)
else:
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,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Save in Py format
try:
os.makedirs(os.join('input/kinetics/libraries/',name))
except:
pass
thermoLibrary.save(os.path.join('input/thermo/libraries', name + '.py'))
kineticsLibrary.save(os.path.join('input/kinetics/libraries/', name, 'reactions.py'))
kineticsLibrary.saveDictionary(os.path.join('input/kinetics/libraries/', name, 'dictionary.txt'))
"""
import argparse
import os
from rmgpy.data.kinetics import KineticsLibrary
from rmgpy import settings
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java kinetics library directory')
parser.add_argument('libraryName', metavar='OUTPUT', type=str, nargs=1,
help='the libraryName for the RMG-Py format kinetics library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = KineticsLibrary()
library.loadOld(inputPath)
try:
os.makedirs(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName))
except:
pass
# Save in Py format
library.save(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName, 'reactions.py'))
library.saveDictionary(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName,'dictionary.txt'))
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'))
