def test_XMLParser_functionality():
"""Test various parts of XMLParser."""
xml_filename = "tests/test_xml_files/rxns.xml"
parser = XMLParser(xml_filename)
# get_species() routine
assert parser.get_species() == ({'H': None,'O': None, 'OH': None,
'H2': None, 'H2O': None, 'O2': None})
# get_rxn_type() routine
assert parser.reaction_list[0].rxn_type == 'Elementary'
# get_rate_coeffs_components() routine
assert (parser.reaction_list[0].rate_coeffs_components ==
{'A': 35200000000.0, 'E': 71400.0})
# get_is_reversible() routine
assert parser.reaction_list[0].is_reversible == False
# get_rxn_equation() routine
assert parser.reaction_list[0].rxn_equation == 'H + O2 =] OH + O'
# get_reactant_stoich_coeffs() routine
assert (parser.reaction_list[0].reactant_stoich_coeffs ==
{'H': 1, 'H2': 0, 'H2O': 0, 'O': 0, 'O2': 1, 'OH': 0})
# get_product_stoich_coeffs() routine
assert (parser.reaction_list[0].product_stoich_coeffs ==
{'H': 0, 'H2': 0, 'H2O': 0, 'O': 1, 'O2': 0, 'OH': 1})
def test_faulty_b_in_arr():
"""Test when b found in Arrhenius (vs. modified Arrhenius)."""
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/faulty_A_arr.xml"
parser = XMLParser(xml_filename)
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/faulty_A_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
def test_convert_to_SI_units_when_no_units():
"""Test when set convert_to_SI_units to True but no units found in XML."""
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/A_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/A_mod_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
def test_rxn_sys_rev_reaction_antioch():
"""Test against Antioch rev rxn results"""
xml_filename = "tests/test_xml_files/rxns_reversible_antioch.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
sql_parser = SQLParser(TEST_DB_PATH, species)
thermo_coeffs = sql_parser.get_thermo_coeffs()
# Condition #1
temp = 900.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 0.0000000000000000e+00,
'OH': 0.0000000000000000e+00,
'H2': 2.0000000000000000e+00,
'H2O': 0.0000000000000000e+00,
'O2': 1.0000000000000000e+00,
'HO2': 0.0000000000000000e+00,
'H2O2': 0.0000000000000000e+00
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -1.2191202810057324e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 1.2191204233198564e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 1.2191204233198564e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], -1.4231412404922757e+06, atol=1e-16)
assert numpy.isclose(rates['H2O'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['O2'], -1.2191205656339805e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], 1.4231412404922757e+06, atol=1e-16)
assert numpy.isclose(rates['H2O2'], 0.0000000000000000e+00, atol=1e-16)
# Condition #2
temp = 2500.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 0.0000000000000000e+00,
'OH': 0.0000000000000000e+00,
'H2': 2.0000000000000000e+00,
'H2O': 0.0000000000000000e+00,
'O2': 1.0000000000000000e+00,
'HO2': 0.0000000000000000e+00,
'H2O2': 0.0000000000000000e+00
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -3.3100422956557074e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], -2.0057001469851071e+11, atol=1e-16)
assert numpy.isclose(rates['H2O'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['O2'], -3.3501562985954098e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], 2.0057001469851071e+11, atol=1e-16)
assert numpy.isclose(rates['H2O2'], 0.0000000000000000e+00, atol=1e-16)
def test_rev_rxn_sys():
"""Returns a valid reaction system with reversible reaction(s)."""
xml_filename = "tests/test_xml_files/rev_rxn.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
sql_parser = SQLParser(TEST_DB_PATH, species)
thermo_coeffs = sql_parser.get_thermo_coeffs()
temp = 500 # "low" temperature range in NASA coeffs database
concentrations = {'H': 1, 'O2': 1, 'H2O': 1}
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
return rxnsys
def test_rxn_sys_get_reaction_rate_for_3_rxns():
"""Tests function to get reaction rate for a given system of reactions (more than 1 reaction)."""
xml_filename = "tests/test_xml_files/rxnsys.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
sql_parser = SQLParser(TEST_DB_PATH, species)
thermo_coeffs = sql_parser.get_thermo_coeffs()
temp = 10
concentrations = {'H': 1, 'O2': 1, 'OH': 1, 'O': 1, 'H2O': 1, 'H2': 1}
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert rates['H'] == -10.
assert rates['O2'] == -15.
assert rates['H2O'] == 40.
assert rates['H2'] == -20.
assert rates['O'] == -10.
assert rates['OH'] == 0.
def test_rxn_sys_invalid_temperature():
"""Tests setting up reaction system with invalid temperatures."""
xml_filename = "tests/test_xml_files/rxns_mixed.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
sql_parser = SQLParser(TEST_DB_PATH, species)
thermo_coeffs = sql_parser.get_thermo_coeffs()
concentrations = {'H': 1, 'O2': 2, 'OH': 1, 'O': 4, 'H2O': 0, 'H2': 1}
temp = 0
with pytest.raises(ValueError):
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
temp = -100
with pytest.raises(ValueError):
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
def test_unit_checks():
"""Tests for unit checks."""
# Arrhenius-type reaction without R
xml_filename = "tests/test_xml_files/unit_check_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
A = parser.reaction_list[0].rate_coeffs_components['A']
E = parser.reaction_list[0].rate_coeffs_components['E']
assert numpy.isclose(A, 35200, atol=1e-16)
assert numpy.isclose(E, 298737.6, atol=1e-16)
# Arrhenius-type reaction with R
xml_filename = "tests/test_xml_files/unit_check_arr_with_R.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=False)
A = parser.reaction_list[0].rate_coeffs_components['A']
E = parser.reaction_list[0].rate_coeffs_components['E']
R = parser.reaction_list[0].rate_coeffs_components['R']
assert numpy.isclose(A, 3.52e+10, atol=1e-16)
assert numpy.isclose(E, 7.14e+04, atol=1e-16)
assert numpy.isclose(R, 8.3144598, atol=1e-16)
# Modified Arrhenius-type reaction without R
xml_filename = "tests/test_xml_files/unit_check_modarr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
A = parser.reaction_list[0].rate_coeffs_components['A']
E = parser.reaction_list[0].rate_coeffs_components['E']
b = parser.reaction_list[0].rate_coeffs_components['b']
assert numpy.isclose(A, 35200, atol=1e-16)
assert numpy.isclose(E, 298737.6, atol=1e-16)
assert numpy.isclose(b, 2.7, atol=1e-16)
# Modified Arrhenius-type reaction with R
xml_filename = "tests/test_xml_files/unit_check_modarr_with_R.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=False)
A = parser.reaction_list[0].rate_coeffs_components['A']
E = parser.reaction_list[0].rate_coeffs_components['E']
b = parser.reaction_list[0].rate_coeffs_components['b']
R = parser.reaction_list[0].rate_coeffs_components['R']
assert numpy.isclose(A, 3.52e+10, atol=1e-16)
assert numpy.isclose(E, 7.14e+04, atol=1e-16)
assert numpy.isclose(b, 2.7, atol=1e-16)
assert numpy.isclose(R, 8.3144598, atol=1e-16)
def test_xml_files_with_missing_info():
"""Test various cases in which input XML files
are missing information."""
# Test when k is missing from constant type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/k_const.xml"
parser = XMLParser(xml_filename)
# Test when A is missing from Arrhenius type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/A_arr.xml"
parser = XMLParser(xml_filename)
# Test when E is missing from Arrhenius type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/E_arr.xml"
parser = XMLParser(xml_filename)
# Test when A is missing from modified Arrhenius type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/A_mod_arr.xml"
parser = XMLParser(xml_filename)
# Test when b is missing from modified Arrhenius type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/b_mod_arr.xml"
parser = XMLParser(xml_filename)
# Test when E is missing from modified Arrhenius type reaction
with pytest.raises(ValueError):
xml_filename = "tests/test_xml_files/E_mod_arr.xml"
parser = XMLParser(xml_filename)
def test_unhandled_xml_components():
"""Test when parts of reaction in the XML file
are unhandled/not implemented."""
# Test when type of reaction is unhandled
xml_filename = "tests/test_xml_files/unhandled_rxn.xml"
with pytest.raises(NotImplementedError):
parser = XMLParser(xml_filename)
# Test when reaction rate coefficient is unhandled
xml_filename = "tests/test_xml_files/unhandled_k.xml"
with pytest.raises(NotImplementedError):
parser = XMLParser(xml_filename)
# Test when units are undhandled
with pytest.raises(NotImplementedError):
xml_filename = "tests/test_xml_files/madeup_units_4_A_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
with pytest.raises(NotImplementedError):
xml_filename = "tests/test_xml_files/madeup_units_4_A_mod_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
with pytest.raises(NotImplementedError):
xml_filename = "tests/test_xml_files/madeup_units_4_E_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
with pytest.raises(NotImplementedError):
xml_filename = "tests/test_xml_files/madeup_units_4_E_mod_arr.xml"
parser = XMLParser(xml_filename, convert_to_SI_units=True)
def test_invalid_component_values():
"""Tests when fields of XML files contain invalid values (non-float)."""
# Test Arrhenius-type reaction when nonsensical R value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_arr_invalidR.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=False)
# Test Arrhenius-type reaction when nonsensical A value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_arr_A.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
# Test Arrhenius-type reaction when nonsensical E value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_arr_E.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
# Test modified Arrhenius-type reaction when nonsensical R value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_modarr_invalidR.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=False)
# Test modified Arrhenius-type reaction when nonsensical A value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_modarr_A.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
# Test modified Arrhenius-type reaction when nonsensical b value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_modarr_b.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
# Test modified Arrhenius-type reaction when nonsensical E value (e.g. string)
xml_filename = "tests/test_xml_files/unit_conversion_fail_modarr_E.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
def test_rxn_sys_irrev_reaction_antioch():
"""Test against Antioch irrev rxn results"""
xml_filename = "tests/test_xml_files/rxns_irreversible_antioch.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
sql_parser = SQLParser(TEST_DB_PATH, species)
thermo_coeffs = sql_parser.get_thermo_coeffs()
# Condition #1
temp = 2500.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 0.0000000000000000e+00,
'OH': 0.0000000000000000e+00,
'H2': 2.0000000000000000e+00,
'H2O': 0.0000000000000000e+00,
'O2': 1.0000000000000000e+00,
'HO2': 0.0000000000000000e+00,
'H2O2': 0.0000000000000000e+00
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['H2O'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['O2'], -3.3300992971255586e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['H2O2'], 0.0000000000000000e+00, atol=1e-16)
# Condition #2
temp = 2500.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 1.0000000000000001e-01,
'OH': 1.0000000000000000e-02,
'H2': 2.0000000000000000e+00,
'H2O': 2.5000000000000000e-01,
'O2': 1.0000000000000000e+00,
'HO2': 2.9999999999999999e-01,
'H2O2': 2.0000000000000000e-02
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -3.7324963347340922e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 2.3071533925003262e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 6.4368180909475500e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], -6.6439941741054521e+12, atol=1e-16)
assert numpy.isclose(rates['H2O'], 4.9820020841399396e+11, atol=1e-16)
assert numpy.isclose(rates['O2'], -2.9843856969218777e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], -1.3498571473703539e+13, atol=1e-16)
assert numpy.isclose(rates['H2O2'], -6.2652907852405969e+11, atol=1e-16)
# Condition #3
temp = 950.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 0.0000000000000000e+00,
'OH': 0.0000000000000000e+00,
'H2': 2.0000000000000000e+00,
'H2O': 0.0000000000000000e+00,
'O2': 1.0000000000000000e+00,
'HO2': 0.0000000000000000e+00,
'H2O2': 0.0000000000000000e+00
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -1.3403448555187156e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 1.3403448555187156e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 1.3403448555187156e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['H2O'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['O2'], -1.3403448555187156e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], 0.0000000000000000e+00, atol=1e-16)
assert numpy.isclose(rates['H2O2'], 0.0000000000000000e+00, atol=1e-16)
# Condition #4
temp = 950.0000000000000000
concentrations = ({
'H': 5.0000000000000000e-01,
'O': 1.0000000000000001e-01,
'OH': 1.0000000000000000e-02,
'H2': 2.0000000000000000e+00,
'H2O': 2.5000000000000000e-01,
'O2': 1.0000000000000000e+00,
'HO2': 2.9999999999999999e-01,
'H2O2': 2.0000000000000000e-02
})
rxnsys = ReactionSystem(xml_parser.reaction_list, thermo_coeffs, temp,
concentrations)
rates = rxnsys.sort_reaction_rates()
assert numpy.isclose(rates['H'], -2.5701654161377395e+13, atol=1e-16)
assert numpy.isclose(rates['O'], 1.1995070447537494e+13, atol=1e-16)
assert numpy.isclose(rates['OH'], 3.5250102331863312e+13, atol=1e-16)
assert numpy.isclose(rates['H2'], 1.9231756318330654e+12, atol=1e-16)
assert numpy.isclose(rates['H2O'], 3.1178427968785107e+11, atol=1e-16)
assert numpy.isclose(rates['O2'], -1.0092501951521918e+13, atol=1e-16)
assert numpy.isclose(rates['HO2'], -1.3353585162517070e+13, atol=1e-16)
assert numpy.isclose(rates['H2O2'], -3.3239141550534125e+11, atol=1e-16)
def test_unit_conversion_fail_arr_onlyE_units():
"""Test when only a few (i.e. not all) components have units."""
xml_filename = "tests/test_xml_files/unit_conversion_fail_arr_onlyEunits.xml"
with pytest.raises(ValueError):
parser = XMLParser(xml_filename, convert_to_SI_units=True)
def test_XMLParser_file_not_found():
"""Test when XML file is nonexistent."""
with pytest.raises(OSError):
parser = XMLParser("no_such_file")
def test_SQLParser_file_not_found():
xml_filename = "tests/test_xml_files/rxn.xml"
xml_parser = XMLParser(xml_filename)
species = xml_parser.get_species()
with pytest.raises(OSError):
sql_parser = SQLParser("no_such_file", species)