def load_transport(self, path, transport_libraries=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, transport_libraries)
def setUp(self):
"""
a function run before each unit test in this class
"""
self.libraries = ['GRI-Mech', 'PrimaryTransportLibrary']
self.groups = ['ring', 'nonring']
self.libraryOrder = []
path = os.path.join(settings['database.directory'], 'transport')
self.transportdb = TransportDatabase()
self.transportdb.load(path, self.libraries)
def __init__(self):
self.database = RMGDatabase()
self.database.kinetics = KineticsDatabase()
self.database.thermo = ThermoDatabase()
self.database.transport = TransportDatabase()
self.database.statmech = StatmechDatabase()
self.database.solvation = SolvationDatabase()
self.database.load_forbidden_structures(
os.path.join(rmgweb.settings.DATABASE_PATH,
'forbiddenStructures.py'))
self.timestamps = {}
def setUpClass(self):
"""A function that is run ONCE before all unit tests in this class."""
self.database = TransportDatabase()
self.database.load(os.path.join(settings['database.directory'], 'transport'),
['GRI-Mech', 'PrimaryTransportLibrary'])
self.speciesList = [
Species().from_smiles('C'),
Species().from_smiles('CCCC'),
Species().from_smiles('O'),
Species().from_smiles('[CH3]'),
Species().from_smiles('[OH]'),
Species().from_smiles('c1ccccc1'),
]
def load_old(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.load_old(path)
self.transport = TransportDatabase()
# self.transport.load_old(path) # Currently no load_old import function available for transport groups
self.forbidden_structures = ForbiddenStructures()
self.forbidden_structures.load_old(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics = KineticsDatabase()
self.kinetics.load_old(path)
self.statmech = StatmechDatabase()
self.statmech.load_old(path)
self.solvation = SolvationDatabase()
def main(dictionary):
database = TransportDatabase()
database.load(path=os.path.join(settings['database.directory'],
'transport'),
libraries=None)
speciesDict = loadSpeciesDictionary(dictionary)
path = 'tran.dat'
with open(path, 'w') as f:
f.write("! {0:15} {1:8} {2:9} {3:9} {4:9} {5:9} {6:9} {7:9}\n".format(
'Species', 'Shape', 'LJ-depth', 'LJ-diam', 'DiplMom', 'Polzblty',
'RotRelaxNum', 'Data'))
f.write("! {0:15} {1:8} {2:9} {3:9} {4:9} {5:9} {6:9} {7:9}\n".format(
'Name', 'Index', 'epsilon/k_B', 'sigma', 'mu', 'alpha', 'Zrot',
'Source'))
for label, spec in speciesDict.iteritems():
transportDataList = database.getAllTransportProperties(spec)
for transportData, _, _ in transportDataList:
if (not transportData):
missingData = True
else:
missingData = False
if missingData:
f.write('! {0:19s} {1!r}\n'.format(label, transportData))
else:
f.write(
'{0:19} {1:d} {2:9.3f} {3:9.3f} {4:9.3f} {5:9.3f} {6:9.3f} ! {7:s}\n'
.format(
label,
transportData.shapeIndex,
transportData.epsilon.value_si / constants.R,
transportData.sigma.value_si * 1e10,
(transportData.dipoleMoment.value_si *
constants.c *
1e21 if transportData.dipoleMoment else 0),
(transportData.polarizability.value_si *
1e30 if transportData.polarizability else 0),
(transportData.rotrelaxcollnum
if transportData.rotrelaxcollnum else 0),
transportData.comment,
))
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
