from __future__ import annotations

import itertools
from pathlib import Path
import logging
import io
import pytest

from . import utilities
from .utilities import allow_deprecated

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, 'Invalid geometry flag value'):
            self.convert('h2o2.inp',
                transport='h2o2-bad-geometry-tran.dat',
                output='h2o2_transport_bad_geometry')

        with self.assertRaisesRegex(ck2yaml.InputError, 'Invalid geometry flag \''):
            self.convert('h2o2.inp',
                transport='h2o2-character-geometry-tran.dat',
                output='h2o2_transport_character_geometry')

    def test_transport_float_geometry(self):
        with self.assertRaisesRegex(ck2yaml.InputError, 'Incorrect geometry flag syntax'):
            self.convert('h2o2.inp',
                transport='h2o2-float-geometry-tran.dat',
                output='h2o2_transport_float_geometry')

        output = self.convert('h2o2.inp',
            transport='h2o2-float-geometry-tran.dat',
            output='h2o2_transport_float_geometry', permissive=True)

        gas = ct.Solution(output)
        self.assertTrue(gas.species("H").transport.geometry == 'atom')
        self.assertTrue(gas.species("H2").transport.geometry == 'linear')
        self.assertTrue(gas.species("H2O").transport.geometry == 'nonlinear')

        with self.assertRaisesRegex(ck2yaml.InputError, 'Invalid float geometry flag'):
            self.convert('h2o2.inp',
                transport='h2o2-float-arithmetic-error-geometry-tran.dat',
                output='h2o2_transport_float_geometry', permissive=True)

    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,
    ) -> str:
        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,
        )
        return mech

    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"
        mech = self.convert(input_file)
        with open(mech) as fid:
            lines = fid.readlines()
        for i, line in enumerate(lines):
            if line.startswith("R1A + R1B"):
                next = lines[i + 1]
                assert next.startswith("LOW") or next.strip() == "DUPLICATE"
        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(NotImplementedError):
                    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(NotImplementedError):
                    yamlPhase.partial_molar_cp
            h_ctml = ctmlPhase.partial_molar_enthalpies
            h_yaml = yamlPhase.partial_molar_enthalpies
            s_ctml = ctmlPhase.partial_molar_entropies
            s_yaml = yamlPhase.partial_molar_entropies
            self.assertNear(ctmlPhase.density, yamlPhase.density)
            for i in range(ctmlPhase.n_species):
                message = ' for species {0} at T = {1}'.format(ctmlPhase.species_names[i], T)
                if check_cp:
                    self.assertNear(cp_ctml[i], cp_yaml[i], tol, msg='cp'+message)
                self.assertNear(h_ctml[i], h_yaml[i], tol, msg='h'+message)
                self.assertNear(s_ctml[i], s_yaml[i], tol, msg='s'+message)

    def checkKinetics(self, ctmlPhase, yamlPhase, temperatures, pressures, tol=1e-7):
        for T,P in itertools.product(temperatures, pressures):
            ctmlPhase.TP = T, P
            yamlPhase.TP = T, P
            kf_ctml = ctmlPhase.forward_rate_constants
            kr_ctml = ctmlPhase.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_ctml[i], kf_yaml[i], rtol=tol, msg='kf '+message)
                self.assertNear(kr_ctml[i], kr_yaml[i], rtol=tol, msg='kr '+message)

    def checkTransport(self, ctmlPhase, yamlPhase, temperatures,
                       model='mixture-averaged'):
        ctmlPhase.transport_model = model
        yamlPhase.transport_model = model
        for T in temperatures:
            ctmlPhase.TP = T, ct.one_atm
            yamlPhase.TP = T, ct.one_atm
            self.assertNear(ctmlPhase.viscosity, yamlPhase.viscosity)
            self.assertNear(ctmlPhase.thermal_conductivity,
                            yamlPhase.thermal_conductivity)
            Dkm_ctml = ctmlPhase.mix_diff_coeffs
            Dkm_yaml = yamlPhase.mix_diff_coeffs
            for i in range(ctmlPhase.n_species):
                message = 'dkm for species {0} at T = {1}'.format(i, T)
                self.assertNear(Dkm_ctml[i], Dkm_yaml[i], msg=message)

    @utilities.slow_test
    def test_gri30(self):
        self.convert("gri30")
        ctmlPhase, yamlPhase = self.checkConversion('gri30')
        X = {'O2': 0.3, 'H2': 0.1, 'CH4': 0.2, 'CO2': 0.4}
        ctmlPhase.X = X
        yamlPhase.X = X
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlPhase, yamlPhase, [900, 1800], [2e5, 20e5])
        self.checkTransport(ctmlPhase, yamlPhase, [298, 1001, 2400])

    def test_pdep(self):
        self.convert("pdep-test")
        ctmlPhase, yamlPhase = self.checkConversion('pdep-test')
        # Chebyshev coefficients in XML are truncated to 6 digits, limiting accuracy
        self.checkKinetics(ctmlPhase, yamlPhase, [300, 1000, 2200],
                           [100, ct.one_atm, 2e5, 2e6, 9.9e6], tol=2e-4)

    def test_ptcombust(self):
        self.convert("ptcombust")
        ctmlSurf, yamlSurf = self.checkConversion("ptcombust", ct.Interface,
            name="Pt_surf")
        ctmlGas = ctmlSurf.adjacent["gas"]
        yamlGas = yamlSurf.adjacent["gas"]

        self.checkKinetics(ctmlGas, yamlGas, [500, 1200], [1e4, 3e5])
        self.checkThermo(ctmlSurf, yamlSurf, [400, 800, 1600])
        self.checkKinetics(ctmlSurf, yamlSurf, [500, 1200], [1e4, 3e5])

    def test_ptcombust_motzwise(self):
        self.convert("ptcombust-motzwise")
        ctmlGas, yamlGas = self.checkConversion('ptcombust-motzwise')
        ctmlSurf, yamlSurf = self.checkConversion('ptcombust-motzwise', ct.Interface,
            name='Pt_surf', ctmlphases=[ctmlGas], yamlphases=[yamlGas])

        self.checkKinetics(ctmlGas, yamlGas, [500, 1200], [1e4, 3e5])
        self.checkThermo(ctmlSurf, yamlSurf, [400, 800, 1600])
        self.checkKinetics(ctmlSurf, yamlSurf, [500, 1200], [1e4, 3e5])

    def test_sofc(self):
        self.convert("sofc")
        ctml_tpb, yaml_tpb = self.checkConversion("sofc", ct.Interface, name="tpb")
        ctmlMetal, ctmlMSurf, ctmlOSurf = ctml_tpb.adjacent.values()
        yamlMetal, yamlMSurf, yamlOSurf = yaml_tpb.adjacent.values()

        self.assertIn("oxide_bulk", ctmlOSurf.adjacent)
        self.assertIn("gas", ctmlOSurf.adjacent)

        self.checkThermo(ctmlMSurf, yamlMSurf, [900, 1000, 1100])
        self.checkThermo(ctmlOSurf, yamlOSurf, [900, 1000, 1100])
        ctmlMetal.electric_potential = yamlMetal.electric_potential = 2
        self.checkKinetics(ctml_tpb, yaml_tpb, [900, 1000, 1100], [1e5])
        ctmlMetal.electric_potential = yamlMetal.electric_potential = 4
        self.checkKinetics(ctml_tpb, yaml_tpb, [900, 1000, 1100], [1e5])

    def test_liquidvapor(self):
        self.convert("liquidvapor")
        for name in ["water", "nitrogen", "methane", "hydrogen", "oxygen", "heptane"]:
            ctmlPhase, yamlPhase = self.checkConversion("liquidvapor", name=name)
            self.checkThermo(ctmlPhase, yamlPhase,
                             [1.3 * ctmlPhase.min_temp, 0.7 * ctmlPhase.max_temp])

    def test_Redlich_Kwong_CO2(self):
        self.convert("co2_RK_example")
        ctmlGas, yamlGas = self.checkConversion('co2_RK_example')
        for P in [1e5, 2e6, 1.3e7]:
            yamlGas.TP = ctmlGas.TP = 300, P
            self.checkThermo(ctmlGas, yamlGas, [300, 400, 500], check_cp=False)

    def test_diamond(self):
        self.convert("diamond")
        ctmlGas, yamlGas = self.checkConversion('diamond', name='gas')
        ctmlSolid, yamlSolid = self.checkConversion('diamond', name='diamond')
        ctmlSurf, yamlSurf = self.checkConversion('diamond',
            ct.Interface, name='diamond_100', ctmlphases=[ctmlGas, ctmlSolid],
            yamlphases=[yamlGas, yamlSolid])
        self.checkThermo(ctmlSolid, yamlSolid, [300, 500])
        self.checkThermo(ctmlSurf, yamlSurf, [330, 490])
        self.checkKinetics(ctmlSurf, yamlSurf, [400, 800], [2e5])

    def test_lithium_ion_battery(self):
        name = 'lithium_ion_battery'
        self.convert(name)
        ctmlAnode, yamlAnode = self.checkConversion(name, name='anode')
        ctmlCathode, yamlCathode = self.checkConversion(name, name='cathode')
        ctmlMetal, yamlMetal = self.checkConversion(name, name='electron')
        ctmlElyt, yamlElyt = self.checkConversion(name, name='electrolyte')
        ctmlAnodeInt, yamlAnodeInt = self.checkConversion(name,
            name='edge_anode_electrolyte',
            ctmlphases=[ctmlAnode, ctmlMetal, ctmlElyt],
            yamlphases=[yamlAnode, yamlMetal, yamlElyt])
        ctmlCathodeInt, yamlCathodeInt = self.checkConversion(name,
            name='edge_cathode_electrolyte',
            ctmlphases=[ctmlCathode, ctmlMetal, ctmlElyt],
            yamlphases=[yamlCathode, yamlMetal, yamlElyt])

        self.checkThermo(ctmlAnode, yamlAnode, [300, 330])
        self.checkThermo(ctmlCathode, yamlCathode, [300, 330])

        ctmlAnode.X = yamlAnode.X = [0.7, 0.3]
        self.checkThermo(ctmlAnode, yamlAnode, [300, 330])
        ctmlCathode.X = yamlCathode.X = [0.2, 0.8]
        self.checkThermo(ctmlCathode, yamlCathode, [300, 330])

        for phase in [ctmlAnode, yamlAnode, ctmlCathode, yamlCathode, ctmlMetal,
                      yamlMetal, ctmlElyt, yamlElyt, ctmlAnodeInt, yamlAnodeInt,
                      ctmlCathodeInt, yamlCathodeInt]:
            phase.TP = 300, 1e5
        ctmlMetal.electric_potential = yamlMetal.electric_potential = 0
        ctmlElyt.electric_potential = yamlElyt.electric_potential = 1.9
        self.checkKinetics(ctmlAnodeInt, yamlAnodeInt, [300], [1e5])

        ctmlMetal.electric_potential = yamlMetal.electric_potential = 2.2
        ctmlElyt.electric_potential = yamlElyt.electric_potential = 0
        self.checkKinetics(ctmlCathodeInt, yamlCathodeInt, [300], [1e5])

    def test_noxNeg(self):
        self.convert("noxNeg")
        ctmlGas, yamlGas = self.checkConversion('noxNeg')
        self.checkThermo(ctmlGas, yamlGas, [300, 1000])
        self.checkKinetics(ctmlGas, yamlGas, [300, 1000], [1e5])

    def test_ch4_ion(self):
        self.convert("ch4_ion")
        ctmlGas, yamlGas = self.checkConversion("ch4_ion")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])
        self.checkTransport(ctmlGas, yamlGas, [298, 1001, 2400])

    def test_nasa9(self):
        self.convert("nasa9-test")
        ctmlGas, yamlGas = self.checkConversion("nasa9-test")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])

    def test_chemically_activated(self):
        self.convert("chemically-activated-reaction")
        ctmlGas, yamlGas = self.checkConversion("chemically-activated-reaction")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])

    def test_explicit_forward_order(self):
        self.convert("explicit-forward-order")
        ctmlGas, yamlGas = self.checkConversion("explicit-forward-order")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        # Accuracy limited by precision of ck2cti
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5], tol=2e-7)

    def test_explicit_reverse_rate(self):
        self.convert("explicit-reverse-rate")
        ctmlGas, yamlGas = self.checkConversion("explicit-reverse-rate")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])

    def test_explicit_third_bodies(self):
        self.convert("explicit-third-bodies")
        ctmlGas, yamlGas = self.checkConversion("explicit-third-bodies")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])

    def test_fractional_stoich_coeffs(self):
        self.convert("frac")
        ctmlGas, yamlGas = self.checkConversion("frac")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])

    def test_water_IAPWS95_thermo(self):
        self.convert("liquid-water")
        ctmlWater, yamlWater = self.checkConversion("liquid-water")
        self.checkThermo(ctmlWater, yamlWater, [300, 500, 1300, 2000], pressure=22064000.0)
        self.assertEqual(ctmlWater.transport_model, yamlWater.transport_model)
        ctmlWater.TP = yamlWater.TP = 300, 22064000.0
        dens = ctmlWater.density
        for T in [298, 1001, 2400]:
            ctmlWater.TD = T, dens
            yamlWater.TD = T, dens
            self.assertNear(ctmlWater.viscosity, yamlWater.viscosity)
            self.assertNear(ctmlWater.thermal_conductivity,
                            yamlWater.thermal_conductivity)

    def test_hmw_nacl_phase(self):
        basename = "HMW_NaCl_sp1977_alt"
        self.convert(basename)
        ctmlPhase, yamlPhase = self.checkConversion(basename)
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_NaCl_solid_phase(self):
        self.convert("NaCl_Solid")
        ctmlPhase, yamlPhase = self.checkConversion("NaCl_Solid")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500, 1300, 2000])

    def test_DH_NaCl_phase(self):
        self.convert("debye-huckel-all")
        for name in [
            "debye-huckel-dilute",
            "debye-huckel-B-dot-ak",
            "debye-huckel-B-dot-a",
            "debye-huckel-pitzer-beta_ij",
            "debye-huckel-beta_ij",
        ]:
            ctmlPhase, yamlPhase = self.checkConversion("debye-huckel-all", name=name)
            self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    @pytest.mark.usefixtures("allow_deprecated")
    def test_Maskell_solid_soln(self):
        self.convert("MaskellSolidSolnPhase_valid")
        ctmlPhase, yamlPhase = self.checkConversion("MaskellSolidSolnPhase_valid")
        # Maskell phase doesn't support partial molar properties, so just check density
        for T in [300, 500, 1300, 2000]:
            ctmlPhase.TP = T, ct.one_atm
            yamlPhase.TP = T, ct.one_atm
            self.assertNear(ctmlPhase.density, yamlPhase.density)

    @pytest.mark.usefixtures("allow_deprecated")
    def test_mock_ion(self):
        self.convert("mock_ion")
        ctmlPhase, yamlPhase = self.checkConversion("mock_ion")
        # ions-from-neutral-molecule phase doesn't support partial molar properties,
        # so just check density
        for T in [300, 500, 1300, 2000]:
            ctmlPhase.TP = T, ct.one_atm
            yamlPhase.TP = T, ct.one_atm
            self.assertNear(ctmlPhase.density, yamlPhase.density)

    def test_Redlich_Kister(self):
        self.convert("RedlichKisterVPSSTP_valid")
        ctmlPhase, yamlPhase = self.checkConversion("RedlichKisterVPSSTP_valid")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_species_names(self):
        self.convert("species-names")
        ctmlGas, yamlGas = self.checkConversion('species-names')
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])

    def test_sri_falloff_reaction(self):
        self.convert("sri-falloff")
        ctmlGas, yamlGas = self.checkConversion("sri-falloff")
        self.checkThermo(ctmlGas, yamlGas, [300, 500, 1300, 2000])
        self.checkKinetics(ctmlGas, yamlGas, [900, 1800], [2e5, 20e5])

    def test_vpss_and_hkft(self):
        self.convert("pdss_hkft")
        ctmlPhase, yamlPhase = self.checkConversion("pdss_hkft")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_lattice_solid(self):
        self.convert("Li7Si3_ls")
        ctmlPhase, yamlPhase = self.checkConversion("Li7Si3_ls",
                                                    name="Li7Si3_and_Interstitials(S)")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_margules(self):
        self.convert("LiKCl_liquid")
        ctmlPhase, yamlPhase = self.checkConversion("LiKCl_liquid")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_idealsolidsoln(self):
        with self.assertWarnsRegex(UserWarning, "SolidKinetics type is not implemented"):
            self.convert("IdealSolidSolnPhaseExample")

        # SolidKinetics is not implemented, so can't create a Kinetics class instance.
        basename = "IdealSolidSolnPhaseExample"
        ctmlPhase = ct.ThermoPhase(basename + "-from-xml.yaml")
        yamlPhase = ct.ThermoPhase(basename + ".yaml")

        self.assertEqual(ctmlPhase.element_names, yamlPhase.element_names)
        self.assertEqual(ctmlPhase.species_names, yamlPhase.species_names)
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_idealmolalsoln(self):
        self.convert("IdealMolalSolnPhaseExample")
        ctmlPhase, yamlPhase = self.checkConversion("IdealMolalSolnPhaseExample")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_transport_models(self):
        self.convert("transport_models_test")
        for name in ["UnityLewis", "CK_Mix", "CK_Multi", "HighP"]:
            ctmlPhase, yamlPhase = self.checkConversion("transport_models_test", name=name)
            self.checkTransport(ctmlPhase, yamlPhase, [298, 1001, 2500])

    def test_nonreactant_orders(self):
        self.convert("reaction-orders")
        ctmlPhase, yamlPhase = self.checkConversion("reaction-orders")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])
        self.checkKinetics(ctmlPhase, yamlPhase, [300, 1001, 2500], [1e5, 10e5])

    def test_species_ss_temperature_polynomials(self):
        self.convert("Li_Liquid")
        ctmlPhase, yamlPhase = self.checkConversion("Li_Liquid")
        self.checkThermo(ctmlPhase, yamlPhase, [300, 500])

    def test_duplicate_section_ids(self):
        with self.assertWarnsRegex(UserWarning, "Duplicate 'speciesData' id"):
            self.convert("duplicate-speciesData-ids")
        with self.assertWarnsRegex(UserWarning, "Duplicate 'reactionData' id"):
            self.convert("duplicate-reactionData-ids")
