def test_bad_coeff():
"""test that input parser correctly identifies that species array is missing"""
try:
input_ = InputParser('tests/test_xml/rxns_bad_coeff.xml')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_missing_equation():
"""test that input parser correctly identifies that species array is missing"""
try:
input_ = InputParser('tests/test_xml/rxns_missing_attribute.xml')
except AttributeError as e:
assert type(e) == AttributeError
print(e)
def test_extradata():
"""test that input parser correctly identifies too many reaction systems present"""
try:
input_ = InputParser('tests/test_xml/rxns_doubleddata.xml')
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_no_reversible():
"""
Check that the empty case can be handled
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
assert len(bc.backward_coeffs(np.array([]), 500)) == 0
def test_missingcoeffdata():
"""test that input parser correctly identifies that coefficient data is missing"""
try:
input_ = InputParser('tests/test_xml/rxns_missingcoeffdata.xml')
except AttributeError as e:
assert type(e) == AttributeError
print(e)
try:
input_ = InputParser('tests/test_xml/rxns_missing_k.xml')
except AttributeError as e:
assert type(e) == AttributeError
print(e)
try:
input_ = InputParser('tests/test_xml/rxns_missing_A.xml')
except AttributeError as e:
assert type(e) == AttributeError
print(e)
def test_singlerxn():
"""test that input parser correctly handles the single reaction case"""
input_ = InputParser('tests/test_xml/rxns_single.xml')
assert len(input_) == 1
assert np.array_equal(input_.nu_prod, np.array([[0], [0], [1], [1]]))
assert np.array_equal(input_.nu_react, np.array([[1], [1], [0], [0]]))
assert input_.rate_coeff_params[0]['k'] == 10000.0
assert input_.rate_coeff_params[0]['type'] == 'Constant'
print(repr(input_))
def test_CPcalc_single():
"""
Test that single reaction case is handled correctly
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
Cp_r = bc.Cp_over_R(500.)
assert np.all(
np.isclose(Cp_r, np.array([2.5, 3.73848592, 2.55540662, 3.54595678])))
def test_Hcalc_single():
"""
Test that single reaction case is handled correctly
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
H_ = bc.H_over_RT(500.)
assert np.all(
np.isclose(
H_, np.array([53.4473198, 1.46400033, 60.98145063, 10.90244139])))
def test_dimension():
"""
Check that incompatible input array sizes are correctly caught
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
try:
bc.backward_coeffs(np.array([1, 2, 3]), 500)
except ValueError as e:
assert type(e) == ValueError
print(e)
def test_coeffs_single():
"""
Test that single reaction case is handled correctly
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
rc_list = [ReactionCoeffs(**params) for params in ip.rate_coeff_params]
for rc in rc_list:
rc.set_params(T=500)
kf = np.array([rc.k_forward() for rc in rc_list])
kb = bc.backward_coeffs(kf, 500)
assert np.isclose(kb[0], 6.03552730e+18)
def test_coeffs_None():
"""
Check that coefficients are being set correctly
"""
ip = InputParser('tests/test_xml/rxns_singlereversible.xml')
sql = SQLParser()
bc = BackwardCoeffs(ip.nu_react, ip.nu_prod, ip.species)
bc.coeffs = None
H_ = bc.H_over_RT(500)
assert np.all(
np.isclose(
H_, np.array([53.4473198, 1.46400033, 60.98145063, 10.90244139])))
bc.coeffs = None
S_ = bc.S_over_R(500)
assert np.all(
np.isclose(
S_, np.array([15.08983739, 26.54400129, 20.70986963,
23.94106991])))
def test_correct():
"""test of standard usage"""
input_ = InputParser('tests/test_xml/rxns.xml')
assert len(input_) == 3
assert len(eval(repr(input_))) == 3
print(repr(input_))