G3CANTHERM = 2.8 # for example
QUANTUM = 3
GUESS = 5
################################################################
import shutil
logger = logging.getLogger()
old_level = logger.getEffectiveLevel()
logger.setLevel(15) # <<< level while reading database
data_source = os.path.join('input','RMG_database')
data_destination = os.path.join('output','RMG_database')
db = loadKineticsDatabase(data_source)
logger.setLevel(old_level)
for family_name,family in db.families.iteritems():
logging.info("Now processing family: %s"%family_name)
_rates = []
library_file_name = os.path.join(data_source,'kinetics_groups',family_name,'library.py')
library_file = open(library_file_name)
global reaction_order
local_context = { '__builtins__':None,
'_rates': _rates,
'rate': rate,
'Arrhenius':Arrhenius,
def testKineticsDatabase(self):
"""
Check the database load functions.
"""
# Create logger
logger = logging.getLogger()
logger.setLevel(10)
# Create console handler and set level to debug; send everything to stdout
# rather than stderr
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(10)
# Create formatter and add to console handler
formatter = logging.Formatter("%(levelname)s - %(message)s")
ch.setFormatter(formatter)
# remove old handlers!
while logger.handlers:
logger.removeHandler(logger.handlers[0])
# Add ch to logger
logger.addHandler(ch)
kineticsDatabase = loadKineticsDatabase("output/RMG_Database")
for label, family in kineticsDatabase.families.iteritems():
# All nodes in library should be in tree and dictionary
# All nodes in tree should be in dictionary
# for nodes in family.library:
# for node in nodes.split(';'):
# self.assertTrue(node in family.tree.parent)
# self.assertTrue(node in family.tree.children)
# self.assertTrue(node in family.dictionary)
for node in family.tree.parent:
self.assertTrue(node in family.tree.children)
self.assertTrue(node in family.dictionary)
for node in family.tree.children:
self.assertTrue(node in family.tree.parent)
self.assertTrue(node in family.dictionary)
# All parents in tree should be in tree
for node in family.tree.parent:
parentNode = family.tree.parent[node]
if parentNode is not None:
self.assertTrue(parentNode in family.tree.parent)
self.assertTrue(parentNode in family.tree.children)
# All children in tree should be in tree
for node in family.tree.children:
for childNode in family.tree.children[node]:
if childNode is not None:
self.assertTrue(childNode in family.tree.parent)
self.assertTrue(childNode in family.tree.children)
# All values in dictionary should be chemical structures
for node in family.dictionary:
self.assertTrue(
isinstance(family.dictionary[node], MoleculePattern)
or isinstance(family.dictionary[node], LogicNode)
)
# All values in library should be ArrheniusEPModel objects or lists of length 2
for node in family.library:
self.assertTrue(
isinstance(family.library[node], KineticsEntry),
'"%s" is of unexpected type "%s".' % (node, family.library[node].__class__),
)
self.assertTrue(family.library[node].model is not None or family.library[node].node != "")
C2H4 = Molecule().fromAdjacencyList(
"""
1 *1 C 0 {2,D} {3,S} {4,S}
2 *2 C 0 {1,D} {5,S} {6,S}
3 H 0 {1,S}
4 H 0 {1,S}
5 H 0 {2,S}
6 H 0 {2,S}
"""
)
H = Molecule().fromAdjacencyList(
"""
1 *3 H 1
"""
)
C2H5 = Molecule().fromAdjacencyList(
"""
1 *1 C 0 {2,S} {3,S} {4,S} {7,S}
2 *2 C 1 {1,S} {5,S} {6,S}
3 H 0 {1,S}
4 H 0 {1,S}
5 H 0 {2,S}
6 H 0 {2,S}
7 *3 H 0 {1,S}
"""
)
rxn = Reaction(reactants=[C2H4, H], products=[C2H5])
print "GENERATING KINETICS DATA:"
print kineticsDatabase.generateKineticsData(rxn, family="R_Addition_MultipleBond")
