def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
from rmgpy.thermo.thermoengine import generateThermoData
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4' #two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.thermo = generateThermoData(spc)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
from rmgpy.thermo.thermoengine import generateThermoData
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4'#two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.thermo = generateThermoData(spc)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
def run_thermo_estimator(input_file, library_flag):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.load_thermo_input(input_file)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.load_thermo(os.path.join(path, 'thermo'),
rmg.thermo_libraries,
depository=False)
if rmg.solvent:
rmg.database.load_solvation(os.path.join(path, 'solvation'))
Species.solvent_data = rmg.database.solvation.get_solvent_data(
rmg.solvent)
Species.solvent_name = rmg.solvent
for species in rmg.initial_species:
submit(species)
if library_flag:
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initial_species:
library.load_entry(
index=len(library.entries) + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.get_thermo_data().to_thermo_data(),
shortDesc=species.get_thermo_data().comment,
)
library.save(os.path.join(rmg.output_directory, 'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
save_chemkin_file(os.path.join(rmg.output_directory, 'chem_annotated.inp'),
species=rmg.initial_species,
reactions=[])
save_species_dictionary(os.path.join(rmg.output_directory,
'species_dictionary.txt'),
species=rmg.initial_species)
def load():
"""
A method that is run before each unit test in this class.
"""
tearDown()
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
# kinetics family loading
rmg.database.loadKinetics(os.path.join(path, 'kinetics'),
kineticsFamilies=[TESTFAMILY],
reactionLibraries=[]
)
def runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'),
rmg.thermoLibraries,
depository=False)
if rmg.solvent:
rmg.database.loadSolvation(os.path.join(path, 'solvation'))
Species.solventData = rmg.database.solvation.getSolventData(
rmg.solvent)
Species.solventName = rmg.solvent
for species in rmg.initialSpecies:
submit(species)
# library = ThermoLibrary(name='Thermo Estimation Library')
# for spc in rmg.initialSpecies:
# library.loadEntry(
# index = len(library.entries) + 1,
# label = species.label,
# molecule = species.molecule[0].toAdjacencyList(),
# thermo = species.getThermoData().toThermoData(),
# shortDesc = species.getThermoData().comment,
# )
# library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
saveChemkinFile(os.path.join(rmg.outputDirectory, 'chem_annotated.inp'),
species=rmg.initialSpecies,
reactions=[])
saveSpeciesDictionary(os.path.join(rmg.outputDirectory,
'species_dictionary.txt'),
species=rmg.initialSpecies)
def load():
"""
A method that is run before each unit test in this class.
"""
tearDown()
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
# kinetics family loading
rmg.database.loadKinetics(os.path.join(path, 'kinetics'),
kineticsFamilies=[TESTFAMILY],
reactionLibraries=[]
)
def runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'), rmg.thermoLibraries, depository=False)
if rmg.solvent:
rmg.database.loadSolvation(os.path.join(path, 'solvation'))
Species.solventData = rmg.database.solvation.getSolventData(rmg.solvent)
Species.solventName = rmg.solvent
# Generate the thermo for all the species and write them to chemkin format as well as
# ThermoLibrary format with values for H, S, and Cp's.
output = open(os.path.join(rmg.outputDirectory, 'output.txt'),'wb')
library = ThermoLibrary(name='Thermo Estimation Library')
for species in rmg.initialSpecies:
species.getThermoData(rmg.database)
library.loadEntry(
index = len(library.entries) + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo.toThermoData(),
shortDesc = species.thermo.comment,
)
output.write(writeThermoEntry(species))
output.write('\n')
output.close()
library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
def setUpClass(cls):
"""
A method that is run before each unit test in this class.
"""
test_family = 'H_Abstraction'
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['test_data.directory'],
'testing_database')
# kinetics family loading
rmg.database.load_kinetics(os.path.join(path, 'kinetics'),
kinetics_families=[test_family],
reaction_libraries=[])
# load empty forbidden structures to avoid any dependence on forbidden structures
# for these tests
for family in rmg.database.kinetics.families.values():
family.forbidden = ForbiddenStructures()
rmg.database.forbidden_structures = ForbiddenStructures()
def runThermoEstimator(inputFile):
"""
Estimate thermo for a list of species using RMG and the settings chosen inside a thermo input file.
"""
rmg = RMG()
rmg.loadThermoInput(inputFile)
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'), rmg.thermoLibraries, depository=False)
if rmg.solvent:
rmg.database.loadSolvation(os.path.join(path, 'solvation'))
Species.solventData = rmg.database.solvation.getSolventData(rmg.solvent)
Species.solventName = rmg.solvent
for species in rmg.initialSpecies:
submit(species)
# library = ThermoLibrary(name='Thermo Estimation Library')
# for spc in rmg.initialSpecies:
# library.loadEntry(
# index = len(library.entries) + 1,
# label = species.label,
# molecule = species.molecule[0].toAdjacencyList(),
# thermo = species.getThermoData().toThermoData(),
# shortDesc = species.getThermoData().comment,
# )
# library.save(os.path.join(rmg.outputDirectory,'ThermoLibrary.py'))
# Save the thermo data to chemkin format output files and dictionary, with no reactions
saveChemkinFile(os.path.join(rmg.outputDirectory, 'chem_annotated.inp'), species=rmg.initialSpecies, reactions=[])
saveSpeciesDictionary(os.path.join(rmg.outputDirectory, 'species_dictionary.txt'), species=rmg.initialSpecies)
def setUpClass(cls):
"""
A method that is run before each unit test in this class.
"""
TESTFAMILY = 'H_Abstraction'
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path=os.path.join(settings['test_data.directory'], 'testing_database')
# kinetics family loading
rmg.database.loadKinetics(os.path.join(path, 'kinetics'),
kineticsFamilies=[TESTFAMILY],
reactionLibraries=[]
)
#load empty forbidden structures to avoid any dependence on forbidden structures
#for these tests
for family in rmg.database.kinetics.families.values():
family.forbidden = ForbiddenStructures()
rmg.database.forbiddenStructures = ForbiddenStructures()
import os
from rmgpy.molecule.molecule import Molecule
from rmgpy.rmg.model import Species
from rmgpy.rmg.model import CoreEdgeReactionModel
from rmgpy.rmg.main import RMG
from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase
rmg = RMG()
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
rmg.database.loadThermo(os.path.join(path,'thermo'))
mol = Molecule().fromSMILES('C1=CC=CC=C1')
tdt = rmg.database.thermo.estimateThermoViaGroupAdditivity(mol)
print tdt.comment
print mol.isAromatic()
spc = Species().fromSMILES('C1=CC=CC=C1')
tdt = rmg.database.thermo.getThermoDataFromGroups(spc)
print tdt.comment
print '\n'
rmg.reactionModel = CoreEdgeReactionModel()
spc, isNew = rmg.reactionModel.makeNewSpecies(mol)
rmg.reactionModel.addSpeciesToEdge(spc)
rmg.initialSpecies = []
rmg.initialSpecies.append(spc)
for species in rmg.initialSpecies:
#species.generateThermoData(rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)
#print species.thermo.comment
tdt = rmg.database.thermo.getThermoDataFromGroups(spc)
import os
import csv
from rmgpy.molecule.molecule import Molecule
from rmgpy.rmg.model import Species
from rmgpy.rmg.model import CoreEdgeReactionModel
from rmgpy.rmg.main import RMG
from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase
rmg = RMG()
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
rmg.database.loadThermo(os.path.join(path,'thermo'))
rmg.reactionModel = CoreEdgeReactionModel()
rmg.initialSpecies = []
delimiter = '\t'
JtoCal = 1.0/4.184
fw = open('output_thermo.txt','w')
fw.write('Name\tSMILES\tH298\tS298\t300 K\t400 K\t500 K\t600 K\t800 K\t1000 K\t1500 K\tComment\n')
count = 0
spc_name = []
spc_smi = []
reader = csv.reader(open('TestSet.csv', 'r'))
for row in reader:
k, v = row
mol = Molecule().fromSMILES(v)
spc, isNew = rmg.reactionModel.makeNewSpecies(mol)
# rmg.reactionModel.addSpeciesToEdge(spc)
