Python RMGDatabase.kinetics方法代码示例

# 需要导入模块: from rmgpy.data.rmg import RMGDatabase [as 别名]
# 或者: from rmgpy.data.rmg.RMGDatabase import kinetics [as 别名]
def convertPrIMe(family):

    print 'Loading kinetics families...'
    database = RMGDatabase()
    database.kinetics = KineticsDatabase()
    database.kinetics.loadFamilies('input/kinetics/families')
    database.loadForbiddenStructures('input/forbiddenStructures.py')
    
    for depository in database.kinetics.families[family].depositories:
        if depository.label == '{0}/PrIMe'.format(family):
            break
    else:
        raise Exception('Could not find PrIMe depository in {0} family.'.format(family))
    
    entries = []
    
    print 'Determining unique list of reactions...'
    for entry0 in depository.entries.values():
        for entry in entries:
            if entry.item.isIsomorphic(entry0.item):
                break
        else:
            entries.append(entry0)
    print 'Found {0:d} unique reactions out of {1:d} entries.'.format(len(entries), len(depository.entries))
    
    print 'Sorting unique reactions...'
    entries.sort(key=lambda entry: sum([1 for r in entry.item.reactants for a in r.atoms if a.isNonHydrogen()]))
    
    print 'Saving reactions...'
    for index, entry in enumerate(entries):
        
        label = entry.label
        reaction = entry.item
        
        # Determine degeneracy in both directions
        reactions = database.kinetics.generateReactionsFromFamilies(reaction.reactants, reaction.products, only_families=[family])
        if len(reactions) != 1:
            print 'Warning: could not determine forward degeneracy for reaction #{0:d}.'.format(index+1)
            forwardDegeneracy = 1
        else:
            forwardDegeneracy = reactions[0].degeneracy
        reactions = database.kinetics.generateReactionsFromFamilies(reaction.products, reaction.reactants, only_families=[family])
        if len(reactions) != 1:
            print 'Warning: could not determine reverse degeneracy for reaction #{0:d}.'.format(index+1)
            reverseDegeneracy = 1
        else:
            reverseDegeneracy = reactions[0].degeneracy
        
        saveReaction('input/kinetics/families/{0}/training/{0}.py'.format(family, index+1), index+1, label, reaction, forwardDegeneracy, reverseDegeneracy)

# 需要导入模块: from rmgpy.data.rmg import RMGDatabase [as 别名]
# 或者: from rmgpy.data.rmg.RMGDatabase import kinetics [as 别名]
def loadDatabase(component='', section=''):
    """
    Load the requested `component` of the RMG database if modified since last loaded.
    """
    global database
    if not database:
        database = RMGDatabase()
        database.thermo = ThermoDatabase()
        database.kinetics = KineticsDatabase()
        database.loadForbiddenStructures(os.path.join(settings.DATABASE_PATH, 'forbiddenStructures.py'))

    if component in ['thermo', '']:
        if section in ['depository', '']:
            dirpath = os.path.join(settings.DATABASE_PATH, 'thermo', 'depository')
            if isDirModified(dirpath):
                database.thermo.loadDepository(dirpath)
                resetDirTimestamps(dirpath)
        if section in ['libraries', '']:
            dirpath = os.path.join(settings.DATABASE_PATH, 'thermo', 'libraries')
            if isDirModified(dirpath):
                database.thermo.loadLibraries(dirpath)
                # put them in our preferred order, so that when we look up thermo in order to estimate kinetics,
                # we use our favourite values first.
                preferred_order = ['primaryThermoLibrary','DFT_QCI_thermo','GRI-Mech3.0','CBS_QB3_1dHR','KlippensteinH2O2']
                new_order = [i for i in preferred_order if i in database.thermo.libraryOrder]
                for i in database.thermo.libraryOrder:
                    if i not in new_order: new_order.append(i) 
                database.thermo.libraryOrder = new_order
                resetDirTimestamps(dirpath)
        if section in ['groups', '']:
            dirpath = os.path.join(settings.DATABASE_PATH, 'thermo', 'groups')
            if isDirModified(dirpath):
                database.thermo.loadGroups(dirpath)
                resetDirTimestamps(dirpath)
    if component in ['kinetics', '']:
        if section in ['libraries', '']:
            dirpath = os.path.join(settings.DATABASE_PATH, 'kinetics', 'libraries')
            if isDirModified(dirpath):
                database.kinetics.loadLibraries(dirpath)
                resetDirTimestamps(dirpath)
        if section in ['families', '']:
            dirpath = os.path.join(settings.DATABASE_PATH, 'kinetics', 'families')
            if isDirModified(dirpath):
                database.kinetics.loadFamilies(dirpath)
                resetDirTimestamps(dirpath)

    return database

# 需要导入模块: from rmgpy.data.rmg import RMGDatabase [as 别名]
# 或者: from rmgpy.data.rmg.RMGDatabase import kinetics [as 别名]
def loadDatabase(component='', section=''):
    """
    Load the requested `component` of the RMG database if modified since last loaded.
    """
    global database
    if not database:
        database = RMGDatabase()
        database.solvation = SolvationDatabase()
        database.thermo = ThermoDatabase()
        database.kinetics = KineticsDatabase()
        database.transport = TransportDatabase()
        database.statmech = StatmechDatabase()
        database.loadForbiddenStructures(os.path.join(rmgweb.settings.DATABASE_PATH, 'forbiddenStructures.py'))

    if component == 'initialize':
        return database
    if component in ['thermo', '']:
        if section in ['depository', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', 'depository')
            if isDirModified(dirpath):
                database.thermo.loadDepository(dirpath)
                resetDirTimestamps(dirpath)
        if section in ['libraries', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', 'libraries')
            if isDirModified(dirpath):
                database.thermo.loadLibraries(dirpath)
                # put them in our preferred order, so that when we look up thermo in order to estimate kinetics,
                # we use our favorite values first.
                preferred_order = ['primaryThermoLibrary','DFT_QCI_thermo','GRI-Mech3.0','CBS_QB3_1dHR','KlippensteinH2O2']
                new_order = [i for i in preferred_order if i in database.thermo.libraryOrder]
                for i in database.thermo.libraryOrder:
                    if i not in new_order: new_order.append(i) 
                database.thermo.libraryOrder = new_order
                resetDirTimestamps(dirpath)
        if section in ['groups', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', 'groups')
            if isDirModified(dirpath):
                database.thermo.loadGroups(dirpath)
                resetDirTimestamps(dirpath)  
                              
    if component in ['transport', '']:
        if section in ['libraries', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'transport', 'libraries')
            if isDirModified(dirpath):
                database.transport.loadLibraries(dirpath)
                resetDirTimestamps(dirpath)
        if section in ['groups', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'transport', 'groups')
            if isDirModified(dirpath):
                database.transport.loadGroups(dirpath)
                resetDirTimestamps(dirpath)
                
    if component in ['solvation', '']:
        dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'solvation')
        if isDirModified(dirpath):
            database.solvation.load(dirpath)
            resetDirTimestamps(dirpath)
                
    if component in ['kinetics', '']:
        if section in ['libraries', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'kinetics', 'libraries')
            if isDirModified(dirpath):
                database.kinetics.loadLibraries(dirpath)
                resetDirTimestamps(dirpath)
        if section in ['families', '']:
            dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'kinetics', 'families')
            if isDirModified(dirpath):
                database.kinetics.loadFamilies(dirpath, families = 'all', depositories = 'all')
                resetDirTimestamps(dirpath)
                
                # Make sure to load the entire thermo database prior to adding training values to the rules
                loadDatabase('thermo','')
                for family in database.kinetics.families.values():
                    oldentries = len(family.rules.entries)
                    family.addKineticsRulesFromTrainingSet(thermoDatabase=database.thermo)
                    newentries = len(family.rules.entries)
                    if newentries != oldentries:
                        print '{0} new entries added to {1} family after adding rules from training set.'.format(newentries-oldentries, family.label)
                    # Filling in rate rules in kinetics families by averaging...
                    family.fillKineticsRulesByAveragingUp()
                    
    if component in ['statmech', '']:
        dirpath = os.path.join(rmgweb.settings.DATABASE_PATH, 'statmech')
        if isDirModified(dirpath):
            database.statmech.load(dirpath)
            resetDirTimestamps(dirpath)

    return database