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exportOldDatabase.py
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exportOldDatabase.py
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#!/usr/bin/env python
# encoding: utf-8
"""
This script exports the database to the old RMG-Java format. The script
requires two command-line arguments: the path to the database to import, and
the path to save the old RMG-Java database to.
"""
import sys
from rmgpy.data.rmg import RMGDatabase
from rmgpy.data.base import Entry
from rmgpy.reaction import Reaction
from rmgpy.kinetics import Arrhenius, ArrheniusEP, KineticsData
################################################################################
def generateAdditionalRateRules(family, database):
"""
For a given reaction `family` label, generate additional rate rules from
the corresponding depository training set. This function does automatically
what users used to do by hand to construct a rate rule from reaction
kinetics found in the literature, i.e. determine the groups involved,
adjust to a per-site basis, etc.
"""
# Find the database components we will need
rules = database.kinetics.depository['{0}/rules'.format(family)]
groups = database.kinetics.groups[family]
index = max([entry.index for entry in rules.entries.values()]) + 1
for depositoryLabel in ['training']:
depository = database.kinetics.depository['{0}/{1}'.format(family, depositoryLabel)]
entries = depository.entries.values()
entries.sort(key=lambda x: (x.index, x.label))
for entry0 in entries:
reaction, template = database.kinetics.getForwardReactionForFamilyEntry(entry=entry0, family=family, thermoDatabase=database.thermo)
# We must convert the kinetics to ArrheniusEP to finish our rate rule
kinetics = reaction.kinetics
# If kinetics are KineticsData, then first convert to Arrhenius
if isinstance(kinetics, KineticsData):
kinetics = Arrhenius().fitToData(
Tdata=kinetics.Tdata.values,
kdata=kinetics.kdata.values,
kunits=kinetics.kdata.units,
T0=1,
)
# Now convert from Arrhenius to ArrheniusEP
# If not Arrhenius (or KineticsData), then skip this entry
if isinstance(kinetics, Arrhenius):
if kinetics.T0.value != 1:
kinetics.changeT0(1)
kinetics = ArrheniusEP(
A = kinetics.A,
n = kinetics.n,
alpha = 0,
E0 = kinetics.Ea,
Tmin = kinetics.Tmin,
Tmax = kinetics.Tmax,
)
else:
break
# Put the kinetics on a per-site basis
kinetics.A.value /= reaction.degeneracy
# Construct a new entry for the new rate rule
label = ';'.join([group.label for group in template])
item = Reaction(
reactants = template[:],
products = None,
)
entry = Entry(
index = index,
label = label,
item = item,
data = kinetics,
reference = entry0.reference,
rank = entry0.rank,
shortDesc = entry0.shortDesc,
longDesc = entry0.longDesc,
history = entry0.history,
)
# Add the new rate rule to the depository of rate rules
rules.entries[entry.index] = entry
index += 1
################################################################################
if __name__ == '__main__':
oldPath = 'output/RMG_database'
newPath = 'input'
print 'Loading the new RMG-Py database...'
database = RMGDatabase()
database.load(newPath)
print 'Constructing additional rate rules from kinetics depository...'
for family in database.kinetics.groups:
generateAdditionalRateRules(family, database)
print 'Saving old RMG-Java database...'
database.saveOld(oldPath)