def test_capitalization_species_target(self):
"""Test that species targets with capitalization not matching model works.
"""
file_path = os.path.join('testfile_st2.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# ignition target is OH
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
file_path = os.path.join('h2o2-lowercase.cti')
mechanism_filename = pkg_resources.resource_filename(
__name__, file_path)
SPEC_KEY = {'H2': 'h2', 'O2': 'o2', 'N2': 'n2', 'Ar': 'ar'}
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY)
# oh is species index 4
assert sim.properties.ignition_target == 4
# now try for uppercase in model and lowercase in file.
properties = ChemKED(filename)
properties.datapoints[0].ignition_type['target'] = 'oh'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
simulations = create_simulations(filename, properties)
sim = simulations[0]
sim.setup_case('h2o2.cti', SPEC_KEY)
# oh is species index 4
assert sim.properties.ignition_target == 4
def test_shock_tube_temperature_target_setup_case(self):
"""Test that shock tube case with temperature target set up properly.
"""
file_path = os.path.join('testfile_st.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
properties.datapoints[0].ignition_type['target'] = 'temperature'
properties.datapoints[1].ignition_type['target'] = 'temperature'
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY)
# Only thing different from last test: ignition target is temperature
assert sim.properties.ignition_target == 'temperature'
sim = simulations[1]
sim.setup_case(mechanism_filename, SPEC_KEY)
# Only thing different from last test: ignition target is temperature
assert sim.properties.ignition_target == 'temperature'
def test_shock_tube_setup_case(self):
"""Test that shock tube cases are set up properly.
"""
file_path = os.path.join('testfile_st.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
assert len(simulations) == 5
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
gas = ct.Solution(mechanism_filename)
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY)
init_pressure = 220. * units.kilopascal
assert sim.apparatus == 'shock tube'
assert np.allclose(sim.time_end, 4.7154e-2)
assert np.allclose(sim.gas.T, 1164.48)
assert np.allclose(sim.gas.P, init_pressure.to('pascal').magnitude)
mass_fracs = np.zeros(sim.gas.n_species)
mass_fracs[sim.gas.species_index(SPEC_KEY['H2'])] = 0.00444
mass_fracs[sim.gas.species_index(SPEC_KEY['O2'])] = 0.00556
mass_fracs[sim.gas.species_index(SPEC_KEY['Ar'])] = 0.99
assert np.allclose(sim.gas.X, mass_fracs)
# no wall velocity
times = np.linspace(0., sim.time_end, 100)
for time in times:
assert np.allclose(sim.reac.walls[0].vdot(time), 0.0)
assert sim.n_vars == gas.n_species + 3
assert sim.properties.ignition_target == 'pressure'
assert sim.properties.ignition_type == 'd/dt max'
sim = simulations[1]
sim.setup_case(mechanism_filename, SPEC_KEY)
assert sim.apparatus == 'shock tube'
assert np.allclose(sim.time_end, 4.4803e-2)
assert np.allclose(sim.gas.T, 1164.97)
assert np.allclose(sim.gas.P, init_pressure.to('pascal').magnitude)
mass_fracs = np.zeros(sim.gas.n_species)
mass_fracs[sim.gas.species_index(SPEC_KEY['H2'])] = 0.00444
mass_fracs[sim.gas.species_index(SPEC_KEY['O2'])] = 0.00556
mass_fracs[sim.gas.species_index(SPEC_KEY['Ar'])] = 0.99
assert np.allclose(sim.gas.X, mass_fracs)
# no wall velocity
times = np.linspace(0., sim.time_end, 100)
for time in times:
assert np.allclose(sim.reac.walls[0].vdot(time), 0.0)
assert sim.n_vars == gas.n_species + 3
assert sim.properties.ignition_target == 'pressure'
assert sim.properties.ignition_type == 'd/dt max'
def test_shock_tube_pressure_rise_setup_case(self):
"""Test that shock tube case with pressure rise is set up properly.
"""
file_path = os.path.join('testfile_st2.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
assert len(simulations) == 1
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
init_temp = 1264.2
init_pres = 2.18 * ct.one_atm
gas = ct.Solution(mechanism_filename)
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY)
assert sim.apparatus == 'shock tube'
assert np.allclose(sim.time_end, 2.9157e-2)
assert np.allclose(sim.gas.T, init_temp)
assert np.allclose(sim.gas.P, init_pres)
mass_fracs = np.zeros(sim.gas.n_species)
mass_fracs[sim.gas.species_index(SPEC_KEY['H2'])] = 0.00444
mass_fracs[sim.gas.species_index(SPEC_KEY['O2'])] = 0.00556
mass_fracs[sim.gas.species_index(SPEC_KEY['Ar'])] = 0.99
assert np.allclose(sim.gas.X, mass_fracs)
assert sim.n_vars == gas.n_species + 3
# Check constructed velocity profile
[times, volumes] = simulation.create_volume_history(
mechanism_filename, init_temp, init_pres,
'H2:0.00444,O2:0.00566,AR:0.9899', 0.10 * 1000., sim.time_end)
volumes = volumes / volumes[0]
dVdt = simulation.first_derivative(times, volumes)
velocities = np.zeros(times.size)
for i, time in enumerate(times):
velocities[i] = sim.reac.walls[0].vdot(time)
assert np.allclose(dVdt, velocities, rtol=1e-3)
def test_rcm_run_cases(self):
"""Test that RCM case runs correctly.
"""
# Read experiment XML file
file_path = os.path.join('testfile_rcm.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
# Setup and run each simulation
with TemporaryDirectory() as temp_dir:
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY, path=temp_dir)
sim.run_case()
# check for presence of data file
assert os.path.exists(sim.meta['save-file'])
with tables.open_file(sim.meta['save-file'], 'r') as h5file:
# Load Table with Group name simulation
table = h5file.root.simulation
# Ensure exact columns present
assert set([
'time', 'temperature', 'pressure', 'volume',
'mass_fractions'
]) == set(table.colnames)
# Ensure final state matches expected
time_end = 1.0e-1
temp = 2385.3726323703772
pres = 7785283.273098443
mass_fracs = np.array([
1.20958787e-04, 2.24531172e-06, 1.00369447e-05,
5.22700388e-04, 4.28382158e-04, 6.78623202e-02,
4.00112919e-07, 1.46544920e-07, 1.20831350e-32,
3.89605241e-34, -3.39400724e-33, -2.46590209e-34,
-1.74786488e-31, -5.36410698e-31, 4.72585636e-27,
7.94725956e-26, 5.20640355e-33, 2.16633481e-32,
2.74982659e-34, 5.20547210e-35, 5.96795929e-33,
-2.98353670e-48, -1.16084981e-45, -2.33518734e-48,
-6.38881605e-47, -3.09502377e-48, -8.14011410e-48,
-6.95137295e-47, -8.71647858e-47, -3.34677877e-46,
2.05479180e-09, 1.59879068e-09, 2.45613053e-09,
2.06962550e-08, 2.82124731e-09, 4.55692132e-04,
3.22230699e-07, 1.49833621e-07, 5.93547268e-08,
-2.74353105e-33, -1.17993222e-30, -5.51437143e-36,
-9.13974801e-37, -1.97028722e-31, -9.69084296e-32,
-1.31976752e-30, -2.12060990e-32, 1.55792718e-01,
7.74803838e-01, 2.72630502e-66, 2.88273784e-67,
-2.18774836e-50, -1.47465442e-48
])
assert np.allclose(table.col('time')[-1], time_end)
assert np.allclose(table.col('temperature')[-1],
temp,
rtol=1e-5,
atol=1e-9)
assert np.allclose(table.col('pressure')[-1],
pres,
rtol=1e-5,
atol=1e-9)
assert np.allclose(table.col('mass_fractions')[-1],
mass_fracs,
rtol=1e-4,
atol=1e-8)
def test_shock_tube_pressure_rise_run_cases(self):
"""Test that shock tube cases with pressure rise run correctly.
"""
# Read experiment XML file
file_path = os.path.join('testfile_st2.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
# Setup and run each simulation
with TemporaryDirectory() as temp_dir:
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY, path=temp_dir)
sim.run_case()
# check for presence of data file
assert os.path.exists(sim.meta['save-file'])
with tables.open_file(sim.meta['save-file'], 'r') as h5file:
# Load Table with Group name simulation
table = h5file.root.simulation
# Ensure exact columns present
assert set([
'time', 'temperature', 'pressure', 'volume',
'mass_fractions'
]) == set(table.colnames)
# Ensure final state matches expected
time_end = 2.9157e-2
temp = 2305.9275837885516
pres = 915452.1978990212
mass_fracs = np.array([
2.55673782e-06, 5.70019832e-07, 3.73361152e-05,
2.61559579e-03, 1.30748753e-04, 1.91579133e-03,
1.04724319e-07, 2.70985419e-09, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
9.95297294e-01, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00
])
assert np.allclose(table.col('time')[-1], time_end)
assert np.allclose(table.col('temperature')[-1], temp)
assert np.allclose(table.col('pressure')[-1], pres)
assert np.allclose(table.col('mass_fractions')[-1],
mass_fracs,
rtol=1e-5,
atol=1e-9)
def test_shock_tube_run_cases(self):
"""Test that shock tube cases run correctly.
"""
# Read experiment XML file
file_path = os.path.join('testfile_st.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
# Setup and run each simulation
with TemporaryDirectory() as temp_dir:
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY, path=temp_dir)
sim.run_case()
# check for presence of data file
assert os.path.exists(sim.meta['save-file'])
with tables.open_file(sim.meta['save-file'], 'r') as h5file:
# Load Table with Group name simulation
table = h5file.root.simulation
# Ensure exact columns present
assert set([
'time', 'temperature', 'pressure', 'volume',
'mass_fractions'
]) == set(table.colnames)
# Ensure final state matches expected
time_end = 4.7154e-2
temp = 1250.440275095967
pres = 235715.78371450436
mass_fracs = np.array([
3.78280811e-09, 6.55635749e-11, 3.88632912e-08,
2.68924922e-03, 9.14481216e-07, 2.01249201e-03,
7.30336393e-09, 4.48899838e-10, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
9.95297294e-01, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00
])
assert np.allclose(table.col('time')[-1], time_end)
assert np.allclose(table.col('temperature')[-1], temp)
assert np.allclose(table.col('pressure')[-1], pres)
assert np.allclose(table.col('mass_fractions')[-1],
mass_fracs,
rtol=1e-5,
atol=1e-9)
sim = simulations[1]
sim.setup_case(mechanism_filename, SPEC_KEY, path=temp_dir)
sim.run_case()
assert os.path.exists(sim.meta['save-file'])
with tables.open_file(sim.meta['save-file'], 'r') as h5file:
# Load Table with Group name simulation
table = h5file.root.simulation
# Ensure exact columns present
assert set([
'time', 'temperature', 'pressure', 'volume',
'mass_fractions'
]) == set(table.colnames)
# Ensure final state matches expected
time_end = 4.4803e-2
temp = 1250.9289794273782
pres = 235708.7300698561
mass_fracs = np.array([
4.09616997e-09, 7.26607683e-11, 4.16076690e-08,
2.68923307e-03, 9.47551606e-07, 2.01247148e-03,
7.82886351e-09, 4.77404824e-10, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00, 0.00000000e+00,
9.95297294e-01, 0.00000000e+00, 0.00000000e+00,
0.00000000e+00, 0.00000000e+00
])
assert np.allclose(table.col('time')[-1], time_end)
assert np.allclose(table.col('temperature')[-1], temp)
assert np.allclose(table.col('pressure')[-1], pres)
assert np.allclose(table.col('mass_fractions')[-1],
mass_fracs,
rtol=1e-5,
atol=1e-9)
def test_rcm_setup_case(self):
"""Test that RCM case is set up properly.
"""
file_path = os.path.join('testfile_rcm.yaml')
filename = pkg_resources.resource_filename(__name__, file_path)
properties = ChemKED(filename)
# Now create list of Simulation objects
simulations = create_simulations(filename, properties)
assert len(simulations) == 1
mechanism_filename = 'gri30.xml'
SPEC_KEY = {'H2': 'H2', 'O2': 'O2', 'N2': 'N2', 'Ar': 'AR'}
gas = ct.Solution(mechanism_filename)
sim = simulations[0]
sim.setup_case(mechanism_filename, SPEC_KEY)
assert sim.apparatus == 'rapid compression machine'
assert np.allclose(sim.time_end, 0.1)
assert np.allclose(sim.gas.T, 297.4)
assert np.allclose(sim.gas.P, 127722.83)
mass_fracs = np.zeros(sim.gas.n_species)
mass_fracs[sim.gas.species_index(SPEC_KEY['H2'])] = 0.12500
mass_fracs[sim.gas.species_index(SPEC_KEY['O2'])] = 0.06250
mass_fracs[sim.gas.species_index(SPEC_KEY['N2'])] = 0.18125
mass_fracs[sim.gas.species_index(SPEC_KEY['Ar'])] = 0.63125
assert np.allclose(sim.gas.X, mass_fracs)
times = np.arange(0, 9.7e-2, 1.e-3)
volumes = np.array([
5.47669375000E+002, 5.46608789894E+002, 5.43427034574E+002,
5.38124109043E+002, 5.30700013298E+002, 5.21154747340E+002,
5.09488311170E+002, 4.95700704787E+002, 4.79791928191E+002,
4.61761981383E+002, 4.41610864362E+002, 4.20399162234E+002,
3.99187460106E+002, 3.77975757979E+002, 3.56764055851E+002,
3.35552353723E+002, 3.14340651596E+002, 2.93128949468E+002,
2.71917247340E+002, 2.50705545213E+002, 2.29493843085E+002,
2.08282140957E+002, 1.87070438830E+002, 1.65858736702E+002,
1.44647034574E+002, 1.23435332447E+002, 1.02223630319E+002,
8.10119281915E+001, 6.33355097518E+001, 5.27296586879E+001,
4.91943750000E+001, 4.97137623933E+001, 5.02063762048E+001,
5.06454851923E+001, 5.10218564529E+001, 5.13374097598E+001,
5.16004693977E+001, 5.18223244382E+001, 5.20148449242E+001,
5.21889350372E+001, 5.23536351113E+001, 5.25157124459E+001,
5.26796063730E+001, 5.28476160610E+001, 5.30202402028E+001,
5.31965961563E+001, 5.33748623839E+001, 5.35527022996E+001,
5.37276399831E+001, 5.38973687732E+001, 5.40599826225E+001,
5.42141273988E+001, 5.43590751578E+001, 5.44947289126E+001,
5.46215686913E+001, 5.47405518236E+001, 5.48529815402E+001,
5.49603582190E+001, 5.50642270863E+001, 5.51660349836E+001,
5.52670070646E+001, 5.53680520985E+001, 5.54697025392E+001,
5.55720927915E+001, 5.56749762728E+001, 5.57777790517E+001,
5.58796851466E+001, 5.59797461155E+001, 5.60770054561E+001,
5.61706266985E+001, 5.62600130036E+001, 5.63449057053E+001,
5.64254496625E+001, 5.65022146282E+001, 5.65761642150E+001,
5.66485675508E+001, 5.67208534842E+001, 5.67944133373E+001,
5.68703658198E+001, 5.69493069272E+001, 5.70310785669E+001,
5.71146023893E+001, 5.71978399741E+001, 5.72779572372E+001,
5.73517897984E+001, 5.74167271960E+001, 5.74721573687E+001,
5.75216388520E+001, 5.75759967785E+001, 5.76575701358E+001,
5.78058719368E+001, 5.80849611077E+001, 5.85928651155E+001,
5.94734357453E+001, 6.09310671165E+001, 6.32487551103E+001,
6.68100309742E+001
])
volumes = volumes / volumes[0]
dVdt = simulation.first_derivative(times, volumes)
velocities = np.zeros(times.size)
for i, time in enumerate(times):
velocities[i] = sim.reac.walls[0].vdot(time)
assert np.allclose(dVdt, velocities)
assert sim.n_vars == gas.n_species + 3
def evaluate_model(
model_name,
spec_keys_file,
dataset_file,
data_path='data',
model_path='models',
results_path='results',
model_variant_file=None,
num_threads=None,
print_results=False,
restart=False,
skip_validation=False,
):
"""Evaluates the ignition delay error of a model for a given dataset.
Parameters
----------
model_name : str
Chemical kinetic model filename
spec_keys_file : str
Name of YAML file identifying important species
dataset_file : str
Name of file with list of data files
data_path : str
Local path for data files. Optional; default = 'data'
model_path : str
Local path for model file. Optional; default = 'models'
results_path : str
Local path for creating results files. Optional; default = 'results'
model_variant_file : str
Name of YAML file identifying ranges of conditions for variants of the
kinetic model. Optional; default = ``None``
num_threads : int
Number of CPU threads to use for performing simulations in parallel.
Optional; default = ``None``, in which case the available number of
cores minus one is used.
print_results : bool
If ``True``, print results of the model evaluation to screen.
restart : bool
If ``True``, process saved results. Mainly intended for testing/development.
skip_validation : bool
If ``True``, skips validation of ChemKED files.
Returns
-------
output : dict
Dictionary with all information about model evaluation results.
"""
# Create results_path if it doesn't exist
if not os.path.exists(results_path):
os.makedirs(results_path)
# Dict to translate species names into those used by models
with open(spec_keys_file, 'r') as f:
model_spec_key = yaml.safe_load(f)
# Keys for models with variants depending on pressure or bath gas
model_variant = None
if model_variant_file:
with open(model_variant_file, 'r') as f:
model_variant = yaml.safe_load(f)
# Read dataset list
with open(dataset_file, 'r') as f:
dataset_list = f.read().splitlines()
error_func_sets = numpy.zeros(len(dataset_list))
dev_func_sets = numpy.zeros(len(dataset_list))
# Dictionary with all output data
output = {'model': model_name, 'datasets': []}
# If number of threads not specified, use either max number of available
# cores minus 1, or use 1 if multiple cores not available.
if not num_threads:
num_threads = multiprocessing.cpu_count() - 1 or 1
# Loop through all datasets
for idx_set, dataset in enumerate(dataset_list):
dataset_meta = {'dataset': dataset, 'dataset_id': idx_set}
# Create individual simulation cases for each datapoint in this set
properties = ChemKED(os.path.join(data_path, dataset),
skip_validation=skip_validation)
simulations = create_simulations(dataset, properties)
ignition_delays_exp = numpy.zeros(len(simulations))
ignition_delays_sim = numpy.zeros(len(simulations))
#############################################
# Determine standard deviation of the dataset
#############################################
ign_delay = [
case.ignition_delay.to('second').magnitude
for case in properties.datapoints
]