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.