import time import math import numpy import pylab import scipy.stats import matplotlib matplotlib.rc('mathtext', fontset='stixsans', default='regular') import re import rmgpy from rmgpy.quantity import constants from rmgpy.kinetics import Arrhenius, ArrheniusEP, KineticsData from rmgpy.data.base import getAllCombinations from rmgpy.species import Species from importOldDatabase import getUsername user = getUsername() ################################################################################ def loadDatabase(): print 'Loading RMG database...' from rmgpy.data.rmg import RMGDatabase database = RMGDatabase() database.load('input') return database def convertKineticsToPerSiteBasis(kinetics, degeneracy): """ Given high-pressure-limit `kinetics` which includes reaction-path `degeneracy`, convert the kinetics to be on a per-site basis. """
nargs=1, help='the input path of the RMG-Java kinetics library directory') parser.add_argument( 'outputPath', metavar='OUTPUT', type=str, nargs=1, help= 'the libraryname.py output file for the RMG-Py format kinetics library' ) args = parser.parse_args() inputPath = args.inputPath[0] outputPath = args.outputPath[0] library = KineticsLibrary() library.loadOld(inputPath) # Assign history to 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 library.entries.iteritems(): entry.history.append(event) # Save in Py format library.save(outputPath)
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)) thermoLibrary.save(os.path.join(outputDir, 'chemkinThermoLibrary.py'), removeH=removeH) kineticsLibrary.save(os.path.join(outputDir, 'chemkinKineticsLibrary.py'), removeH=removeH)
import os.path import time import math import numpy import pylab import scipy.stats import matplotlib matplotlib.rc('mathtext', fontset='stixsans', default='regular') import re import rmgpy from rmgpy.quantity import constants from rmgpy.kinetics import Arrhenius, ArrheniusEP, KineticsData from rmgpy.data.base import getAllCombinations from importOldDatabase import getUsername user = getUsername() ################################################################################ def loadDatabase(): print 'Loading RMG database...' from rmgpy.data.rmg import RMGDatabase database = RMGDatabase() database.load('input') return database def getRateCoefficientUnits(family): """ For the given reaction `family`, return the units of its forward kinetics. This is hardcoding of reaction families, but at least it will fail loudly if it encounters an unexpected family.