def thermo(mech1_str,
mech2_str,
temps,
mech1_csv_str=None,
mech2_csv_str=None,
dct_idx='name'):
""" Read the thermo sections of two CHEMKIN files and
produce plots of the thermochemical parameters together
"""
# Build dictionaries containing the thermo data strings for each species
if dct_idx == 'name':
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_name_dcts(
mech1_str, mech2_str, temps)
elif dct_idx == 'inchi':
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_inchi_dcts(
mech1_str, mech2_str, mech1_csv_str, mech2_csv_str, temps)
# Combine the two thermo dictionaries together under a common index
thermo_vals_dct = combine.mechanism_thermo(mech1_thermo_dct,
mech2_thermo_dct)
# Build list of CHEMKIN mechanism names for plotting
if dct_idx == 'name':
names = [key for key in thermo_vals_dct]
elif dct_idx == 'inchi':
names = [
combine.spc_name_from_inchi(mech1_csv_str, mech2_csv_str, key)
for key in thermo_vals_dct
]
# Plot the data from both mechanisms for each species
plotter.thermo.build(thermo_vals_dct, temps, names)
def test__compare_thermo():
""" test chemkin_io.calculator.combine.mechanism_thermo
"""
# Build dictionaries containing the thermo data strings for each species
# Dictionaries indexed by the given mechanism names or InCHI string
if INDEX == 'name':
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_name_dcts(
MECH1_STR, MECH2_STR, TEMPS)
elif INDEX == 'inchi':
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_inchi_dcts(
MECH1_STR, MECH2_STR, MECH1_CSV_STR, MECH2_CSV_STR, TEMPS)
print('\nMech1 thermo dct')
for key, val in mech1_thermo_dct.items():
print(key)
print(val)
print('\n\nMech2 thermo dct')
for key, val in mech2_thermo_dct.items():
print(key)
print(val)
# Calculate Enthalpy, Entropy, Gibbs, & Heat Capacity for each species
# Mech 1 and 2 thermo data collated for each species
thermo_vals_dct = combine.mechanism_thermo(mech1_thermo_dct,
mech2_thermo_dct)
print('\n\n\nCombined thermo vals')
for idx in thermo_vals_dct:
# # Obtain the name of each species to print for ID purposes
# if INDEX == 'name':
# mech1_name = idx
# mech2_name = idx
# elif INDEX == 'inchi':
# print('\n\nInChI: ', idx)
# mech1_name, mech2_name = combine.mech_name_from_inchi(
# MECH1_CSV_STR, MECH2_CSV_STR, idx)
# print('M1 Name: ', mech1_name)
# print('M2 Name: ', mech2_name)
# Print all of the thermo quantities
mech1_vals = thermo_vals_dct[idx]['mech1']
mech2_vals = thermo_vals_dct[idx]['mech2']
print('\nM1 Enthalpy', mech1_vals[0])
print('M2 Enthalpy', mech2_vals[0])
print('M1 Heat Capacity', mech1_vals[1])
print('M2 Heat Capacity', mech2_vals[1])
print('M1 Entropy', mech1_vals[2])
print('M2 Entropy', mech2_vals[2])
print('M1 Gibbs', mech1_vals[3])
print('M2 Gibbs', mech2_vals[3])
print('\n\n\n\n\n\n')
print(thermo_vals_dct)
def test__compare_rates():
""" test chemkin_io.mechparser.compare.rates
"""
# Build dictionaries containing:
# thermo data strings for each species, k data strings for each reaction
# Dictionaries indexed by the given mechanism names or InCHI string
# Build name for test but use inchi
_, mech2_thermo_dct = combine.build_thermo_name_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR, TEMPS)
mech1_ktp_dct, mech2_ktp_dct = combine.build_reaction_name_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR, T_REF, TEMPS, PRESSURES)
_, mech2_thermo_dct = combine.build_thermo_inchi_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR, FAKE_CSV_STR, FAKE_CSV_STR, TEMPS)
mech1_ktp_dct, mech2_ktp_dct = combine.build_reaction_inchi_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR, FAKE_CSV_STR, FAKE_CSV_STR, T_REF,
TEMPS, PRESSURES)
print('\nMech1 reaction dct')
for key, val in mech1_ktp_dct.items():
print(key)
print(val)
print('\n\nMech2 reaction dct')
for key, val in mech2_ktp_dct.items():
print(key)
print(val)
# Rate constant
ktp_dct = combine.mechanism_rates(mech1_ktp_dct, mech2_ktp_dct,
mech2_thermo_dct, TEMPS)
# print dict
print('\n\nktp dct')
for rxn, mechs in ktp_dct.items():
print(rxn)
mech1, mech2 = mechs['mech1'], mechs['mech2']
for (pr1, ktp1), (pr2, ktp2) in zip(mech1.items(), mech2.items()):
print('Pressure: ', pr1, pr2)
print('Mech1 ks: ', ktp1)
print('Mech2 ks: ', ktp2)
print(' ')
print('\n\nktp dct')
print(ktp_dct)
def test__compare_thermo():
""" test chemkin_io.calculator.combine.mechanism_thermo
"""
# Build dictionaries containing the thermo data strings for each species
# Dictionaries indexed by the given mechanism names or InCHI string
# Build name for test but use inchi
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_name_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR, TEMPS)
mech1_thermo_dct, mech2_thermo_dct = combine.build_thermo_inchi_dcts(
FAKE1_MECH_STR, FAKE2_MECH_STR,
FAKE_CSV_STR, FAKE_CSV_STR, TEMPS)
print('\nMech1 thermo dct')
for key, val in mech1_thermo_dct.items():
print(key)
print(val)
print('\n\nMech2 thermo dct')
for key, val in mech2_thermo_dct.items():
print(key)
print(val)
# Calculate Enthalpy, Entropy, Gibbs, & Heat Capacity for each species
# Mech 1 and 2 thermo data collated for each species
thermo_vals_dct = combine.mechanism_thermo(
mech1_thermo_dct, mech2_thermo_dct)
print('\n\n\nCombined thermo vals')
for idx in thermo_vals_dct:
# Print all of the thermo quantities
print(idx, '\n')
mech1_vals = thermo_vals_dct[idx]['mech1']
mech2_vals = thermo_vals_dct[idx]['mech2']
print('\nM1 Enthalpy', mech1_vals[0])
print('M2 Enthalpy', mech2_vals[0])
print('M1 Heat Capacity', mech1_vals[1])
print('M2 Heat Capacity', mech2_vals[1])
print('M1 Entropy', mech1_vals[2])
print('M2 Entropy', mech2_vals[2])
print('M1 Gibbs', mech1_vals[3])
print('M2 Gibbs', mech2_vals[3])
print(thermo_vals_dct)
def rates(mech1_str,
mech2_str,
t_ref,
temps,
pressures,
mech1_csv_str=None,
mech2_csv_str=None,
dct_idx='name'):
""" Read the reaction sections of two CHEMKIN files and
produce plots of the rate constants together
"""
# Build dictionaries containing the thermo data strings for each species
if dct_idx == 'name':
_, mech2_thermo_dct = combine.build_thermo_name_dcts(
mech1_str, mech2_str, temps)
mech1_ktp_dct, mech2_ktp_dct = combine.build_reaction_name_dcts(
mech1_str, mech2_str, t_ref, temps, pressures)
elif dct_idx == 'inchi':
_, mech2_thermo_dct = combine.build_thermo_inchi_dcts(
mech1_str, mech2_str, mech1_csv_str, mech2_csv_str, temps)
mech1_ktp_dct, mech2_ktp_dct = combine.build_reaction_inchi_dcts(
mech1_str, mech2_str, mech1_csv_str, mech2_csv_str, t_ref, temps,
pressures)
# Combine the two thermo dictionaries together under a common index
ktp_dct = combine.mechanism_rates(mech1_ktp_dct, mech2_ktp_dct,
mech2_thermo_dct, temps)
# Build list of CHEMKIN mechanism names for plotting
if dct_idx == 'name':
names = [key for key in ktp_dct]
# elif dct_idx == 'inchi':
# names = [combine.rxn_name_from_inchi(mech1_csv_str, mech2_csv_str, key)
# for key in ktp_dct]
# Plot the data from both mechanisms for each species
plotter.rates.build(ktp_dct, temps, names)