def __init__(self,
title='',
old_dir='',
new_dir='',
observables=None,
expt_data=None,
ck2cti=True):
self.title = title
self.new_dir = new_dir
self.old_dir = old_dir
self.conditions = None
self.expt_data = expt_data if expt_data else []
self.observables = observables if observables else {}
# Detect if the transport file exists
old_transport_path = None
if os.path.exists(os.path.join(old_dir, 'tran.dat')):
old_transport_path = os.path.join(old_dir, 'tran.dat')
new_transport_path = None
if os.path.exists(os.path.join(new_dir, 'tran.dat')):
new_transport_path = os.path.join(new_dir, 'tran.dat')
# load the species and reactions from each model
old_species_list, old_reaction_list = load_chemkin_file(
os.path.join(old_dir, 'chem_annotated.inp'),
os.path.join(old_dir, 'species_dictionary.txt'),
old_transport_path)
new_species_list, new_reaction_list = load_chemkin_file(
os.path.join(new_dir, 'chem_annotated.inp'),
os.path.join(new_dir, 'species_dictionary.txt'),
new_transport_path)
self.old_sim = Cantera(species_list=old_species_list,
reaction_list=old_reaction_list,
output_directory=old_dir)
self.new_sim = Cantera(species_list=new_species_list,
reaction_list=new_reaction_list,
output_directory=new_dir)
# load each chemkin file into the cantera model
if not ck2cti:
self.old_sim.load_model()
self.new_sim.load_model()
else:
self.old_sim.load_chemkin_model(os.path.join(
old_dir, 'chem_annotated.inp'),
transport_file=old_transport_path,
quiet=True)
self.new_sim.load_chemkin_model(os.path.join(
new_dir, 'chem_annotated.inp'),
transport_file=new_transport_path,
quiet=True)
def __init__(self,
title='',
oldDir='',
newDir='',
observables={},
exptData=[],
ck2cti=True):
self.title = title
self.newDir = newDir
self.oldDir = oldDir
self.conditions = None
self.exptData = exptData
self.observables = observables
# Detect if the transport file exists
oldTransportPath = None
if os.path.exists(os.path.join(oldDir, 'tran.dat')):
oldTransportPath = os.path.join(oldDir, 'tran.dat')
newTransportPath = None
if os.path.exists(os.path.join(newDir, 'tran.dat')):
newTransportPath = os.path.join(newDir, 'tran.dat')
# load the species and reactions from each model
oldSpeciesList, oldReactionList = loadChemkinFile(
os.path.join(oldDir, 'chem_annotated.inp'),
os.path.join(oldDir, 'species_dictionary.txt'), oldTransportPath)
newSpeciesList, newReactionList = loadChemkinFile(
os.path.join(newDir, 'chem_annotated.inp'),
os.path.join(newDir, 'species_dictionary.txt'), newTransportPath)
self.oldSim = Cantera(speciesList=oldSpeciesList,
reactionList=oldReactionList,
outputDirectory=oldDir)
self.newSim = Cantera(speciesList=newSpeciesList,
reactionList=newReactionList,
outputDirectory=newDir)
# load each chemkin file into the cantera model
if not ck2cti:
self.oldSim.loadModel()
self.newSim.loadModel()
else:
self.oldSim.loadChemkinModel(os.path.join(oldDir,
'chem_annotated.inp'),
transportFile=oldTransportPath,
quiet=True)
self.newSim.loadChemkinModel(os.path.join(newDir,
'chem_annotated.inp'),
transportFile=newTransportPath,
quiet=True)
def setUp(self):
"""
A function run before each unit test in this class.
"""
from rmgpy.chemkin import load_chemkin_file
folder = os.path.join(os.path.dirname(rmgpy.__file__),
'tools/data/various_kinetics')
chemkin_path = os.path.join(folder, 'chem_annotated.inp')
dictionary_path = os.path.join(folder, 'species_dictionary.txt')
transport_path = os.path.join(folder, 'tran.dat')
species, reactions = load_chemkin_file(chemkin_path, dictionary_path,
transport_path)
self.rmg_ctSpecies = [
spec.to_cantera(use_chemkin_identifier=True) for spec in species
]
self.rmg_ctReactions = []
for rxn in reactions:
converted_reactions = rxn.to_cantera(species,
use_chemkin_identifier=True)
if isinstance(converted_reactions, list):
self.rmg_ctReactions.extend(converted_reactions)
else:
self.rmg_ctReactions.append(converted_reactions)
job = Cantera()
job.load_chemkin_model(chemkin_path,
transport_file=transport_path,
quiet=True)
self.ctSpecies = job.model.species()
self.ctReactions = job.model.reactions()
def run_cantera_job(
smiles_dictionary,
specie_initial_mol_frac,
final_time,
temp_initial,
initial_p,
chemkin_file='',
species_dictionary_file='',
transport_file=None,
reactor_type='IdealGasConstPressureTemperatureReactor',
time_units='s',
temp_units='K',
p_units='atm',
species_list=None,
reaction_list=None,
):
"""General function for running Cantera jobs from chemkin files with common defaults
=========================== =======================================================================
Input (Required) Description
=========================== =======================================================================
smiles_dictionary A dictionary with user names as keys and SMILES strings as values
specie_initial_mol_frac A dictionary with user specie names as keys and mol fractions as values
final_time Termination time for the simulation
temp_initial Initial temperature for the simulation
initial_p Initial pressure for the simulation
=========================== =======================================================================
Inputs with Defaults Description
=========================== =======================================================================
chemkin_file String relative path of the chem.inp or chem_annotated.inp file
species_dictionary_file String relative path of species_dictionary file
reactor_type String with Cantera reactor type
time_units Default is s (min and h are also supported)
temp_units Default is K (C is also supported)
p_units Default is atm (bar and Pa are also supported)
=========================== =======================================================================
Optional Inputs Description
=========================== =======================================================================
transport_file String relative path of trans.dat file
species_list Output from loadChemkinFile for faster simulation (otherwise generated)
reaction_list Output from loadChemkinFile for faster simulation (otherwise generated)
===================================================================================================
=========================== =======================================================================
Output Description
=========================== =======================================================================
all_data Cantera Simulation Data Object [time, [temp, pressure, spc1, spc2,..]]
===================================================================================================
"""
logging.info(
'Running a cantera job using the chemkin file {}'.format(chemkin_file))
logging.debug('loading chemkin and species dictionary file')
cwd = os.getcwd()
if chemkin_file == '':
chemkin_file = os.path.join(cwd, 'chem_annotated.inp')
if species_dictionary_file == '':
species_dictionary_file = os.path.join(cwd, 'species_dictionary.txt')
user_species_dictionary = create_species_from_smiles(smiles_dictionary)
specie_initial_mol_frac = set_species_mol_fractions(
specie_initial_mol_frac, user_species_dictionary)
if (not species_list) or (not reaction_list):
(species_list,
reaction_list) = loadChemkinFile(chemkin_file,
species_dictionary_file)
name_dictionary = getRMGSpeciesFromUserSpecies(
user_species_dictionary.values(), species_list)
mol_fractions = {}
for (user_name, chemkin_name) in name_dictionary.iteritems():
try:
mol_fractions[chemkin_name] = specie_initial_mol_frac[user_name]
except KeyError:
logging.debug(
'{} initial mol fractions set to 0'.format(user_name))
if temp_units == 'C':
temp_initial += 273.0
temp_initial = ([temp_initial], 'K')
initial_p = ([initial_p], p_units)
job = Cantera(speciesList=species_list,
reactionList=reaction_list,
outputDirectory='')
job.loadChemkinModel(chemkin_file, transportFile=transport_file)
job.generateConditions([reactor_type], ([final_time], time_units),
[mol_fractions], temp_initial, initial_p)
logging.debug('Starting Cantera Simulation')
all_data = job.simulate()
all_data = all_data[0]
logging.info('Cantera Simulation Complete')
logging.debug('Setting labels to user defined species labels')
species_index = {}
for i in range(len(species_list)):
species_index[species_list[i]] = i + 2
user_index = {}
for (user_name, specie) in user_species_dictionary.iteritems():
try:
user_index[species_index[name_dictionary[specie]]] = user_name
except KeyError:
logging.info('{0} is not in the model for {1}'.format(
user_name, chemkin_file))
for (indices, user_label) in user_index.iteritems():
try:
all_data[1][indices].label = user_label
except KeyError:
pass
return all_data
