Пример #1
0
 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)
Пример #2
0
 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)
Пример #3
0
 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()
Пример #4
0
 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)
Пример #5
0
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)
Пример #6
0
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)
Пример #7
0
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)