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 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 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 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):
"""
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)
broadcast(self.forbiddenStructures, 'forbidden')
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 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 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 initialize(wd, rxns):
global working_dir, reactions
working_dir = wd
assert os.path.isdir(working_dir)
#set global variable here such that functions executed in the root worker have access to it.
reactions = [ReductionReaction(rxn) for rxn in rxns]
broadcast(reactions, 'reactions')
def initialize(wd, rxns):
global working_dir, reactions
working_dir = wd
assert os.path.isdir(working_dir)
#set global variable here such that functions executed in the root worker have access to it.
reactions = [ReductionReaction(rxn) for rxn in rxns]
broadcast(reactions, 'reactions')
def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise
logging.info('Reading input file "{0}"...'.format(full_path))
rmg = rmg0
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'catalystProperties': catalystProperties,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'solvation': solvation,
'adjacencyList': adjacencyList,
'quantumMechanics': quantumMechanics,
'mlEstimator': mlEstimator,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError) as e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
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 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')
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
logging.info('')
################################################################################
def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
logging.info('')
################################################################################
def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
"pressureDependence": pressureDependence,
"options": options,
"generatedSpeciesConstraints": generatedSpeciesConstraints,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints["explicitlyAllowedMolecules"] = []
broadcast(rmg.speciesConstraints, "speciesConstraints")
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
logging.info("")
################################################################################
def readThermoInputFile(path, rmg0):
"""
Read an thermo estimation input file at `path` on disk into the :class:`RMG` object
`rmg`.
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError), e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
################################################################################
def readThermoInputFile(path, rmg0):
def readInputFile(path, rmg0):
"""
Read an RMG input file at `path` on disk into the :class:`RMG` object
`rmg`.
"""
global rmg, speciesDict
full_path = os.path.abspath(os.path.expandvars(path))
try:
f = open(full_path)
except IOError:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise
logging.info('Reading input file "{0}"...'.format(full_path))
logging.info(f.read())
f.seek(0)# return to beginning of file
setGlobalRMG(rmg0)
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
rmg.reactionSystems = []
speciesDict = {}
global_context = { '__builtins__': None }
local_context = {
'__builtins__': None,
'True': True,
'False': False,
'database': database,
'catalystProperties': catalystProperties,
'species': species,
'SMARTS': SMARTS,
'SMILES': SMILES,
'InChI': InChI,
'adjacencyList': adjacencyList,
'simpleReactor': simpleReactor,
'liquidReactor': liquidReactor,
'surfaceReactor': surfaceReactor,
'simulator': simulator,
'solvation': solvation,
'model': model,
'quantumMechanics': quantumMechanics,
'mlEstimator': mlEstimator,
'pressureDependence': pressureDependence,
'options': options,
'generatedSpeciesConstraints': generatedSpeciesConstraints,
'thermoCentralDatabase': thermoCentralDatabase
}
try:
exec f in global_context, local_context
except (NameError, TypeError, SyntaxError) as e:
logging.error('The input file "{0}" was invalid:'.format(full_path))
logging.exception(e)
raise
finally:
f.close()
rmg.speciesConstraints['explicitlyAllowedMolecules'] = []
broadcast(rmg.speciesConstraints, 'speciesConstraints')
# convert keys from species names into species objects.
for reactionSystem in rmg.reactionSystems:
reactionSystem.convertInitialKeysToSpeciesObjects(speciesDict)
if rmg.quantumMechanics:
rmg.quantumMechanics.setDefaultOutputDirectory(rmg.outputDirectory)
rmg.quantumMechanics.initialize()
broadcast(rmg.quantumMechanics, 'quantumMechanics')
logging.info('')
