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test_convert.py
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test_convert.py
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from __future__ import annotations
import itertools
from pathlib import Path
import logging
import io
import pytest
from . import utilities
import cantera as ct
from cantera import ck2yaml, cti2yaml, ctml2yaml, yaml2ck
class ck2yamlTest(utilities.CanteraTest):
def convert(self, inputFile, thermo=None, transport=None,
surface=None, output=None, extra=None, **kwargs):
if output is None:
output = Path(inputFile).stem # strip '.inp'
if inputFile is not None:
inputFile = self.test_data_path / inputFile
if thermo is not None:
thermo = self.test_data_path / thermo
if transport is not None:
transport = self.test_data_path / transport
if surface is not None:
surface = self.test_data_path / surface
if extra is not None:
extra = self.test_data_path / extra
output = self.test_work_path / (output + "-from-ck.yaml")
# In Python >= 3.8, this can be replaced by the missing_ok argument
if output.is_file():
output.unlink()
ck2yaml.convert_mech(inputFile, thermo_file=thermo,
transport_file=transport, surface_file=surface, out_name=output,
extra_file=extra, quiet=True, **kwargs)
return output
def checkConversion(self, refFile, testFile):
ref = ct.Solution(refFile)
gas = ct.Solution(testFile)
self.assertEqual(ref.element_names, gas.element_names)
self.assertEqual(ref.species_names, gas.species_names)
coeffs_ref = ref.reactant_stoich_coeffs
coeffs_gas = gas.reactant_stoich_coeffs
self.assertEqual(coeffs_gas.shape, coeffs_ref.shape)
self.assertTrue((coeffs_gas == coeffs_ref).all())
compositionA = [[ref.n_atoms(i,j) for j in range(ref.n_elements)]
for i in range(ref.n_species)]
compositionB = [[gas.n_atoms(i,j) for j in range(gas.n_elements)]
for i in range(gas.n_species)]
self.assertEqual(compositionA, compositionB)
return ref, gas
def checkThermo(self, ref, gas, temperatures):
for T in temperatures:
ref.TP = T, ct.one_atm
gas.TP = T, ct.one_atm
ref_cp = ref.standard_cp_R
gas_cp = gas.standard_cp_R
ref_h = ref.standard_enthalpies_RT
gas_h = gas.standard_enthalpies_RT
ref_s = ref.standard_entropies_R
gas_s = gas.standard_entropies_R
for i in range(gas.n_species):
message = ' for species {0} at T = {1}'.format(i, T)
self.assertNear(ref_cp[i], gas_cp[i], 1e-7, msg='cp'+message)
self.assertNear(ref_h[i], gas_h[i], 1e-7, msg='h'+message)
self.assertNear(ref_s[i], gas_s[i], 1e-7, msg='s'+message)
def checkKinetics(self, ref, gas, temperatures, pressures, tol=1e-8):
for T,P in itertools.product(temperatures, pressures):
ref.TP = T, P
gas.TP = T, P
ref_kf = ref.forward_rate_constants
ref_kr = ref.reverse_rate_constants
gas_kf = gas.forward_rate_constants
gas_kr = gas.reverse_rate_constants
for i in range(gas.n_reactions):
message = ' for reaction {0} at T = {1}, P = {2}'.format(i, T, P)
self.assertNear(ref_kf[i], gas_kf[i], rtol=tol, msg='kf' + message)
self.assertNear(ref_kr[i], gas_kr[i], rtol=tol, msg='kr' + message)
@utilities.slow_test
def test_gri30(self):
output = self.convert('gri30.inp', thermo='gri30_thermo.dat',
transport='gri30_tran.dat', output='gri30_test')
ref, gas = self.checkConversion("gri30.yaml", output)
self.checkKinetics(ref, gas, [300, 1500], [5e3, 1e5, 2e6])
def test_soot(self):
output = self.convert("soot.inp", thermo="soot-therm.dat", output="soot_test")
ref, gas = self.checkConversion("soot.yaml", output)
self.checkThermo(ref, gas, [300, 1100])
self.checkKinetics(ref, gas, [300, 1100], [5e3, 1e5, 2e6])
def test_pdep(self):
output = self.convert('pdep-test.inp')
ref, gas = self.checkConversion('pdep-test.yaml', output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_species_only(self):
self.convert(None, thermo='dummy-thermo.dat', output='dummy-thermo')
yaml = ("{phases: [{name: gas, species: "
"[{dummy-thermo-from-ck.yaml/species: [R1A, R1B, P1]}], "
"thermo: ideal-gas}]}")
gas = ct.Solution(yaml=yaml)
self.assertEqual(gas.n_species, 3)
self.assertEqual(gas.n_reactions, 0)
def test_missingThermo(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'No thermo data'):
self.convert('h2o2_missingThermo.inp')
def test_duplicate_thermo(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'additional thermo'):
self.convert('duplicate-thermo.inp')
output = self.convert('duplicate-thermo.inp', permissive=True)
gas = ct.Solution(output)
self.assertEqual(gas.n_species, 3)
self.assertEqual(gas.n_reactions, 2)
def test_duplicate_species(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'additional declaration'):
self.convert('duplicate-species.inp')
output = self.convert('duplicate-species.inp', permissive=True)
gas = ct.Solution(output)
self.assertEqual(gas.species_names, ['foo','bar','baz'])
def test_pathologicalSpeciesNames(self):
output = self.convert('species-names.inp')
gas = ct.Solution(output)
self.assertEqual(gas.n_species, 10)
self.assertEqual(gas.species_name(0), '(Parens)')
self.assertEqual(gas.species_name(1), '@#$%^-2')
self.assertEqual(gas.species_index('co:lons:'), 2)
self.assertEqual(gas.species_name(3), '[xy2]*{.}')
self.assertEqual(gas.species_name(4), 'plus+')
self.assertEqual(gas.species_name(5), 'eq=uals')
self.assertEqual(gas.species_name(6), 'plus')
self.assertEqual(gas.species_name(7), 'trans_butene')
self.assertEqual(gas.species_name(8), 'co')
self.assertEqual(gas.species_name(9), "amp&ersand")
self.assertEqual(gas.n_reactions, 13)
nu = gas.product_stoich_coeffs - gas.reactant_stoich_coeffs
self.assertEqual(list(nu[:,0]), [-1, -1, 0, 2, 0, 0, 0, 0, 0, 0])
self.assertEqual(list(nu[:,1]), [-2, 3, 0, -1, 0, 0, 0, 0, 0, 0])
self.assertEqual(list(nu[:,2]), [-1, 0, 0, 0, 1, 0, 0, 0, 0, 0])
self.assertEqual(list(nu[:,3]), [3, 0, 0, 0, -2, -1, 0, 0, 0, 0])
self.assertEqual(list(nu[:,4]), [2, 0, 0, 0, -1, 0, -1, 0, 0, 0])
self.assertEqual(list(nu[:,5]), [1, 0, 0, 0, 1, -1, -1, 0, 0, 0])
self.assertEqual(list(nu[:,6]), [2, 0, -1, 0, 0, -1, 0, 0, 0, 0])
self.assertEqual(list(nu[:,7]), [0, 0, 0, 0, -1, 1, 0, 0, 0, 0])
self.assertEqual(list(nu[:,8]), [0, 0, 0, 0, -1, 1, 0, 0, 0, 0])
self.assertEqual(list(nu[:,9]), [0, 0, 0, 0, -1, 1, 0, 0, 0, 0])
self.assertEqual(list(nu[:,10]), [0, 0, -1, 0, 2, 0, 0, -1, 0, 0])
self.assertEqual(list(nu[:,11]), [0, 0, -1, 0, 2, 0, 0, 0, -1, 0])
self.assertEqual(list(nu[:,12]), [0, 0, 0, 0, 1, 0, 0, 0, 0, -1])
def test_unterminatedSections(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'implicitly ended'):
self.convert('unterminated-sections.inp')
output = self.convert('unterminated-sections.inp', permissive=True)
gas = ct.Solution(output)
self.assertEqual(gas.n_species, 3)
self.assertEqual(gas.n_reactions, 2)
def test_unterminatedSections2(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'implicitly ended'):
self.convert('unterminated-sections2.inp')
output = self.convert('unterminated-sections2.inp', permissive=True)
gas = ct.Solution(output)
self.assertEqual(gas.n_species, 3)
self.assertEqual(gas.n_reactions, 2)
def test_unrecognized_section(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'SPAM'):
self.convert('unrecognized-section.inp', thermo='dummy-thermo.dat',
permissive=True)
def test_nasa9(self):
output = self.convert("nasa9-test.inp", thermo="nasa9-test-therm.dat")
ref, gas = self.checkConversion("nasa9-test.yaml", output)
self.checkThermo(ref, gas, [300, 500, 1200, 5000])
def test_nasa9_subset(self):
output = self.convert("nasa9-test-subset.inp", thermo="nasa9-test-therm.dat")
ref, gas = self.checkConversion("nasa9-test-subset.yaml", output)
self.checkThermo(ref, gas, [300, 500, 1200, 5000])
def test_sri_falloff(self):
output = self.convert("sri-falloff.inp", thermo="dummy-thermo.dat")
ref, gas = self.checkConversion("sri-falloff.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_chemically_activated(self):
output = self.convert("chemically-activated-reaction.inp")
ref, gas = self.checkConversion("chemically-activated-reaction.yaml",
output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6, 1e7])
def test_explicit_third_bodies(self):
output = self.convert("explicit-third-bodies.inp", thermo="dummy-thermo.dat")
ref, gas = self.checkConversion("explicit-third-bodies.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_explicit_reverse_rate(self):
output = self.convert("explicit-reverse-rate.inp", thermo="dummy-thermo.dat")
ref, gas = self.checkConversion("explicit-reverse-rate.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
# Reactions with explicit reverse rate constants are transformed into
# two irreversible reactions with reactants and products swapped, unless
# the explicit reverse rate is zero so only the forward reaction is used.
Rr = gas.reverse_rate_constants
self.assertEqual(Rr[0], 0.0)
self.assertEqual(Rr[1], 0.0)
self.assertEqual(Rr[2], 0.0)
self.assertEqual(Rr[3], 0.0)
self.assertEqual(Rr[4], 0.0)
Rstoich = gas.reactant_stoich_coeffs
Pstoich = gas.product_stoich_coeffs
self.assertEqual(list(Rstoich[:, 0]), list(Pstoich[:, 1]))
self.assertEqual(list(Rstoich[:, 1]), list(Pstoich[:, 0]))
self.assertEqual(list(Rstoich[:, 2]), list(Pstoich[:, 3]))
self.assertEqual(list(Rstoich[:, 3]), list(Pstoich[:, 2]))
self.assertEqual(gas.n_reactions, 5)
def test_explicit_forward_order(self):
output = self.convert("explicit-forward-order.inp", thermo="dummy-thermo.dat")
ref, gas = self.checkConversion("explicit-forward-order.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_negative_order(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'Negative reaction order'):
self.convert('negative-order.inp', thermo='dummy-thermo.dat')
def test_negative_order_permissive(self):
output = self.convert('negative-order.inp', thermo='dummy-thermo.dat',
permissive=True)
ref, gas = self.checkConversion("negative-order.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_negative_A_factor(self):
output = self.convert('negative-rate.inp', thermo='dummy-thermo.dat')
gas = ct.Solution(output) # Validate the mechanism
self.assertLess(gas.reaction(4).rate.pre_exponential_factor, 0)
self.assertLess(gas.reaction(1).rate.pre_exponential_factor, 0)
self.assertLess(gas.reaction(2).rate.pre_exponential_factor, 0)
self.assertLess(gas.forward_rate_constants[5], 0)
def test_bad_troe_value(self):
with self.assertRaises(ValueError):
self.convert('bad-troe.inp', thermo='dummy-thermo.dat')
def test_invalid_reaction_equation(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'Unparsable'):
self.convert('invalid-equation.inp', thermo='dummy-thermo.dat')
@utilities.slow_test
def test_reaction_units(self):
out_def = self.convert('units-default.inp', thermo='dummy-thermo.dat')
out_cus = self.convert('units-custom.inp', thermo='dummy-thermo.dat')
default, custom = self.checkConversion(out_def, out_cus)
self.checkKinetics(default, custom,
[300, 800, 1450, 2800], [5e0, 5e3, 1e5, 2e6, 1e8], 1e-7)
def test_float_stoich_coeffs(self):
output = self.convert('float-stoich.inp', thermo='dummy-thermo.dat')
gas = ct.Solution(output)
R = gas.reactant_stoich_coeffs
P = gas.product_stoich_coeffs
self.assertArrayNear(R[:,0], [0, 1.5, 0.5, 0])
self.assertArrayNear(P[:,0], [1, 0, 0, 1])
self.assertArrayNear(R[:,1], [1, 0, 0, 1])
self.assertArrayNear(P[:,1], [0, 0.33, 1.67, 0])
def test_photon(self):
output = self.convert('photo-reaction.inp', thermo='dummy-thermo.dat',
permissive=True)
ref, gas = self.checkConversion("photo-reaction.yaml", output)
self.checkKinetics(ref, gas, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_transport_normal(self):
output = self.convert('h2o2.inp', transport='gri30_tran.dat',
output='h2o2_transport_normal')
gas = ct.Solution(output)
gas.TPX = 300, 101325, 'H2:1.0, O2:1.0'
self.assertAlmostEqual(gas.thermal_conductivity, 0.07663, 4)
def test_transport_embedded(self):
output = self.convert('with-transport.inp')
gas = ct.Solution(output)
gas.X = [0.2, 0.3, 0.5]
D = gas.mix_diff_coeffs
for d in D:
self.assertTrue(d > 0.0)
def test_transport_missing_species(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'No transport data'):
self.convert('h2o2.inp', transport='h2o2-missing-species-tran.dat',
output='h2o2_transport_missing_species')
def test_transport_extra_column_entries(self):
with self.assertRaisesRegex(ck2yaml.InputError, '572.400'):
self.convert('h2o2.inp',
transport='h2o2-extra-column-entries-tran.dat',
output='h2o2_extra-column-entries-tran')
def test_transport_duplicate_species(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'duplicate transport'):
self.convert('h2o2.inp',
transport='h2o2-duplicate-species-tran.dat',
output='h2o2_transport_duplicate_species')
self.convert('h2o2.inp',
transport='h2o2-duplicate-species-tran.dat',
output='h2o2_transport_duplicate_species', permissive=True)
def test_transport_bad_geometry(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'geometry flag'):
self.convert('h2o2.inp',
transport='h2o2-bad-geometry-tran.dat',
output='h2o2_transport_bad_geometry')
def test_transport_float_geometry(self):
with self.assertRaisesRegex(ck2yaml.InputError, 'geometry flag'):
self.convert('h2o2.inp',
transport='h2o2-float-geometry-tran.dat',
output='h2o2_transport_float_geometry')
def test_empty_reaction_section(self):
output = self.convert('h2o2_emptyReactions.inp')
gas = ct.Solution(output)
self.assertEqual(gas.n_species, 9)
self.assertEqual(gas.n_reactions, 0)
def test_reaction_comments1(self):
output = self.convert('pdep-test.inp')
text = output.read_text()
self.assertIn('Generic mechanism header', text)
self.assertIn('Single PLOG reaction', text)
self.assertIn('Multiple PLOG expressions at the same pressure', text)
def test_reaction_comments2(self):
output = self.convert('explicit-third-bodies.inp', thermo='dummy-thermo.dat')
text = output.read_text()
self.assertIn('An end of line comment', text)
self.assertIn('A comment after the last reaction', text)
def test_custom_element(self):
output = self.convert('custom-elements.inp')
gas = ct.Solution(output)
self.assertEqual(gas.n_elements, 4)
self.assertNear(gas.atomic_weight(2), 13.003)
self.assertEqual(gas.n_atoms('ethane', 'C'), 2)
self.assertEqual(gas.n_atoms('CC', 'C'), 1)
self.assertEqual(gas.n_atoms('CC', 'Ci'), 1)
def test_surface_mech(self):
output = self.convert('surface1-gas.inp', surface='surface1.inp',
output='surface1')
surf = ct.Interface(output, 'PT_SURFACE')
gas = surf.adjacent["gas"]
self.assertEqual(gas.n_reactions, 11)
self.assertEqual(surf.n_reactions, 15)
self.assertEqual(surf.species('O2_Pt').size, 3)
# Different units for rate constants in each input file
# 62.1 kJ/gmol = 6.21e7 J/kmol
self.assertNear(gas.reaction(0).rate.activation_energy, 6.21e7)
# 67400 J/mol = 6.74e7 J/kmol
self.assertNear(surf.reaction(1).rate.activation_energy, 6.74e7)
# Sticking coefficients
self.assertTrue(surf.reaction(4).duplicate)
self.assertNotIsInstance(surf.reaction(1).rate, ct.StickingArrheniusRate)
self.assertIsInstance(surf.reaction(2).rate, ct.StickingArrheniusRate)
self.assertTrue(surf.reaction(2).rate.motz_wise_correction)
self.assertIsInstance(surf.reaction(4).rate, ct.StickingArrheniusRate)
self.assertFalse(surf.reaction(4).rate.motz_wise_correction)
self.assertTrue(surf.reaction(6).rate.motz_wise_correction)
# Coverage dependencies
covdeps = surf.reaction(1).rate.coverage_dependencies
self.assertEqual(len(covdeps), 2)
self.assertIn("H_Pt", covdeps)
self.assertEqual(covdeps["OH_Pt"]["m"], 1.0)
self.assertNear(covdeps["H_Pt"]["E"], -6e6) # 6000 J/gmol = 6e6 J/kmol
def test_surface_mech2(self):
output = self.convert('surface1-gas-noreac.inp', surface='surface1.inp',
output='surface1-nogasreac')
gas = ct.Solution(output, 'gas')
surf = ct.Interface(output, 'PT_SURFACE', [gas])
self.assertEqual(gas.n_reactions, 0)
self.assertEqual(surf.n_reactions, 15)
covdeps = surf.reaction(1).rate.coverage_dependencies
self.assertIn("H_Pt", covdeps)
self.assertEqual(covdeps["OH_Pt"]["m"], 1.0)
self.assertNear(covdeps["H_Pt"]["E"], -6e6)
def test_third_body_plus_falloff_reactions(self):
output = self.convert("third_body_plus_falloff_reaction.inp")
gas = ct.Solution(output)
self.assertEqual(gas.n_reactions, 2)
def test_blank_line_in_header(self):
output = self.convert("blank_line_in_header.inp")
gas = ct.Solution(output)
self.assertEqual(gas.n_reactions, 1)
@utilities.slow_test
def test_extra(self):
output = self.convert("gri30.inp", thermo="gri30_thermo.dat",
transport="gri30_tran.dat", output="gri30_extra",
extra="extra.yaml")
yml = utilities.load_yaml(output)
desc = yml['description'].split('\n')[-1]
self.assertEqual(desc, 'This is an alternative description.')
for key in ['foo', 'bar']:
self.assertIn(key, yml.keys())
def test_sri_zero(self):
# This test tests it can convert the SRI parameters when D or E equal to 0
output = self.convert('sri_convert_test.txt')
mech = utilities.load_yaml(output)
D = mech['reactions'][0]['SRI']['D']
E = mech['reactions'][0]['SRI']['E']
self.assertEqual(D, 0)
self.assertEqual(E, 0)
def test_duplicate_reactions(self):
# Running a test this way instead of using the convertMech function
# tests the behavior of the ck2yaml.main function and the mechanism
# validation step.
# Replace the ck2yaml logger with our own in order to capture the output
log_stream = io.StringIO()
logger = logging.getLogger('cantera.ck2yaml')
original_handler = logger.handlers.pop()
logformatter = logging.Formatter('%(message)s')
handler = logging.StreamHandler(log_stream)
handler.setFormatter(logformatter)
logger.addHandler(handler)
with self.assertRaises(SystemExit):
ck2yaml.main([
f"--input={self.test_data_path}/undeclared-duplicate-reactions.inp",
f"--thermo={self.test_data_path}/dummy-thermo.dat",
f"--output={self.test_work_path}/undeclared-duplicate-reactions.yaml"])
# Put the original logger back in place
logger.handlers.clear()
logger.addHandler(original_handler)
message = log_stream.getvalue()
for token in ('FAILED', 'lines 12 and 14', 'R1A', 'R1B'):
self.assertIn(token, message)
def test_single_Tint(self):
output = self.convert(None, thermo="thermo_single_Tint.dat",
output="thermo_single_Tint",
single_intermediate_temperature=True)
mech = utilities.load_yaml(output)
# Al(cr)
thermo = mech["species"][0]["thermo"]
assert thermo["temperature-ranges"] == [200.0, 933.61]
assert len(thermo["data"]) == 1
assert thermo["data"][0][0] == 1.01040191
# AlBr3(L)
thermo = mech["species"][1]["thermo"]
assert thermo["temperature-ranges"] == [370.6, 5000.0]
assert len(thermo["data"]) == 1
assert thermo["data"][0][0] == 15.02975
# AlF3(b)
thermo = mech["species"][2]["thermo"]
assert thermo["temperature-ranges"] == [728.0, 1000.0, 2523.0]
assert len(thermo["data"]) == 2
assert thermo["data"][1][0] == 10.41947
# AlF3(L)
thermo = mech["species"][3]["thermo"]
assert thermo["temperature-ranges"] == [2523.0, 5000.0]
assert len(thermo["data"]) == 1
assert thermo["data"][0][0] == 15.096679
def test_error_for_big_element_number(self):
with self.assertRaisesRegex(ck2yaml.InputError,
'Element amounts can have no more than 3 digits.'):
self.convert('big_element_num_err.inp')
class yaml2ckTest(utilities.CanteraTest):
"""Test yaml2ck by converting to CK then back to YAML to read with Cantera."""
ext: str = "-from-yaml2ck.yaml"
def _convert_to_ck(
self,
input_file: Path,
phase_name: str = "",
output: tuple[str, str, str] | tuple = (),
) -> tuple[Path | None, Path | None, Path | None]:
mechanism_path: Path | str
if not output:
stem = Path(input_file).stem # strip '.inp'
mechanism_path = self.test_work_path / (stem + "-from-yaml.ck")
thermo_path = transport_path = None
else:
if len(output) != 3:
raise ValueError(
"convert_to_ck output must be a tuple of length three "
"containing the mechanism, thermo, and transport file names."
)
mechanism_path, thermo_path, transport_path = output
mech, thermo, transport = yaml2ck.convert(
input_file,
phase_name=phase_name,
mechanism_path=mechanism_path,
thermo_path=thermo_path,
transport_path=transport_path,
overwrite=True,
sort_elements=None,
sort_species=None
)
return mech, thermo, transport
def convert(
self,
input_file: Path,
phase_name: str = "",
mech: str | Path | None = None,
thermo: str | Path | None = None,
transport: str | Path | None = None,
permissive: bool = False,
) -> None:
if mech is not None:
mech, thermo, transport = self._convert_to_ck(
input_file,
phase_name,
(mech, thermo, transport),
)
else:
mech, thermo, transport = self._convert_to_ck(input_file, phase_name)
output = self.test_work_path / (Path(input_file).stem + self.ext)
ck2yaml.convert_mech(
mech,
thermo_file=thermo,
transport_file=transport,
out_name=output,
quiet=True,
permissive=permissive,
)
def check_conversion(self, basename, cls=ct.Solution, **kwargs):
# The round-trip YAML->CK->YAML will always have the single phase name 'gas'
# even if the input YAML phase has a different name
if "name" in kwargs:
phase_name = kwargs.pop("name")
else:
phase_name = ""
ckname = self.test_work_path / (basename.stem + self.ext)
ck_phase = cls(ckname, **kwargs)
yaml_phase = cls(basename, phase_name, **kwargs)
self.assertEqual(set(ck_phase.element_names), set(yaml_phase.element_names))
self.assertEqual(set(ck_phase.species_names), set(yaml_phase.species_names))
yamlSpecies = [yaml_phase.species(s) for s in ck_phase.species_names]
for C, Y in zip(ck_phase.species(), yamlSpecies):
self.assertEqual(C.composition, Y.composition)
self.assertEqual(ck_phase.n_reactions, yaml_phase.n_reactions)
for C, Y in zip(ck_phase.reactions(), yaml_phase.reactions()):
self.assertEqual(C.__class__, Y.__class__)
self.assertEqual(C.reactants, Y.reactants)
self.assertEqual(C.products, Y.products)
self.assertEqual(C.duplicate, Y.duplicate)
for i, sp in zip(range(ck_phase.n_reactions), ck_phase.kinetics_species_names):
self.assertEqual(ck_phase.reactant_stoich_coeff(sp, i),
yaml_phase.reactant_stoich_coeff(sp, i))
return ck_phase, yaml_phase
def check_thermo(self, ck_phase, yaml_phase, temperatures, tol=1e-7):
yaml_idx = {ck_phase.species_index(s): yaml_phase.species_index(s) for s in ck_phase.species_names}
for T in temperatures:
ck_phase.TP = T, ct.one_atm
yaml_phase.TP = T, ct.one_atm
cp_ck = ck_phase.partial_molar_cp
cp_yaml = yaml_phase.partial_molar_cp
h_ck = ck_phase.partial_molar_enthalpies
h_yaml = yaml_phase.partial_molar_enthalpies
s_ck = ck_phase.partial_molar_entropies
s_yaml = yaml_phase.partial_molar_entropies
self.assertNear(ck_phase.density, yaml_phase.density)
for i in range(ck_phase.n_species):
message = ' for species {0} at T = {1}'.format(i, T)
self.assertNear(cp_ck[i], cp_yaml[yaml_idx[i]], tol, msg='cp'+message)
self.assertNear(h_ck[i], h_yaml[yaml_idx[i]], tol, msg='h'+message)
self.assertNear(s_ck[i], s_yaml[yaml_idx[i]], tol, msg='s'+message)
def check_kinetics(self, ck_phase, yaml_phase, temperatures, pressures, tol=1e-7):
for T, P in itertools.product(temperatures, pressures):
ck_phase.TP = T, P
yaml_phase.TP = T, P
kf_ck = ck_phase.forward_rate_constants
kr_ck = ck_phase.reverse_rate_constants
kf_yaml = yaml_phase.forward_rate_constants
kr_yaml = yaml_phase.reverse_rate_constants
for i in range(yaml_phase.n_reactions):
message = f"for reaction {i+1}: {yaml_phase.reaction(i)} at T = {T}, P = {P}"
self.assertNear(kf_ck[i], kf_yaml[i], rtol=tol, msg="kf " + message)
self.assertNear(kr_ck[i], kr_yaml[i], rtol=tol, msg="kr " + message)
def check_transport(self, ck_phase, yaml_phase, temperatures, model="mixture-averaged"):
yaml_idx = {ck_phase.species_index(s): yaml_phase.species_index(s) for s in ck_phase.species_names}
ck_phase.transport_model = model
yaml_phase.transport_model = model
for T in temperatures:
ck_phase.TP = T, ct.one_atm
yaml_phase.TP = T, ct.one_atm
self.assertNear(ck_phase.viscosity, yaml_phase.viscosity)
self.assertNear(ck_phase.thermal_conductivity,
yaml_phase.thermal_conductivity)
Dkm_ck = ck_phase.mix_diff_coeffs
Dkm_yaml = yaml_phase.mix_diff_coeffs
for i in range(ck_phase.n_species):
message = 'dkm for species {0} at T = {1}'.format(i, T)
self.assertNear(Dkm_ck[i], Dkm_yaml[yaml_idx[i]], msg=message)
@utilities.slow_test
def test_gri30(self):
input_file = self.cantera_data_path / "gri30.yaml"
self.convert(input_file)
X = {'O2': 0.3, 'H2': 0.1, 'CH4': 0.2, 'CO2': 0.4}
ck_phase, yaml_phase = self.check_conversion(input_file)
ck_phase.X = X
yaml_phase.X = X
self.check_thermo(ck_phase, yaml_phase, [300, 500, 1300, 2000])
self.check_kinetics(ck_phase, yaml_phase, [900, 1800], [2e5, 20e5])
self.check_transport(ck_phase, yaml_phase, [298, 1001, 2400])
def test_nonreactant_orders(self):
input_file = self.test_data_path / "reaction-orders.yaml"
self.convert(input_file, permissive=True)
ck_phase, yaml_phase = self.check_conversion(input_file)
self.check_thermo(ck_phase, yaml_phase, [300, 500])
self.check_kinetics(ck_phase, yaml_phase, [300, 1001, 2500], [1e5, 10e5])
def test_phase_id(self):
input_file = self.cantera_data_path / "nDodecane_Reitz.yaml"
self.convert(input_file, "nDodecane_IG")
ck_phase, yaml_phase = self.check_conversion(input_file, name="nDodecane_IG")
ck_phase.X = "h2:1"
yaml_phase.X = "h2:1"
self.check_kinetics(
ck_phase, yaml_phase, [300, 800, 1450, 2800], [5e3, 1e5, 2e6], tol=4e-6
)
def test_third_body_reactions(self):
input_file = self.test_data_path / "explicit-third-bodies.yaml"
self.convert(input_file)
ck_phase, yaml_phase = self.check_conversion(input_file)
self.check_kinetics(
ck_phase, yaml_phase, [300, 800, 1450, 2800], [5e3, 1e5, 2e6]
)
def test_pdep(self):
input_file = self.test_data_path / "pdep-test.yaml"
self.convert(input_file)
ck_phase, yaml_phase = self.check_conversion(input_file)
# Chebyshev coefficients in XML are truncated to 6 digits, limiting accuracy
self.check_kinetics(ck_phase, yaml_phase, [300, 1000, 2200],
[100, ct.one_atm, 2e5, 2e6, 9.9e6], tol=2e-4)
def test_sri_falloff(self):
input_file = self.test_data_path / "sri-falloff.yaml"
self.convert(input_file)
ck_phase, yaml_phase = self.check_conversion(input_file)
self.check_kinetics(ck_phase, yaml_phase, [300, 800, 1450, 2800], [5e3, 1e5, 2e6])
def test_chemically_activated(self):
input_file = self.test_data_path / "chemically-activated-reaction.yaml"
self.convert(input_file)
ck_phase, yaml_phase = self.check_conversion(input_file)
# pre-exponential factor in XML is truncated to 7 sig figs, limiting accuracy
self.check_kinetics(
ck_phase, yaml_phase, [300, 800, 1450, 2800], [5e3, 1e5, 2e6, 1e7], tol=1e-7
)
def test_yaml_2_ck_reactions(self):
input_file = self.test_data_path / "yaml-ck-reactions.yaml"
self.convert(input_file)
ck_phase, yaml_phase = self.check_conversion(input_file)
X = {'O2': 0.3, 'H': 0.1, 'H2': 0.2, 'AR': 0.4}
ck_phase.X = X
yaml_phase.X = X
self.check_thermo(ck_phase, yaml_phase, [300, 500, 1300, 2000])
self.check_kinetics(ck_phase, yaml_phase, [900, 1800], [2e5, 20e5], tol=2e-7)
self.check_transport(ck_phase, yaml_phase, [298, 1001, 2400])
class cti2yamlTest(utilities.CanteraTest):
def convert(self, basename, src_dir=None, encoding=None):
if src_dir is None:
src_dir = self.test_data_path
cti2yaml.convert(
filename=Path(src_dir) / f"{basename}.cti",
output_name=self.test_work_path / f"{basename}-from-cti.yaml",
encoding=encoding,
)
def checkConversion(self, basename, cls=ct.Solution, ctiphases=(),
yamlphases=(), **kwargs):
ctiPhase = cls(f"{basename}-from-cti.yaml", adjacent=ctiphases, **kwargs)
yamlPhase = cls(f"{basename}.yaml", adjacent=yamlphases, **kwargs)
self.assertEqual(ctiPhase.element_names, yamlPhase.element_names)
self.assertEqual(ctiPhase.species_names, yamlPhase.species_names)
self.assertEqual(ctiPhase.n_reactions, yamlPhase.n_reactions)
for C, Y in zip(ctiPhase.species(), yamlPhase.species()):
self.assertEqual(C.composition, Y.composition)
for C, Y in zip(ctiPhase.reactions(), yamlPhase.reactions()):
self.assertEqual(C.__class__, Y.__class__)
self.assertEqual(C.reactants, Y.reactants)
self.assertEqual(C.products, Y.products)
self.assertEqual(C.duplicate, Y.duplicate)
for i, sp in zip(range(ctiPhase.n_reactions), ctiPhase.kinetics_species_names):
self.assertEqual(ctiPhase.reactant_stoich_coeff(sp, i),
yamlPhase.reactant_stoich_coeff(sp, i))
return ctiPhase, yamlPhase
def checkThermo(self, ctiPhase, yamlPhase, temperatures, tol=1e-7, check_cp=True):
for T in temperatures:
ctiPhase.TP = T, ct.one_atm
yamlPhase.TP = T, ct.one_atm
if check_cp:
cp_cti = ctiPhase.partial_molar_cp
cp_yaml = yamlPhase.partial_molar_cp
else:
with pytest.raises(ct.CanteraError):
yamlPhase.partial_molar_cp
h_cti = ctiPhase.partial_molar_enthalpies
h_yaml = yamlPhase.partial_molar_enthalpies
s_cti = ctiPhase.partial_molar_entropies
s_yaml = yamlPhase.partial_molar_entropies
self.assertNear(ctiPhase.density, yamlPhase.density)
for i in range(ctiPhase.n_species):
message = ' for species {0} at T = {1}'.format(i, T)
if check_cp:
self.assertNear(cp_cti[i], cp_yaml[i], tol, msg='cp'+message)
self.assertNear(h_cti[i], h_yaml[i], tol, msg='h'+message)
self.assertNear(s_cti[i], s_yaml[i], tol, msg='s'+message)
def checkKinetics(self, ctiPhase, yamlPhase, temperatures, pressures, tol=1e-7):
for T,P in itertools.product(temperatures, pressures):
ctiPhase.TP = T, P
yamlPhase.TP = T, P
kf_cti = ctiPhase.forward_rate_constants
kr_cti = ctiPhase.reverse_rate_constants
kf_yaml = yamlPhase.forward_rate_constants
kr_yaml = yamlPhase.reverse_rate_constants
for i in range(yamlPhase.n_reactions):
message = ' for reaction {0} at T = {1}, P = {2}'.format(i, T, P)
self.assertNear(kf_cti[i], kf_yaml[i], rtol=tol, msg='kf '+message)
self.assertNear(kr_cti[i], kr_yaml[i], rtol=tol, msg='kr '+message)
def checkTransport(self, ctiPhase, yamlPhase, temperatures,
model='mixture-averaged'):
ctiPhase.transport_model = model
yamlPhase.transport_model = model
for T in temperatures:
ctiPhase.TP = T, ct.one_atm
yamlPhase.TP = T, ct.one_atm
self.assertNear(ctiPhase.viscosity, yamlPhase.viscosity)
self.assertNear(ctiPhase.thermal_conductivity,
yamlPhase.thermal_conductivity)
Dkm_cti = ctiPhase.mix_diff_coeffs
Dkm_yaml = yamlPhase.mix_diff_coeffs
for i in range(ctiPhase.n_species):
message = 'dkm for species {0} at T = {1}'.format(i, T)
self.assertNear(Dkm_cti[i], Dkm_yaml[i], msg=message)
@utilities.slow_test
def test_gri30(self):
self.convert("gri30")
ctiPhase, yamlPhase = self.checkConversion('gri30')
X = {'O2': 0.3, 'H2': 0.1, 'CH4': 0.2, 'CO2': 0.4}
ctiPhase.X = X
yamlPhase.X = X
self.checkThermo(ctiPhase, yamlPhase, [300, 500, 1300, 2000])
self.checkKinetics(ctiPhase, yamlPhase, [900, 1800], [2e5, 20e5])
self.checkTransport(ctiPhase, yamlPhase, [298, 1001, 2400])
def test_pdep(self):
self.convert("pdep-test")
ctiPhase, yamlPhase = self.checkConversion('pdep-test')
# Agreement limited by low precision used by ck2cti for Chebyshev coeffs
self.checkKinetics(ctiPhase, yamlPhase, [300, 1000, 2200],
[100, ct.one_atm, 2e5, 2e6, 9.9e6], tol=2e-4)
def test_ptcombust(self):
self.convert("ptcombust")
ctiSurf, yamlSurf = self.checkConversion("ptcombust", ct.Interface,
name="Pt_surf")
yamlGas = yamlSurf.adjacent["gas"]
ctiGas = ctiSurf.adjacent["gas"]
self.checkKinetics(ctiGas, yamlGas, [500, 1200], [1e4, 3e5])
self.checkThermo(ctiSurf, yamlSurf, [400, 800, 1600])
self.checkKinetics(ctiSurf, yamlSurf, [500, 1200], [1e4, 3e5])
@utilities.slow_test
def test_ptcombust_motzwise(self):
self.convert("ptcombust-motzwise")
ctiSurf, yamlSurf = self.checkConversion("ptcombust-motzwise", ct.Interface,
name="Pt_surf")
yamlGas = yamlSurf.adjacent["gas"]
ctiGas = ctiSurf.adjacent["gas"]
self.checkKinetics(ctiGas, yamlGas, [500, 1200], [1e4, 3e5])
self.checkThermo(ctiSurf, yamlSurf, [400, 800, 1600])
self.checkKinetics(ctiSurf, yamlSurf, [900], [101325])
def test_sofc(self):
self.convert("sofc")
cti_tpb, yaml_tpb = self.checkConversion("sofc", ct.Interface, name="tpb")
ctiMetal, ctiMSurf, ctiOSurf = cti_tpb.adjacent.values()
yamlMetal, yamlMSurf, yamlOSurf = yaml_tpb.adjacent.values()
self.assertIn("oxide_bulk", ctiOSurf.adjacent)
self.assertIn("gas", ctiOSurf.adjacent)
self.checkThermo(ctiMSurf, yamlMSurf, [900, 1000, 1100])
self.checkThermo(ctiOSurf, yamlOSurf, [900, 1000, 1100])
ctiMetal.electric_potential = yamlMetal.electric_potential = 2
self.checkKinetics(cti_tpb, yaml_tpb, [900, 1000, 1100], [1e5])
ctiMetal.electric_potential = yamlMetal.electric_potential = 4
self.checkKinetics(cti_tpb, yaml_tpb, [900, 1000, 1100], [1e5])
@utilities.slow_test
def test_liquidvapor(self):
self.convert("liquidvapor")
for name in ["water", "nitrogen", "methane", "hydrogen", "oxygen", "heptane"]:
ctiPhase, yamlPhase = self.checkConversion("liquidvapor", name=name)
self.checkThermo(ctiPhase, yamlPhase,
[1.3 * ctiPhase.min_temp, 0.7 * ctiPhase.max_temp])
def test_Redlich_Kwong_CO2(self):
self.convert("co2_RK_example")
ctiGas, yamlGas = self.checkConversion('co2_RK_example')
for P in [1e5, 2e6, 1.3e7]:
yamlGas.TP = ctiGas.TP = 300, P
self.checkThermo(ctiGas, yamlGas, [300, 400, 500], check_cp=False)
def test_diamond(self):
self.convert("diamond")
ctiSurf, yamlSurf = self.checkConversion("diamond", ct.Interface,
name="diamond_100")
ctiSolid = ctiSurf.adjacent["diamond"]
yamlSolid = yamlSurf.adjacent["diamond"]
self.checkThermo(ctiSolid, yamlSolid, [300, 500])
self.checkThermo(ctiSurf, yamlSurf, [330, 490])
self.checkKinetics(ctiSurf, yamlSurf, [400, 800], [2e5])
def test_lithium_ion_battery(self):
name = 'lithium_ion_battery'
self.convert(name, encoding="utf-8")
ctiAnode, yamlAnode = self.checkConversion(name, name='anode')
ctiCathode, yamlCathode = self.checkConversion(name, name='cathode')
ctiMetal, yamlMetal = self.checkConversion(name, name='electron')
ctiElyt, yamlElyt = self.checkConversion(name, name='electrolyte')
ctiAnodeInt, yamlAnodeInt = self.checkConversion(name,
name='edge_anode_electrolyte',
ctiphases=[ctiAnode, ctiMetal, ctiElyt],
yamlphases=[yamlAnode, yamlMetal, yamlElyt])
ctiCathodeInt, yamlCathodeInt = self.checkConversion(name,
name='edge_cathode_electrolyte',
ctiphases=[ctiCathode, ctiMetal, ctiElyt],
yamlphases=[yamlCathode, yamlMetal, yamlElyt])
self.checkThermo(ctiAnode, yamlAnode, [300, 330])
self.checkThermo(ctiCathode, yamlCathode, [300, 330])
ctiAnode.X = yamlAnode.X = [0.7, 0.3]
self.checkThermo(ctiAnode, yamlAnode, [300, 330])
ctiCathode.X = yamlCathode.X = [0.2, 0.8]
self.checkThermo(ctiCathode, yamlCathode, [300, 330])
for phase in [ctiAnode, yamlAnode, ctiCathode, yamlCathode, ctiMetal,
yamlMetal, ctiElyt, yamlElyt, ctiAnodeInt, yamlAnodeInt,
ctiCathodeInt, yamlCathodeInt]:
phase.TP = 300, 1e5
ctiMetal.electric_potential = yamlMetal.electric_potential = 0
ctiElyt.electric_potential = yamlElyt.electric_potential = 1.9
self.checkKinetics(ctiAnodeInt, yamlAnodeInt, [300], [1e5])
ctiMetal.electric_potential = yamlMetal.electric_potential = 2.2
ctiElyt.electric_potential = yamlElyt.electric_potential = 0
self.checkKinetics(ctiCathodeInt, yamlCathodeInt, [300], [1e5])
def test_ch4_ion(self):
self.convert("ch4_ion")
ctiGas, yamlGas = self.checkConversion("ch4_ion")
self.checkThermo(ctiGas, yamlGas, [300, 500, 1300, 2000])
self.checkKinetics(ctiGas, yamlGas, [900, 1800], [2e5, 20e5])
self.checkTransport(ctiGas, yamlGas, [298, 1001, 2400])
def test_description(self):
self.convert("haca2")
ctiGas, yamlGas = self.checkConversion("haca2")
assert ctiGas.input_header["description"].startswith("HACA Mechanism")
assert yamlGas.input_header["description"].startswith("HACA Mechanism")
def test_nonreactant_orders(self):
self.convert("reaction-orders")
ctiGas, yamlGas = self.checkConversion("reaction-orders")
assert ctiGas.input_header["description"].startswith("Input file to test")
self.checkThermo(ctiGas, yamlGas, [300, 500])
self.checkKinetics(ctiGas, yamlGas, [300, 1001, 2500], [1e5, 10e5])
class ctml2yamlTest(utilities.CanteraTest):
def convert(self, basename, src_dir=None):
if src_dir is None:
src_dir = self.test_data_path
ctml2yaml.convert(
Path(src_dir) / f"{basename}.xml",
self.test_work_path / f"{basename}-from-xml.yaml",
)
def checkConversion(self, basename, cls=ct.Solution, ctmlphases=(),
yamlphases=(), **kwargs):
ctmlPhase = cls(f"{basename}-from-xml.yaml", adjacent=ctmlphases, **kwargs)
yamlPhase = cls(f"{basename}.yaml", adjacent=yamlphases, **kwargs)
self.assertEqual(ctmlPhase.element_names, yamlPhase.element_names)
self.assertEqual(ctmlPhase.species_names, yamlPhase.species_names)
self.assertEqual(ctmlPhase.n_reactions, yamlPhase.n_reactions)
for C, Y in zip(ctmlPhase.species(), yamlPhase.species()):
self.assertEqual(C.composition, Y.composition)
for C, Y in zip(ctmlPhase.reactions(), yamlPhase.reactions()):
self.assertEqual(C.__class__, Y.__class__)
self.assertEqual(C.reactants, Y.reactants)
self.assertEqual(C.products, Y.products)
self.assertEqual(C.duplicate, Y.duplicate)
for i, sp in zip(range(ctmlPhase.n_reactions), ctmlPhase.kinetics_species_names):
self.assertEqual(ctmlPhase.reactant_stoich_coeff(sp, i),
yamlPhase.reactant_stoich_coeff(sp, i))
return ctmlPhase, yamlPhase
def checkThermo(self, ctmlPhase, yamlPhase, temperatures, pressure=ct.one_atm,
tol=1e-7, check_cp=True):
for T in temperatures:
ctmlPhase.TP = T, pressure
yamlPhase.TP = T, pressure
if check_cp:
cp_ctml = ctmlPhase.partial_molar_cp
cp_yaml = yamlPhase.partial_molar_cp
else:
with pytest.raises(ct.CanteraError):
yamlPhase.partial_molar_cp