and seedMechanisms is not None:
kineticsLibraries.extend(seedMechanisms)
else:
kineticsLibraries = None
self.kinetics = KineticsDatabase()
self.kinetics.load(path,
families=kineticsFamilies,
libraries=kineticsLibraries,
depositories=kineticsDepositories
)
def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
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.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)
def save(self, path):
"""
Save the RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.forbiddenStructures.save(os.path.join(path, 'forbiddenStructures.py'))
self.thermo.save(os.path.join(path, 'thermo'))
self.kinetics.save(os.path.join(path, 'kinetics'))
self.statmech.save(os.path.join(path, 'statmech'))
def saveOld(self, path):
"""
Save the old RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.thermo.saveOld(path)
self.forbiddenStructures.saveOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics.saveOld(path)
self.statmech.saveOld(path)
class RMGDatabase:
"""
The primary class for working with the RMG database.
"""
def __init__(self):
self.thermo = None
self.transport = None
self.forbiddenStructures = None
self.kinetics = None
self.statmech = None
self.solvation = None
# Store the newly created database in the module.
global database
# assert database is None, "Should only make one instance of RMGDatabase because it's stored as a module-level variable."
if database is None:
database = self
else:
logging.warning(
"Should only make one instance of RMGDatabase because it's stored as a module-level variable!"
)
logging.warning("Unexpected behaviour may result!")
def load(self,
path,
thermoLibraries=None,
transportLibraries=None,
reactionLibraries=None,
seedMechanisms=None,
kineticsFamilies=None,
kineticsDepositories=None,
statmechLibraries=None,
depository=True,
solvation=True,
testing=False):
"""
Load the RMG database from the given `path` on disk, where `path`
points to the top-level folder of the RMG database. If none of the
optional arguments are provided, then the entire database will be
loaded. You can use the optional arguments to specify that only certain
components of the database be loaded.
Argument testing will load a lighter version of the database used for unit-tests
"""
self.loadThermo(os.path.join(path, 'thermo'), thermoLibraries,
depository)
if not testing:
self.loadTransport(os.path.join(path, 'transport'),
transportLibraries)
self.loadForbiddenStructures(
os.path.join(path, 'forbiddenStructures.py'))
self.loadKinetics(os.path.join(path, 'kinetics'), reactionLibraries,
seedMechanisms, kineticsFamilies,
kineticsDepositories)
if not testing:
self.loadStatmech(os.path.join(path, 'statmech'),
statmechLibraries, depository)
if solvation:
self.loadSolvation(os.path.join(path, 'solvation'))
def loadThermo(self, path, thermoLibraries=None, depository=True):
"""
Load the RMG thermo database from the given `path` on disk, where
`path` points to the top-level folder of the RMG thermo database.
"""
self.thermo = ThermoDatabase()
self.thermo.load(path, thermoLibraries, depository)
broadcast(self.thermo, 'thermo')
def loadTransport(self, path, transportLibraries=None):
"""
Load the RMG transport database from the given 'path' on disk, where
'path' points to the top-level folder of the RMG transport database.
"""
self.transport = TransportDatabase()
self.transport.load(path, transportLibraries)
broadcast(self.transport, 'transport')
def loadForbiddenStructures(self, path=None):
"""
Load the RMG forbidden structures from the given `path` on disk, where
`path` points to the forbidden structures file.
If no path is given, a blank forbidden structures object is created.
"""
self.forbiddenStructures = ForbiddenStructures()
if path is not None:
self.forbiddenStructures.load(path)
broadcast(self.forbiddenStructures, 'forbidden')
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 loadSolvation(self, path):
"""
Load the RMG solvation database from the given `path` on disk, where
`path` points to the top-level folder of the RMG solvation database.
"""
self.solvation = SolvationDatabase()
self.solvation.load(path)
broadcast(self.solvation, 'solvation')
def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
broadcast(self.statmech, 'statmech')
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()
# Not completely implemented
# self.solvation.loadOld(path)
def save(self, path):
"""
Save the RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.forbiddenStructures.save(
os.path.join(path, 'forbiddenStructures.py'))
self.thermo.save(os.path.join(path, 'thermo'))
# self.transport.save(os.path.join(path, 'transport')) #Currently no function for saving transport groups
self.kinetics.save(os.path.join(path, 'kinetics'))
self.statmech.save(os.path.join(path, 'statmech'))
self.solvation.save(os.path.join(path, 'solvation'))
self.transport.save(os.path.join(path, 'transport'))
def saveOld(self, path):
"""
Save the old RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.thermo.saveOld(path)
self.transport.saveOld(path)
self.forbiddenStructures.saveOld(
os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics.saveOld(path)
self.statmech.saveOld(path)
class RMGDatabase(object):
"""
The primary class for working with the RMG database.
"""
def __init__(self):
self.thermo = None
self.transport = None
self.forbiddenStructures = None
self.kinetics = None
self.statmech = None
self.solvation = None
# Store the newly created database in the module.
global database
if database is not None:
logging.warning('An instance of RMGDatabase already exists. Re-initializing it.')
database = self
def load(self,
path,
thermoLibraries=None,
transportLibraries=None,
reactionLibraries=None,
seedMechanisms=None,
kineticsFamilies=None,
kineticsDepositories=None,
statmechLibraries=None,
depository=True,
solvation=True,
testing = False):
"""
Load the RMG database from the given `path` on disk, where `path`
points to the top-level folder of the RMG database. If none of the
optional arguments are provided, then the entire database will be
loaded. You can use the optional arguments to specify that only certain
components of the database be loaded.
Argument testing will load a lighter version of the database used for unit-tests
"""
self.loadThermo(os.path.join(path, 'thermo'), thermoLibraries, depository)
if not testing:
self.loadTransport(os.path.join(path, 'transport'), transportLibraries)
self.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
self.loadKinetics(os.path.join(path, 'kinetics'),
reactionLibraries,
seedMechanisms,
kineticsFamilies,
kineticsDepositories
)
if not testing:
self.loadStatmech(os.path.join(path, 'statmech'), statmechLibraries, depository)
if solvation:
self.loadSolvation(os.path.join(path, 'solvation'))
def loadThermo(self, path, thermoLibraries=None, depository=True):
"""
Load the RMG thermo database from the given `path` on disk, where
`path` points to the top-level folder of the RMG thermo database.
"""
self.thermo = ThermoDatabase()
self.thermo.load(path, thermoLibraries, depository)
broadcast(self.thermo, 'thermo')
def loadTransport(self, path, transportLibraries=None):
"""
Load the RMG transport database from the given 'path' on disk, where
'path' points to the top-level folder of the RMG transport database.
"""
self.transport = TransportDatabase()
self.transport.load(path, transportLibraries)
broadcast(self.transport, 'transport')
def loadForbiddenStructures(self, path = None):
"""
Load the RMG forbidden structures from the given `path` on disk, where
`path` points to the forbidden structures file.
If no path is given, a blank forbidden structures object is created.
"""
self.forbiddenStructures = ForbiddenStructures()
if path is not None:
self.forbiddenStructures.load(path)
broadcast(self.forbiddenStructures, 'forbidden')
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 loadSolvation(self, path):
"""
Load the RMG solvation database from the given `path` on disk, where
`path` points to the top-level folder of the RMG solvation database.
"""
self.solvation = SolvationDatabase()
self.solvation.load(path)
broadcast(self.solvation, 'solvation')
def loadStatmech(self, path, statmechLibraries=None, depository=True):
"""
Load the RMG statmech database from the given `path` on disk, where
`path` points to the top-level folder of the RMG statmech database.
"""
self.statmech = StatmechDatabase()
self.statmech.load(path, statmechLibraries, depository)
broadcast(self.statmech, 'statmech')
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()
# Not completely implemented
# self.solvation.loadOld(path)
def save(self, path):
"""
Save the RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.forbiddenStructures.save(os.path.join(path, 'forbiddenStructures.py'))
self.thermo.save(os.path.join(path, 'thermo'))
# self.transport.save(os.path.join(path, 'transport')) #Currently no function for saving transport groups
self.kinetics.save(os.path.join(path, 'kinetics'))
self.statmech.save(os.path.join(path, 'statmech'))
self.solvation.save(os.path.join(path, 'solvation'))
self.transport.save(os.path.join(path, 'transport'))
def saveOld(self, path):
"""
Save the old RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.makedirs(path)
self.thermo.saveOld(path)
self.transport.saveOld(path)
self.forbiddenStructures.saveOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics.saveOld(path)
self.statmech.saveOld(path)