for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
try:
entry.longDesc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
# Mark as duplicates where there are mixed pressure dependent and non-pressure dependent duplicate kinetics
# Even though CHEMKIN does not require a duplicate flag, RMG needs it.
# Using flag markDuplicates = True
kineticsLibrary.checkForDuplicates(markDuplicates=True)
kineticsLibrary.convertDuplicatesToMulti()
# Save in Py format
databaseDirectory = settings['database.directory']
try:
os.makedirs(os.path.join(databaseDirectory, 'kinetics', 'libraries',name))
except:
pass
thermoLibrary.save(os.path.join(databaseDirectory, 'thermo' ,'libraries', name + '.py'))
kineticsLibrary.save(os.path.join(databaseDirectory, 'kinetics', 'libraries', name, 'reactions.py'))
kineticsLibrary.saveDictionary(os.path.join(databaseDirectory, 'kinetics', 'libraries', name, 'dictionary.txt'))
logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
user = getUsername() # Pulls username from current git repository
#user = '******'.format(name, email) # If not in git repository, then enter user information manually
event = [time.asctime(),user,'action','{0} imported this entry from the old RMG database.'.format(user)]
for label, entry in thermoLibrary.entries.iteritems():
entry.history.append(event)
for label, entry in kineticsLibrary.entries.iteritems():
entry.history.append(event)
# Save in Py format
if not os.path.exists(outputDir):
os.makedirs(os.path.join(self.path))
.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index=i + 1,
item=reaction,
data=reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i + 1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
user = getUsername() # Pulls username from current git repository
#user = '******'.format(name, email) # If not in git repository, then enter user information manually
event = [
time.asctime(), user, 'action',
'{0} imported this entry from the old RMG database.'.format(user)
]
for label, entry in thermoLibrary.entries.iteritems():
entry.history.append(event)
for label, entry in kineticsLibrary.entries.iteritems():
entry.history.append(event)
# Save in Py format