################################################################################
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java database directory')
parser.add_argument('outputPath', metavar='OUTPUT', type=str, nargs=1,
help='output path for the desired RMG-Py database directory')
args = parser.parse_args()
inputPath = args.inputPath[0]
outputPath = args.outputPath[0]
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(inputPath)
try:
os.makedirs(outputPath)
except:
pass
print 'Saving the new RMG-Py database...'
database.save(outputPath)
print "Done!"
################################################################################
if __name__ == '__main__':
#figure out the username
user = getUsername()
# Comment out the line above and uncomment the one below, filling in user information manually if
# it cannot be obtained from git or you do not want to extract user info from git.
# user = "******"
# Set the import and export paths
oldPath = 'output/RMG_database'
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(oldPath)
print 'Loading the current database to look for changes...'
current_database = RMGDatabase()
current_database.load(newPath)
print 'Setting history of all entries in database...'
setHistory(database, current_database, user=user)
print 'Saving the new RMG-Py database...'
database.save(newPath)
print "Done!"
for label, entry in library.entries.iteritems():
entry.history.append(event)
groups = database.states.groups
for label, entry in groups.entries.iteritems():
entry.history.append(event)
for label, entry in database.forbiddenStructures.entries.iteritems():
entry.history.append(event)
################################################################################
if __name__ == '__main__':
#figure out the username
user = getUsername()
# Set the import and export paths
oldPath = 'output/RMG_database'
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(oldPath)
print 'Setting history of all entries in database...'
setHistory(database, user=user)
print 'Saving the new RMG-Py database...'
database.save(newPath)
return groupValues, groupUncertainties
################################################################################
if __name__ == '__main__':
# Parse the command-line arguments
args = parseCommandLineArguments()
inputDirectory = os.path.abspath(args.input[0])
outputDirectory = os.path.abspath(args.output[0])
# Load the old RMG-Java database
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(inputDirectory)
# Generate kinetics group additivity values from old rate rules
print 'Generating kinetics group additivity values...'
Tdata = [300,400,500,600,800,1000,1500,2000]
for familyLabel, family in database.kinetics.groups.iteritems():
print ' %s...' % (familyLabel)
# Determine units of generated rate coefficients
numReactants = len(family.forwardTemplate.reactants)
if numReactants == 1:
kunits = 's^-1'
elif numReactants == 2:
kunits = 'm^3/(mol*s)'
else:
raise Exception("Unexpected number of reactants %i in forward template of reaction family %s." % (numReactants, familyLabel))
