def test_get_sa_coefficients():
"""
Run RMG's minimal example with SA.
Then run the `get_sa_coefficients()` method to test that the adapter correctly parses the bsol object
to obtain sa_dict.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
observable_list = ['OH', 'H']
rms_simulator_adapter = RMSConstantHP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=observable_list,
sa_atol=t3.t3['sensitivity']['atol'],
sa_rtol=t3.t3['sensitivity']['rtol'],
)
rms_simulator_adapter.simulate()
sa_dict = rms_simulator_adapter.get_sa_coefficients()
# check that there are over 20 time steps (as an arbitrary number) to indicate that the solver completed
assert len(sa_dict['time']) > 20
# check that there are SA data for the 2 requested species
assert len(sa_dict['kinetics']) == 2
assert len(sa_dict['thermo']) == 2
def test_get_species_by_label():
"""Test getting species by label"""
t3 = run_minimal(
project_directory=os.path.join(DATA_BASE_PATH, 'minimal_data'),
iteration=1,
set_paths=True,
)
rmg_species, rmg_reactions = t3.load_species_and_reactions_from_chemkin_file(
)
label = 'H2O'
species = common.get_species_by_label(label, rmg_species)
assert species.label == label
assert species.index == 7
def test_find_equilibrium():
"""
Find equilibrium mole fractions of RMG's minimal example.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
cantera_simulator_adapter = CanteraConstantHP(t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
cantera_simulator_adapter.conditions
equilibrium_dictionaries = cantera_simulator_adapter.find_equilibrium('TP')
assert len(equilibrium_dictionaries[0].keys()) == 8
def test_get_t50():
"""
Find half life of give species from RMG's minimal example.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
cantera_simulator_adapter = CanteraConstantHP(t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
cantera_simulator_adapter.simulate()
t50_list = cantera_simulator_adapter.get_t50('H2(1)')
assert len(t50_list) == 1
def test_get_idt_by_T():
"""
Calculate the ignition delay time for RMG's minimal example. Check that the dictionary found an idt.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
cantera_simulator_adapter = CanteraConstantHP(t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
cantera_simulator_adapter.simulate()
idt_dict = cantera_simulator_adapter.get_idt_by_T()
assert len(idt_dict['idt']) == 1
assert len(idt_dict['idt_index']) == 1
def test_set_up_no_sa():
"""
Simulate RMG's minimal example without SA. By setting observable_list = list(), no SA is run.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
cantera_simulator_adapter = CanteraConstantHP(t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
cantera_simulator_adapter.simulate()
# check that there are over 20 time steps (as an arbitrary number) to indicate that the solver completed
time = cantera_simulator_adapter.all_data[0][0].data
assert len(time) > 20
def test_get_idt_by_T():
"""
Calculate the ignition delay time for RMG's minimal example.
Since this adapter simulates at constant T, this method returns a dictionary whose values are empty lists.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
rmg_simulator_adapter = RMGConstantTP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
rmg_simulator_adapter.simulate()
idt_dict = rmg_simulator_adapter.get_idt_by_T()
assert len(idt_dict['idt']) == 0
assert len(idt_dict['idt_index']) == 0
def test_set_up_no_sa():
"""
Run RMG's minimal example without SA by testing the `set_up` method within the RMSSimulator init method.
By setting observable_list = list(), no SA is run. Instead, RMS is used to just simulate the mechanism.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
rms_simulator_adapter = RMSConstantHP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
rms_simulator_adapter.simulate()
# check that there are over 20 time steps (as an arbitrary number) to indicate that the solver completed
assert len(rms_simulator_adapter.sol.t) > 20
def test_get_idt_by_T():
"""
Calculate the ignition delay time for RMG's minimal example.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
rms_simulator_adapter = RMSConstantHP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
sa_atol=t3.t3['sensitivity']['atol'],
sa_rtol=t3.t3['sensitivity']['rtol'],
)
rms_simulator_adapter.simulate()
idt_dict = rms_simulator_adapter.get_idt_by_T()
assert len(idt_dict['idt']) == 1
assert len(idt_dict['idt_index']) == 1
def test_get_sa_coefficients():
"""
Run RMG's minimal example with SA by testing the `set_up` method within the RMGConstantTP init method.
Then run the `get_sa_coefficients()` method to test that RMGConstantTP correctly parses the SA csv files
to obtain sa_dict.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
observable_list = ['OH', 'H']
rmg_simulator_adapter = RMGConstantTP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=observable_list,
sa_atol=t3.t3['sensitivity']['atol'],
sa_rtol=t3.t3['sensitivity']['rtol'],
)
rmg_simulator_adapter.simulate()
# check that RMG ran SA
performed_sa = os.path.isdir(t3.paths['SA'])
assert performed_sa
# check that RMG produced the corresponding csv files
files = [
'sensitivity_1_SPC_3.csv', 'sensitivity_1_SPC_4.csv',
'simulation_1_12.csv'
]
for file in files:
exist = os.path.isfile(os.path.join(t3.paths['SA solver'], file))
assert exist
# check that RMG can correctly parse the csv files to product the SA dictionary
sa_dict = rmg_simulator_adapter.get_sa_coefficients()
# check that there are over 100 time steps (as an arbitrary number) to indicate that the solver completed
assert len(sa_dict['time']) > 100
# check that there are SA data for the 2 requested species
assert len(sa_dict['kinetics']) == 2
assert len(sa_dict['thermo']) == 2
def test_set_up_no_sa():
"""
Run RMG's minimal example without SA by testing the `set_up` method within the RMGSimulator init method.
By setting observable_list = list(), no SA is run. Instead, RMG is just used to simulate the mechanism.
"""
t3 = run_minimal(project_directory=TEST_DIR)
t3.set_paths()
rmg_simulator_adapter = RMGConstantTP(
t3=t3.t3,
rmg=t3.rmg,
paths=t3.paths,
logger=t3.logger,
atol=t3.rmg['model']['atol'],
rtol=t3.rmg['model']['rtol'],
observable_list=list(),
)
rmg_simulator_adapter.simulate()
# check that RMG produced the concentration profiles
concentration_profiles = os.path.isfile(
os.path.join(t3.paths['RMG'], 'solver', 'simulation_1_12.csv'))
assert concentration_profiles
