def test_to_table_multi():
path1 = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
path2 = os.path.join(BASE_DIR, 'test_xmls/rxns_rev.xml')
rs1 = ReactionSet(path1)
rs2 = ReactionSet(path2)
mr = MultiReactionOutput([rs1, rs2])
con1 = np.array([[1.], [2.], [1.]])
con2 = np.array([2., 1., .5, 1., 1., 1., .5, 1.]).T
mr.to_table_multi(['H2', 'O'], [con1, con2], [300, 1300, 3000],
'test_tables', 'latex', False)
with open(os.path.join(BASE_DIR, 'test_tables/multireaction_check.tex'),
'r') as f:
check = f.read()
with open(os.path.join(BASE_DIR, 'test_tables/multireaction.tex'),
'r') as f:
tab = f.read()
assert (tab == check)
try:
mr.to_table_multi(True, [con1, con2], [120, 1300, 6000], 'test_tables')
except TypeError as err:
assert (type(err) == TypeError)
try:
mr.to_table_multi('r', [con1, con2], [120, 1300, 6000], 'test_tables')
except KeyError as err:
assert (type(err) == KeyError)
try:
mr.to_table_multi('H2', [np.array([[2.], [1.]]), con2],
[120, 1300, 6000], 'test_tables')
except TypeError as err:
assert (type(err) == TypeError)
try:
mr.to_table_multi(['H2', 'O'], [con1, con2], ['q', 1300, 6000],
'test_tables')
except TypeError as err:
assert (type(err) == TypeError)
def test_set_param_error_coeftype():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
try:
rrr.set_params(1, coeftype='seyretttg')
except ValueError as err:
assert (type(err) == ValueError)
def test_set_param_error_k_type():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
try:
rrr.set_params(0, k=[-1, 2, 33])
except TypeError as err:
assert (type(err) == TypeError)
def test_reaction_rates_rev():
x = np.array([2., 1., .5, 1., 1., 1., .5, 1.]).T
path = os.path.join(BASE_DIR, 'test_xmls/rxns_rev.xml')
rrr = ReactionSet(path)
assert(np.isclose(rrr.progress_rates(x,750), [-3.43641832e+16, -5.88589924e+11, 1.36640381e+12, \
-5.51788793e+14, 1.45474612e+13, 6.75189291e+13, \
1.62500000e+13, 7.82443985e+12, 2.55000887e+13, \
2.69382512e+13, 2.84197199e+12]).all())
assert(np.isclose(rrr.reaction_rates(x,750),[3.42304562795e16,-3.38308977852e16,-3.52979102957e+16, \
4.07078984572e+13,5.86479724945e+14,3.44028050967e+16, \
-7.63606068937e+13,-5.52803118677e+13]).all())
def test_reversible_input():
# Test a standard output
expected_dict = {'reactions': [{'reversible': False, 'coeftype': 'Arrhenius', 'b': 0, 'k': 0, 'A': 35200000000.0, 'E': 71400.0, \
'vprime': np.array([[1.],[0.],[0.],[0.],[0.],[1.]]), 'v2prime': np.array([[0.],[1.],[1.],[0.],[0.],[0.]])},\
{'reversible': True, 'coeftype': 'modifiedArrhenius', 'k': 0, 'A': 0.0506, 'b': 2.7, 'E': 26300.0,\
'vprime': np.array([[0.],[1.],[0.],[1.],[0.],[0.]]), 'v2prime': np.array([[1.],[0.],[1.],[0.],[0.],[0.]])},\
{'reversible': False, 'coeftype': 'Constant', 'A': 0, 'b': 0, 'E': 0, 'k': 1000.0, \
'vprime': np.array([[0.],[0.],[1.],[1.],[0.],[0.]]), 'v2prime': np.array([[1.],[0.],[0.],[0.],[1.],[0.]])}],\
'species': np.array(['H', 'O', 'OH', 'H2', 'H2O', 'O2'])}
path = os.path.join(BASE_DIR, "test_xmls/rxns_test_reversible_input.xml")
actual_dict = ReactionSet(path).get_params()
# Test for each reactions relevant information
for index, expected_dict_index in enumerate(expected_dict['reactions']):
cur_dict_index = actual_dict['reactions'][index]
#assert cur_dict_index['reversible'] == expected_dict_index['reversible']
assert cur_dict_index['coeftype'] == expected_dict_index['coeftype']
assert cur_dict_index['b'] == expected_dict_index['b']
assert cur_dict_index['k'] == expected_dict_index['k']
assert cur_dict_index['A'] == expected_dict_index['A']
assert cur_dict_index['E'] == expected_dict_index['E']
for i, ele in enumerate(cur_dict_index['vprime']):
assert ele == expected_dict_index['vprime'][i]
for i, ele in enumerate(cur_dict_index['v2prime']):
assert ele == expected_dict_index['v2prime'][i]
expected_species = np.array(['H', 'O', 'OH', 'H2', 'H2O', 'O2'])
# Test for the new species entry
for index, ele in enumerate(expected_dict):
assert expected_species[index] == actual_dict['species'][index]
def test_empty_xml_file():
# Test for an empty xml file
try:
path = os.path.join(BASE_DIR, "test_xmls/rxns_test_empty_file.xml")
ReactionSet(path)
except FileNotFoundError as err:
assert (type(err) == FileNotFoundError)
def test_multireaction():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rs = ReactionSet(path)
try:
MultiReactionOutput(rs)
except TypeError as err:
assert (type(err) == TypeError)
def test_mod_arrhenius_k_overflow():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_arr_over_2.xml')
rrr = ReactionSet(path)
try:
rrr.reactions[0]._mod_arrhenius(100)
except OverflowError as err:
assert (type(err) == OverflowError)
def test_xml_file_not_found():
# Test for an empty xml file
try:
path = os.path.join(BASE_DIR, "test_xmls/the_ghost_of_files.xml")
ReactionSet(path)
except FileNotFoundError as err:
assert (type(err) == FileNotFoundError)
def test_reaction_rate_T_error_2():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
try:
rrr.reactions[0].reaction_rate(np.array([[1], [2], [3]]), 'f')
except ValueError as err:
assert (type(err) == ValueError)
def test_progress_rate_T_error_3():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
try:
rrr.reactions[0].progress_rate(np.array([[1], [2], [3]]), [1, 2, 3])
except TypeError as err:
assert (type(err) == TypeError)
def test_progress_rate_x_shape_error():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
try:
rrr.reactions[0].progress_rate(np.array([[1], [2], [3], [4]]), 1)
except ValueError as err:
assert (type(err) == ValueError)
def test_missing_species():
# Test for an empty xml file
try:
path = os.path.join(BASE_DIR,
"test_xmls/rxns_test_missing_species.xml")
ReactionSet(path)
except AttributeError as err:
assert (type(err) == AttributeError)
def test_missing_reactions():
# Test for an empty xml file
try:
path = os.path.join(BASE_DIR,
"test_xmls/rxns_test_missing_reactions.xml")
ReactionSet(path)
except ValueError as err:
assert (type(err) == ValueError)
def test_T_val_error():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
T = -1
try:
rrr.reactions[0].reaction_coef(T)
except ValueError as err:
assert (type(err) == ValueError)
def test_type_missing_tag():
# Test for missing type tag
try:
path = os.path.join(BASE_DIR,
"test_xmls/rxns_test_type_missing_tag.xml")
ReactionSet(path)
except ValueError as err:
assert (type(err) == ValueError)
def test_unexpected_reactant():
# Test for an empty xml file
try:
path = os.path.join(BASE_DIR,
"test_xmls/rxns_test_unexpected_reactant.xml")
ReactionSet(path)
except ValueError as err:
assert (type(err) == ValueError)
def test_T_type_error():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rrr = ReactionSet(path)
T = 'fsag'
try:
rrr.reactions[0].reaction_coef(T)
except TypeError as err:
assert (type(err) == TypeError)
def test_reversible_tag_error():
# Test for invalid reversible tag attribute: i.e. not yes nor no
try:
path = os.path.join(BASE_DIR,
"test_xmls/rxns_test_reversible_tag_error.xml")
ReactionSet(path)
except ValueError as err:
assert (type(err) == ValueError)
def test_missing_modified_arrhenius_parameters():
# Test for an empty xml file
try:
path = os.path.join(
BASE_DIR,
"test_xmls/rxns_test_missing_modified_arrhenius_parameters.xml")
ReactionSet(path)
except AttributeError as err:
assert (type(err) == AttributeError)
def test_uneven_out_bounds():
x = np.array([2., 1., .5, 1., 1., 1., .5, 1.]).T
path = os.path.join(BASE_DIR, 'test_xmls/rxns_rev_ob_test.xml')
rrr = ReactionSet(path)
try:
rrr.reaction_rates(x, 210)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.reaction_rates(x, 3020)
except ValueError as err:
assert (type(err) == ValueError)
def test_to_table_helper():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rs = ReactionSet(path)
con = np.array([[1.], [2.], [1.]])
try:
rs.to_table(['H2', 'O'], con, 1200, 'trash', 'mike')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.to_table(['H2', 'O'], con, 1200, 129910, 'mike')
except TypeError as err:
assert (type(err) == TypeError)
def test_reaction_rates_rev_high():
x = np.array([2., 1., .5, 1., 1., 1., .5, 1.]).T
path = os.path.join(BASE_DIR, 'test_xmls/rxns_rev.xml')
rrr = ReactionSet(path)
try:
rrr.progress_rates(x, 3501)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.reaction_rates(x, 10000)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.reaction_rates(x, float('inf'))
except FloatingPointError as err:
assert (type(err) == FloatingPointError)
# bonus test
try:
rrr.reaction_rates('12,34,5,2,1', 1300)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.progress_rates('12,34,5,2,1', 1300)
except ValueError as err:
assert (type(err) == ValueError)
def test_reaction_coef():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_coef_1.xml')
rrr = ReactionSet(path)
assert (rrr.reaction_coefs(900)[0][0] == 0.00044989777442266471)
assert (rrr.reaction_coefs(900)[1][0] == 1.5783556022951033)
def test_reaction_coef_rev():
path = os.path.join(BASE_DIR, 'test_xmls/rxns_rev.xml')
rrr = ReactionSet(path)
assert (np.isclose(rrr.reaction_coefs(200)[0][0], 19066566282.668961))
assert (np.isclose(rrr.reaction_coefs(200)[0][1], 2.43147163435558e+27))
def test_find_rates():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rs = ReactionSet(path)
con = np.array([[1.], [2.], [1.]])
tab = rs.find_rates(['H2', 'O'], con, [120, 1300, 6000], 'min')
assert (tab[0] == (-60.0, 120))
assert (tab[1] == (-70.0, 120))
try:
rs.find_rates(True, con, [1200], 'min')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.find_rates('r', con, [1200], 'min')
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.find_rates(['H2', 'r'], con, [1200], 'min')
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.find_rates(['H2', 12], con, [1200], 'min')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.find_rates(['H2', 'O'], con, [1010, 'e'], 'max')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.find_rates(['H2', 'O'], con, [1200, 1300, 1400], 'trash')
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.find_rates(['H2', 'O'], con, [1200, 1300, 1400], 3)
except TypeError as err:
assert (type(err) == TypeError)
def test_to_table():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rs = ReactionSet(path)
con = np.array([[1.], [2.], [1.]])
tab = rs.to_table(['H2', 'O'],
con, [120, 1300, 6000],
'trash',
save_output=False)
check = np.array([['T', 'H2', 'O'], [120, -60.0, -70.0],
[1300, -60.0, -70.0], [6000, -60.0, -70.0]],
dtype=object)
assert (np.array_equal(tab, check))
try:
rs.to_table(True, con, 1200, 'trash')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.to_table(True, con, [1200, 1300, 1400], 'trash')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.to_table('r', con, 1200, 'trash')
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.to_table(['H2', 'r'], con, 1200, 'trash')
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.to_table(['H2', 12], con, 1200, 'trash')
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.to_table(['H2', 'O'], con, [1010, 'e'], 'trash')
except TypeError as err:
assert (type(err) == TypeError)
def test_plot_rates_against_temp():
path = os.path.join(BASE_DIR, 'test_xmls/reaction_rate_1.xml')
rs = ReactionSet(path)
con = np.array([[1.], [2.], [1.]])
try:
rs.plot_rates_against_temperature(True, con, 1200)
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.plot_rates_against_temperature(True, con, [1200, 1300, 1400])
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.plot_rates_against_temperature('r', con, 1200)
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.plot_rates_against_temperature(['H2', 'r'], con, 1200)
except ValueError as err:
assert (type(err) == ValueError)
try:
rs.plot_rates_against_temperature(['H2', 12], con, 1200)
except TypeError as err:
assert (type(err) == TypeError)
try:
rs.plot_rates_against_temperature(['H2', 'O'], con, [1010, 'e'])
except TypeError as err:
assert (type(err) == TypeError)
def test_coef_type_error():
try:
path = os.path.join(BASE_DIR, 'test_xmls/reaction_init_type_1.xml')
rrr = ReactionSet(path)
except ValueError as err:
assert (type(err) == ValueError)
def test_reaction_rates_rev_low():
x = np.array([2., 1., .5, 1., 1., 1., .5, 1.]).T
path = os.path.join(BASE_DIR, 'test_xmls/rxns_rev.xml')
rrr = ReactionSet(path)
try:
rrr.progress_rates(x, 190)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.reaction_rates(x, 190)
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.reaction_rates(x, 10)
except FloatingPointError as err:
assert (type(err) == FloatingPointError)
# bonus test
try:
rrr.reaction_rates(x, 'f')
except ValueError as err:
assert (type(err) == ValueError)
try:
rrr.progress_rates(x, 'f')
except ValueError as err:
assert (type(err) == ValueError)