def loadNecessaryDatabases():
"""
loads transport and statmech databases
"""
from rmgpy.data.statmech import StatmechDatabase
from rmgpy.data.transport import TransportDatabase
#only load if they are not there already.
try:
getDB('transport')
getDB('statmech')
except DatabaseError:
logging.info("Databases not found. Making databases")
db = RMGDatabase()
db.statmech = StatmechDatabase()
db.statmech.load(os.path.join(settings['database.directory'],'statmech'))
db.transport = TransportDatabase()
db.transport.load(os.path.join(settings['database.directory'],'transport'))
def loadNecessaryDatabases():
"""
loads transport and statmech databases
"""
from rmgpy.data.statmech import StatmechDatabase
from rmgpy.data.transport import TransportDatabase
#only load if they are not there already.
try:
getDB('transport')
getDB('statmech')
except DatabaseError:
logging.info("Databases not found. Making databases")
db = RMGDatabase()
db.statmech = StatmechDatabase()
db.statmech.load(os.path.join(settings['database.directory'],'statmech'))
db.transport = TransportDatabase()
db.transport.load(os.path.join(settings['database.directory'],'transport'))
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
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
