def test_arr():
""" Tests the Arrhenius reader
"""
ckin_str1 = (
'REACTIONS CAL/MOLE MOLES\n\n'
'H+O2+M=OH+O+M 1.000E+15 0.000 25000\n'
' N2/1.400/ AR/1.000/ \n\n\n' # note three spaces before \n
'END\n\n')
ckin_str2 = ('REACTIONS CAL/MOLE MOLES\n\n'
'H+O2=OH+O 1.000E+15 0.000 25000\n'
'DUP\n'
'H+O2=OH+O 1.000E+15 0.000 25000\n'
'DUP\n\n\n'
'END\n\n')
rxn_param_dct1 = parser(ckin_str1, 'cal/mole', 'moles')
rxn_param_dct2 = parser(ckin_str2, 'cal/mole', 'moles')
for params in rxn_param_dct1.values(): # should only be one rxn
arr_tuples = params.arr
arr_collid = params.arr_collid
assert len(arr_tuples) == 1
for arr_tuple in arr_tuples:
assert np.allclose(arr_tuple, [1e15, 0, 25000])
for spc, eff in arr_collid.items():
assert spc in ('N2', 'AR')
assert np.isclose(1.4, eff) or np.isclose(1.0, eff)
for params in rxn_param_dct2.values():
arr_tuples = params.arr
assert len(arr_tuples) == 2 # should be a duplicate
for arr_tuple in arr_tuples:
assert np.allclose(arr_tuple, [1e15, 0, 25000])
def test_plog():
""" Tests the PLOG reader and writer
"""
ckin_str1 = 'REACTIONS CAL/MOLE MOLES\n\n' \
'H+O2=OH+O 1.000E+15 0.000 25000 ! Duplicates exist at ' \
'1 atm (see below); only single 1-atm fit is written\n' \
' PLOG /1.000E-01 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+02 1.000E+15 0.000 25000 /\n\n\nEND\n\n'
# This one is for checking the incorrect way of writing duplicate PLOGS
ckin_str2 = 'REACTIONS CAL/MOLE MOLES\n\n' \
'H+O2=OH+O 1.000E+15 0.000 25000 ! Duplicates exist at ' \
'1 atm (see below); only single 1-atm fit is written\n' \
' PLOG /1.000E-01 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+02 1.000E+15 0.000 25000 /\nDUP\n' \
'H+O2=OH+O 1.000E+15 0.000 25000 ! Duplicates exist at ' \
'1 atm (see below); only single 1-atm fit is written\n' \
' PLOG /1.000E-01 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+00 1.000E+15 0.000 25000 /\n' \
' PLOG /1.000E+02 1.000E+15 0.000 25000 /\nDUP\n\n\nEND' \
'\n\n'
rxn_param_dct1 = parser(ckin_str1, 'cal/mole', 'moles')
for params in rxn_param_dct1.values():
plog_dct = params.plog
for pressure, arr_tuples in plog_dct.items():
for arr_tuple in arr_tuples:
assert np.allclose(arr_tuple, [1e15, 0, 25000])
if pressure == 1: # this pressure should have duplicate Arrhenius
assert len(arr_tuples) == 2
# Check the duplicate case
rxn_param_dct2 = parser(ckin_str2, 'cal/mole', 'moles')
for params in rxn_param_dct2.values():
plog_dct = params.plog
plog_dups = params.plog_dups
# Check the plog_dct
for pressure, arr_tuples in plog_dct.items():
for arr_tuple in arr_tuples:
assert np.allclose(arr_tuple, [1e15, 0, 25000])
if pressure == 1: # this pressure should have duplicate Arrhenius
assert len(arr_tuples) == 2
# Check the plog_dups
assert len(plog_dups) == 1
dup_dct = plog_dups[0]
for pressure, arr_tuples in dup_dct.items():
for arr_tuple in arr_tuples:
assert np.allclose(arr_tuple, [1e15, 0, 25000])
if pressure == 1: # this pressure should have duplicate Arrhenius
assert len(arr_tuples) == 2
def test_troe():
""" Tests the Troe reader and writer
"""
ckin_str1 = (
'REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' TROE / 1.500E+00 8.000E+03 1.000E+02 1.000E+03 /\n'
' AR/1.400/ N2/1.700/ \n\n\nEND\n\n')
ckin_str2 = (
'REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' TROE / 1.500E+00 8.000E+03 1.000E+02 1.000E+03 /\n'
' AR/1.400/ N2/1.700/ \n'
'DUP\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' TROE / 1.500E+00 8.000E+03 1.000E+02 1.000E+03 /\n'
' AR/1.400/ N2/1.700/ \n'
'DUP\n\n\nEND\n\n')
rxn_param_dct1 = parser(ckin_str1, 'cal/mole', 'moles')
for params in rxn_param_dct1.values():
troe_dct = params.troe
highp_arr = troe_dct['highp_arr']
lowp_arr = troe_dct['lowp_arr']
troe_params = troe_dct['troe_params']
for arr_tuple in highp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
for arr_tuple in lowp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
assert np.allclose(troe_params, [1.5, 8e3, 1e2, 1e3])
# Do the duplicates check
rxn_param_dct2 = parser(ckin_str2, 'cal/mole', 'moles')
for params in rxn_param_dct2.values():
troe_dct = params.troe
highp_arr = troe_dct['highp_arr']
lowp_arr = troe_dct['lowp_arr']
troe_params = troe_dct['troe_params']
for arr_tuple in highp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
for arr_tuple in lowp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
assert np.allclose(troe_params, [1.5, 8e3, 1e2, 1e3])
assert len(params.troe_dups) == 1
def _get_strs(rxn_param_dct):
""" Gets two strs after passing a rxn_param_dct through
the writer and reader
"""
first_str = writer(rxn_param_dct)
new_rxn_param_dct = parser(first_str, 'cal/mole', 'moles')
second_str = writer(new_rxn_param_dct)
return first_str, second_str
def test_lind():
""" Tests the Lindemann reader and writer
"""
ckin_str1 = ('REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' AR/1.400/ N2/1.700/ \n\n\nEND\n\n')
ckin_str2 = ('REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' AR/1.400/ N2/1.700/ \n'
'DUP\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+12 1.500 50000\n'
' LOW / 1.000E+12 1.500 50000 /\n'
' AR/1.400/ N2/1.700/ \n'
'DUP\n\n\nEND\n\n')
rxn_param_dct1 = parser(ckin_str1, 'cal/mole', 'moles')
for params in rxn_param_dct1.values():
lind_dct = params.lind
highp_arr = lind_dct['highp_arr']
lowp_arr = lind_dct['lowp_arr']
for arr_tuple in highp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
for arr_tuple in lowp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
# Do the duplicates check
rxn_param_dct2 = parser(ckin_str2, 'cal/mole', 'moles')
for params in rxn_param_dct2.values():
lind_dct = params.lind
highp_arr = lind_dct['highp_arr']
lowp_arr = lind_dct['lowp_arr']
for arr_tuple in highp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
for arr_tuple in lowp_arr:
assert np.allclose(arr_tuple, [1e12, 1.5, 50000])
assert len(params.lind_dups) == 1
def test_rxn_names():
""" test mechanalyzer.parser.reaction
"""
ckin_str = ioformat.pathtools.read_file(DAT_PATH, 'rxn_block.dat')
rxn_param_dct = parser(ckin_str, 'cal/mole', 'moles')
print(rxn_param_dct)
def test_cheb():
""" Tests the Chebyshev reader and writer
"""
ckin_str1 = (
'REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+00 0.000 0\n'
' TCHEB/ 500.00 2000.00 /\n'
' PCHEB/ 0.03 100.00 /\n'
' CHEB / 6 4 /\n'
' CHEB / -1.620E+01 -1.183E-01 -5.423E-02 -1.476E-02 /\n'
' CHEB / 2.578E+00 1.614E-01 7.359E-02 1.880E-02 /\n'
' CHEB / 1.068E-01 -7.235E-02 -2.733E-02 -3.778E-03 /\n'
' CHEB / 3.955E-02 1.207E-02 3.402E-04 -2.695E-03 /\n'
' CHEB / 8.557E-03 4.345E-03 3.670E-03 1.608E-03 /\n'
' CHEB / 8.599E-04 -1.758E-03 -7.502E-04 7.396E-07 /\n\n\n'
'END\n\n')
# For duplicates
ckin_str2 = (
'REACTIONS CAL/MOLE MOLES\n\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+00 0.000 0\n'
' TCHEB/ 500.00 2000.00 /\n'
' PCHEB/ 0.03 100.00 /\n'
' CHEB / 6 4 /\n'
' CHEB / -1.620E+01 -1.183E-01 -5.423E-02 -1.476E-02 /\n'
' CHEB / 2.578E+00 1.614E-01 7.359E-02 1.880E-02 /\n'
' CHEB / 1.068E-01 -7.235E-02 -2.733E-02 -3.778E-03 /\n'
' CHEB / 3.955E-02 1.207E-02 3.402E-04 -2.695E-03 /\n'
' CHEB / 8.557E-03 4.345E-03 3.670E-03 1.608E-03 /\n'
' CHEB / 8.599E-04 -1.758E-03 -7.502E-04 7.396E-07 /\n'
'DUP\n'
'H+O2(+N2)=OH+O(+N2) 1.000E+00 0.000 0\n'
' TCHEB/ 500.00 2000.00 /\n'
' PCHEB/ 0.03 100.00 /\n'
' CHEB / 6 4 /\n'
' CHEB / -1.620E+01 -1.183E-01 -5.423E-02 -1.476E-02 /\n'
' CHEB / 2.578E+00 1.614E-01 7.359E-02 1.880E-02 /\n'
' CHEB / 1.068E-01 -7.235E-02 -2.733E-02 -3.778E-03 /\n'
' CHEB / 3.955E-02 1.207E-02 3.402E-04 -2.695E-03 /\n'
' CHEB / 8.557E-03 4.345E-03 3.670E-03 1.608E-03 /\n'
' CHEB / 8.599E-04 -1.758E-03 -7.502E-04 7.396E-07 /\n'
'DUP\n\n\nEND\n\n')
rxn_param_dct1 = parser(ckin_str1, 'cal/mole', 'moles')
for params in rxn_param_dct1.values():
cheb_dct = params.cheb
tlim = cheb_dct['tlim']
plim = cheb_dct['plim']
alpha = cheb_dct['alpha']
assert tlim == (500, 2000)
assert plim == (0.03, 100)
assert np.shape(alpha) == (6, 4)
# Do the duplicates check
rxn_param_dct2 = parser(ckin_str2, 'cal/mole', 'moles')
for params in rxn_param_dct2.values():
cheb_dct = params.cheb
tlim = cheb_dct['tlim']
plim = cheb_dct['plim']
alpha = cheb_dct['alpha']
cheb_dups = params.cheb_dups
assert tlim == (500, 2000)
assert plim == (0.03, 100)
assert np.shape(alpha) == (6, 4)
assert len(cheb_dups) == 1