def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_pmutt_parameters = {
'name':
'CO2',
'elements': {
'C': 1,
'O': 2
},
'trans_model':
trans.FreeTrans,
'n_degrees':
3,
'molecular_weight':
get_molecular_weight('CO2'),
'rot_model':
rot.RigidRotor,
'rot_temperatures':
rot.get_rot_temperatures_from_atoms(CO2, geometry='linear'),
'geometry':
'linear',
'symmetrynumber':
2,
'elec_model':
elec.GroundStateElec,
'potentialenergy':
-22.994202,
'spin':
0.,
'vib_model':
vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms':
CO2,
'potentialenergy':
-22.994202,
'vib_energies': [
c.wavenumber_to_energy(x) *
c.convert_unit(initial='J', final='eV')
for x in CO2_pmutt_parameters['vib_wavenumbers']
],
'geometry':
'linear',
'symmetrynumber':
2,
'spin':
0.
}
self.CO2_pmutt = StatMech(**CO2_pmutt_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
self.mw = get_molecular_weight({'C': 1, 'O': 2})
def setUp(self):
slope = 0.5
intercept = 10. # kcal/mol
del_E = -1. # kcal/mol
del_E_eV = del_E * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
E_surf = -2. # kcal/mol
E_surf_eV = E_surf * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
E_gas = -3. # kcal/mol
E_gas_eV = E_gas * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
species = {
'A(g)_shomate':
Shomate(name='A(g)_shomate',
T_low=100.,
T_high=500.,
a=np.zeros(8)),
'A(g)_statmech':
StatMech(),
'*':
StatMech(),
'A*':
StatMech(U=del_E_eV, H=del_E_eV, **presets['constant']),
'surf':
StatMech(U=E_surf_eV, H=E_surf_eV, **presets['constant']),
'gas':
StatMech(U=E_gas_eV, H=E_gas_eV, **presets['constant'])
}
reaction_shomate = Reaction.from_string('A(g)_shomate + * = A*',
species)
reaction_statmech = Reaction.from_string('A(g)_statmech + * = A*',
species)
self.lsr_const = LSR(slope=slope,
intercept=intercept,
reaction=del_E,
surf_species=E_surf,
gas_species=E_gas)
self.lsr_shomate = LSR(slope=slope,
intercept=intercept,
reaction=reaction_shomate,
surf_species=species['surf'],
gas_species=species['gas'])
self.lsr_statmech = LSR(slope=slope,
intercept=intercept,
reaction=reaction_statmech,
surf_species=species['surf'],
gas_species=species['gas'])
def setUp(self):
unittest.TestCase.setUp(self)
self.Nasa9_direct = Nasa9(
name='CO2',
elements={'C': 1, 'O': 2},
phase='g',
nasas = [
SingleNasa9(T_low=200., T_high=1000.,
a=np.array([4.943650540E+04, -6.264116010E+02,
5.301725240E+00, 2.503813816E-03,
-2.127308728E-07, -7.689988780E-10,
2.849677801E-13, -4.528198460E+04,
-7.048279440E+00])),
SingleNasa9(T_low=1000., T_high=6000.,
a=np.array([1.176962419E+05, -1.788791477E+03,
8.291523190E+00, -9.223156780E-05,
4.863676880E-09, -1.891053312E-12,
6.330036590E-16, -3.908350590E+04,
-2.652669281E+01])),
SingleNasa9(T_low=6000., T_high=20000.,
a=np.array([-1.544423287E+09, 1.016847056E+06,
-2.561405230E+02, 3.369401080E-02,
-2.181184337E-06, 6.991420840E-11,
-8.842351500E-16, -8.043214510E+06,
2.254177493E+03]))]
)
H2O_statmech = StatMech(name='H2O', spin=0, symmetrynumber=2,
atoms=molecule('H2O'), potentialenergy=-14.2209,
vib_wavenumbers=np.array([3825.434, 3710.2642, 1582.432]),
**presets['idealgas'])
self.Nasa9_statmech = Nasa9.from_model(
name='H2O', elements={'H': 2, 'O': 1}, phase='g', T_low=100.,
T_high=5000., model=H2O_statmech)
def _float_to_specie(self, val):
"""Converts a float to a :class:`~pmutt.statmech.StatMech` object
Parameters
----------
val : float
Value (in kcal/mol)
Returns
-------
obj : :class:`~pmutt.statmech.StatMech` object
:class:`~pmutt.statmech.StatMech` object that gives the val
when `get_E` is called
"""
val = val*c.convert_unit(initial='kcal/mol', final='eV/molecule')
return StatMech(U=val, H=val, F=val, G=val, **presets['constant'])
def _float_to_reaction(self, val):
"""Converts a float to a :class:`~pmutt.reaction.Reaction` object
Parameters
----------
val : float
Value (in kcal/mol)
Returns
-------
obj : :class:`~pmutt.reaction.Reaction` object
:class:`~pmutt.reaction.Reaction` object that gives the val
when `get_delta_E` is called
"""
reactant = StatMech()
product = self._float_to_specie(val=val)
return Reaction(reactants=[reactant], reactants_stoich=[1.],
products=[product], products_stoich=[1.])
1150.401492, 1027.841298, 1018.203753,
945.310074, 929.15992, 911.661049,
808.685354, 730.986587, 475.287654,
339.164649, 264.682213, 244.584138,
219.956713, 115.923768, 35.56194])
'''Rotational'''
butane_rot = rot.RigidRotor(symmetrynumber=2, atoms=butane_atoms)
'''Electronic'''
butane_elec = elec.GroundStateElec(potentialenergy=-73.7051, spin=0)
'''StatMech Initialization'''
butane_statmech = StatMech(name='butane',
trans_model=butane_trans,
vib_model=butane_vib,
rot_model=butane_rot,
elec_model=butane_elec)
H_statmech = butane_statmech.get_H(T=298., units='kJ/mol')
S_statmech = butane_statmech.get_S(T=298., units='J/mol/K')
print('H_butane(T=298) = {:.1f} kJ/mol'.format(H_statmech))
print('S_butane(T=298) = {:.2f} J/mol/K'.format(S_statmech))
# ### Presets
# The [``presets``][0] dictionary stores commonly used models to ease the initialization of [``StatMech``][1] objects. The same water molecule before can be initialized this way instead.
#
# [0]: https://vlachosgroup.github.io/pmutt/statmech.html#presets
# [1]: https://vlachosgroup.github.io/pmutt/statmech.html#pmutt.statmech.StatMech
from pmutt.statmech import StatMech, trans, vib, rot, elec
H2_atoms = molecule('H2')
'''Translational'''
H2_trans = trans.FreeTrans(n_degrees=3, atoms=H2_atoms)
'''Vibrational'''
H2_vib = vib.HarmonicVib(vib_wavenumbers=[4342.]) # vib_wavenumbers in cm-1
'''Rotational'''
H2_rot = rot.RigidRotor(symmetrynumber=2, atoms=H2_atoms)
'''Electronic'''
H2_elec = elec.GroundStateElec(potentialenergy=-6.77,
spin=0) # potentialenergy in eV
'''StatMech Initialization'''
H2_statmech = StatMech(name='H2',
trans_model=H2_trans,
vib_model=H2_vib,
rot_model=H2_rot,
elec_model=H2_elec)
'''Calculate thermodynamic properties'''
H_statmech = H2_statmech.get_H(T=298., units='kJ/mol')
S_statmech = H2_statmech.get_S(T=298., units='J/mol/K')
print('H_H2(T=298 K) = {:.1f} kJ/mol'.format(H_statmech))
print('S_H2(T=298 K) = {:.2f} J/mol/K'.format(S_statmech))
# <a id='section_5_3'></a>
# ## 5.3. Initializing StatMech modes using presets
#
# Commonly used models can be accessed via [``presets``](https://vlachosgroup.github.io/pMuTT/statmech.html#presets). The currently supported models are:
#
# - [``idealgas``](https://vlachosgroup.github.io/pMuTT/statmech.html#ideal-gas-idealgas) - Ideal gases
class TestStatMech(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_pmutt_parameters = {
'name':
'CO2',
'elements': {
'C': 1,
'O': 2
},
'trans_model':
trans.FreeTrans,
'n_degrees':
3,
'molecular_weight':
get_molecular_weight('CO2'),
'rot_model':
rot.RigidRotor,
'rot_temperatures':
rot.get_rot_temperatures_from_atoms(CO2, geometry='linear'),
'geometry':
'linear',
'symmetrynumber':
2,
'elec_model':
elec.GroundStateElec,
'potentialenergy':
-22.994202,
'spin':
0.,
'vib_model':
vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms':
CO2,
'potentialenergy':
-22.994202,
'vib_energies': [
c.wavenumber_to_energy(x) *
c.convert_unit(initial='J', final='eV')
for x in CO2_pmutt_parameters['vib_wavenumbers']
],
'geometry':
'linear',
'symmetrynumber':
2,
'spin':
0.
}
self.CO2_pmutt = StatMech(**CO2_pmutt_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
self.mw = get_molecular_weight({'C': 1, 'O': 2})
def test_get_q(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_q(T=self.T0, ignore_q_elec=True, V=self.V0),
6.163652058396284e+25)
def test_get_CvoR(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_CvoR(T=self.T0, V=self.V0), 2.9422622359004853)
def test_get_Cv(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_Cv(T=self.T0, V=self.V0, units='J/mol/K'),
2.9422622359004853 * c.R('J/mol/K'))
np.testing.assert_almost_equal(
self.CO2_pmutt.get_Cv(T=self.T0, V=self.V0, units='J/g/K'),
2.9422622359004853 * c.R('J/mol/K') / self.mw)
def test_get_CpoR(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_CpoR(T=self.T0, V=self.V0), 3.9422622359004853)
def test_get_Cp(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_Cp(T=self.T0, V=self.V0, units='J/mol/K'),
3.9422622359004853 * c.R('J/mol/K'))
np.testing.assert_almost_equal(
self.CO2_pmutt.get_Cp(T=self.T0, V=self.V0, units='J/g/K'),
3.9422622359004853 * c.R('J/mol/K') / self.mw)
def test_get_EoRT(self):
np.testing.assert_almost_equal(self.CO2_pmutt.get_EoRT(T=self.T0),
-894.97476277965)
np.testing.assert_almost_equal(
self.CO2_pmutt.get_EoRT(T=self.T0, include_ZPE=True),
-877.703643641077)
def test_get_E(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_E(T=self.T0, units='J/mol'),
-894.97476277965 * c.R('J/mol/K') * self.T0)
np.testing.assert_almost_equal(self.CO2_pmutt.get_E(T=self.T0,
units='J/mol',
include_ZPE=True),
-877.703643641077 * c.R('J/mol/K') *
self.T0,
decimal=2)
np.testing.assert_almost_equal(
self.CO2_pmutt.get_E(T=self.T0, units='J/g'),
-894.97476277965 * c.R('J/mol/K') * self.T0 / self.mw)
def test_get_UoRT(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_UoRT(T=self.T0, V=self.V0), -875.1095022368354)
def test_get_U(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_U(T=self.T0, V=self.V0, units='J/mol'),
-875.1095022368354 * c.R('J/mol/K') * self.T0)
np.testing.assert_almost_equal(
self.CO2_pmutt.get_U(T=self.T0, V=self.V0, units='J/g'),
-875.1095022368354 * c.R('J/mol/K') * self.T0 / self.mw)
def test_get_HoRT(self):
expected_HoRT_CO2 = \
self.CO2_ASE.get_enthalpy(temperature=self.T0, verbose=False) \
/ c.R('eV/K')/self.T0
calc_HoRT_CO2 = self.CO2_pmutt.get_HoRT(T=self.T0)
np.testing.assert_almost_equal(expected_HoRT_CO2, calc_HoRT_CO2, 3)
def test_get_H(self):
expected_H_CO2 = \
self.CO2_ASE.get_enthalpy(temperature=self.T0, verbose=False)
calc_H_CO2 = self.CO2_pmutt.get_H(T=self.T0, units='eV')
np.testing.assert_almost_equal(expected_H_CO2, calc_H_CO2, 3)
def test_get_SoR(self):
expected_SoR_CO2 = \
self.CO2_ASE.get_entropy(temperature=self.T0, pressure=self.P0,
verbose=False)/c.R('eV/K')
calc_SoR_CO2 = self.CO2_pmutt.get_SoR(T=self.T0, V=self.V0)
np.testing.assert_almost_equal(expected_SoR_CO2, calc_SoR_CO2, 3)
def test_get_S(self):
expected_S_CO2 = \
self.CO2_ASE.get_entropy(temperature=self.T0, pressure=self.P0,
verbose=False)
calc_S_CO2 = self.CO2_pmutt.get_S(T=self.T0, V=self.V0, units='eV/K')
np.testing.assert_almost_equal(expected_S_CO2, calc_S_CO2, 1)
def test_get_FoRT(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_FoRT(T=self.T0, V=self.V0), -900.6031596134445)
def test_get_F(self):
np.testing.assert_almost_equal(
self.CO2_pmutt.get_F(T=self.T0, V=self.V0, units='J/mol'),
-900.6031596134445 * c.R('J/mol/K') * self.T0)
np.testing.assert_almost_equal(
self.CO2_pmutt.get_F(T=self.T0, V=self.V0, units='J/g'),
-900.6031596134445 * c.R('J/mol/K') * self.T0 / self.mw)
def test_get_GoRT(self):
expected_GoRT_CO2 = \
self.CO2_ASE.get_gibbs_energy(temperature=self.T0,
pressure=self.P0,
verbose=False)/c.R('eV/K')/self.T0
calc_GoRT_CO2 = self.CO2_pmutt.get_GoRT(T=self.T0, V=self.V0)
np.testing.assert_almost_equal(expected_GoRT_CO2, calc_GoRT_CO2, 3)
def test_get_G(self):
expected_G_CO2 = \
self.CO2_ASE.get_gibbs_energy(temperature=self.T0,
pressure=self.P0,
verbose=False)
calc_G_CO2 = self.CO2_pmutt.get_G(T=self.T0, V=self.V0, units='eV')
np.testing.assert_almost_equal(expected_G_CO2, calc_G_CO2, 3)
potentialenergy=-14.2209,
symmetrynumber=2,
spin=0.,
atoms=molecule('H2O'),
vib_wavenumbers=[3825.434, 3710.2642, 1582.432],
T_ref=298.,
HoRT_ref=-97.60604334,
**presets['idealgas'])
refs = References(references=[H2_ref, H2O_ref])
H2O_statmech = StatMech(name='H2O',
phase='G',
atoms=molecule('H2O'),
potentialenergy=-14.2209,
symmetrynumber=2,
spin=0,
references=refs,
vib_wavenumbers=[3825.434, 3710.264, 1582.432],
**presets['idealgas'])
H2O_TS_statmech = StatMech(name='H2O',
elements={
'H': 2,
'O': 1
},
phase='G',
atoms=molecule('H2O'),
potentialenergy=0.,
symmetrynumber=2,
spin=0,
12.47757489, 12.52697445, 12.64787689, 12.7652535, 12.87931824,
12.99026871, 13.09828757, 13.20354395, 13.3061946, 13.40638501,
13.50425036, 13.59991643, 13.69350035, 13.78511133, 13.87485131,
13.96281555, 14.04909315, 14.13376754, 14.21691692, 14.29861465,
14.37892962, 14.45792659, 14.53566649, 14.6122067, 14.68760129,
14.76190128, 14.83515483, 14.90740747, 14.97870223, 15.04907987,
15.11857898, 15.18723616, 15.25508613, 15.32216185, 15.38849466,
15.45411434, 15.51904926, 15.58332641, 15.64697155, 15.71000921,
15.77246282, 15.83435478
])
HoRT_Fe2O3 = -333.1719719
SoR_Fe2O3 = 10.49736076
O2 = StatMech(vib_wavenumbers=np.array([1580.2]),
potentialenergy=-0.1879339246281043,
spin=1.,
symmetrynumber=2,
atoms=molecule('O2'),
**presets['idealgas'])
species = {
'Fe':
Nasa.from_data(name='Fe',
T=T,
CpoR=CpoR_Fe,
T_ref=T_ref,
HoRT_ref=HoRT_Fe,
SoR_ref=SoR_Fe),
'FeO':
Nasa.from_data(name='FeO',
T=T,
CpoR=CpoR_FeO,
def setUp(self):
self.T = c.T0('K')
# Factor to convert potential energy to dimensionless number
dim_factor = c.R('eV/K')*self.T
self.m = 0.5 # BEP Slope
self.c = 20. # BEP Intercept in kcal/mol
species = {
'H2': StatMech(name='H2', potentialenergy=2.*dim_factor,
**presets['electronic']),
'O2': StatMech(name='O2', potentialenergy=4.*dim_factor,
**presets['electronic']),
'H2O': StatMech(name='H2O', potentialenergy=3.*dim_factor,
**presets['electronic']),
'BEP': BEP(slope=self.m, intercept=self.c, name='BEP')
}
self.rxn_delta_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='delta_H')
self.bep_delta_H = self.rxn_delta_H.transition_state[0]
rxn_rev_delta_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='rev_delta_H')
self.bep_rev_delta_H = rxn_rev_delta_H.transition_state[0]
rxn_reactants_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='reactants_H')
self.bep_reactants_H = rxn_reactants_H.transition_state[0]
rxn_products_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='products_H')
self.bep_products_H = rxn_products_H.transition_state[0]
self.rxn_delta_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='delta_E')
self.bep_delta_E = self.rxn_delta_E.transition_state[0]
rxn_rev_delta_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='rev_delta_E')
self.bep_rev_delta_E = rxn_rev_delta_E.transition_state[0]
rxn_reactants_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='reactants_E')
self.bep_reactants_E = rxn_reactants_E.transition_state[0]
rxn_products_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='products_E')
self.bep_products_E = rxn_products_E.transition_state[0]
def setUp(self):
'''Reactions using Nasa polynomial'''
self.H2O_nasa = Nasa(name='H2O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'H': 2,
'O': 1
},
a_low=[
4.19864056E+00, -2.03643410E-03,
6.52040211E-06, -5.48797062E-09,
1.77197817E-12, -3.02937267E+04,
-8.49032208E-01
],
a_high=[
3.03399249E+00, 2.17691804E-03,
-1.64072518E-07, -9.70419870E-11,
1.68200992E-14, -3.00042971E+04,
4.96677010E+00
])
self.H2_nasa = Nasa(name='H2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 2},
a_low=[
2.34433112E+00, 7.98052075E-03,
-1.94781510E-05, 2.01572094E-08,
-7.37611761E-12, -9.17935173E+02,
6.83010238E-01
],
a_high=[
3.33727920E+00, -4.94024731E-05,
4.99456778E-07, -1.79566394E-10,
2.00255376E-14, -9.50158922E+02,
-3.20502331E+00
])
self.O2_nasa = Nasa(name='O2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 2},
a_low=[
3.78245636E+00, -2.99673416E-03,
9.84730201E-06, -9.68129509E-09,
3.24372837E-12, -1.06394356E+03, 3.65767573E+00
],
a_high=[
3.28253784E+00, 1.48308754E-03,
-7.57966669E-07, 2.09470555E-10,
-2.16717794E-14, -1.08845772E+03,
5.45323129E+00
])
self.rxn_nasa = rxn.Reaction(reactants=[self.H2_nasa, self.O2_nasa],
reactants_stoich=[1., 0.5],
products=[self.H2O_nasa],
products_stoich=[1.])
self.rxn_nasa_dict = {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07, -9.7041987e-11,
1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06, -5.48797062e-09,
1.77197817e-12, -30293.7267, -0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922, -3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05, 2.01572094e-08,
-7.37611761e-12, -917.935173, 0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.28253784, 0.00148308754, -7.57966669e-07, 2.09470555e-10,
-2.16717794e-14, -1088.45772, 5.45323129
],
'a_low': [
3.78245636, -0.00299673416, 9.84730201e-06,
-9.68129509e-09, 3.24372837e-12, -1063.94356, 3.65767573
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 2
},
'name':
'O2',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 0.5],
'transition_state':
None,
'transition_state_stoich':
None,
'reaction_str':
'H2+0.50O2=H2O',
}
'''Reactions using StatMech'''
ideal_gas_param = presets['idealgas']
self.H2O_sm = StatMech(name='H2O',
atoms=molecule('H2O'),
symmetrynumber=2,
vib_wavenumbers=[3825.434, 3710.2642, 1582.432],
potentialenergy=-6.7598,
spin=0.,
**ideal_gas_param)
self.H2_sm = StatMech(name='H2',
atoms=molecule('H2'),
symmetrynumber=2,
vib_wavenumbers=[4306.1793],
potentialenergy=-14.2209,
spin=0.,
**ideal_gas_param)
self.O2_sm = StatMech(name='O2',
atoms=molecule('O2'),
symmetrynumber=2,
vib_wavenumbers=[1556.],
potentialenergy=-9.862407,
spin=1.,
**ideal_gas_param)
# This is an arbitrary transition state for testing
self.H2O_TS_sm = StatMech(name='H2O_TS',
atoms=molecule('H2O'),
symmetrynumber=1.,
vib_wavenumbers=[4000., 3900., 1600.],
potentialenergy=-5.7598,
spin=0.,
**ideal_gas_param)
self.rxn_sm = rxn.Reaction(reactants=[self.H2_sm, self.O2_sm],
reactants_stoich=[1., 0.5],
products=[self.H2O_sm],
products_stoich=[1.],
transition_state=[self.H2O_TS_sm],
transition_state_stoich=[1.])
self.species_dict = {
'H2O': self.H2O_sm,
'H2': self.H2_sm,
'O2': self.O2_sm,
'H2O_TS': self.H2O_TS_sm
}
self.maxDiff = None
class TestReaction(unittest.TestCase):
def setUp(self):
'''Reactions using Nasa polynomial'''
self.H2O_nasa = Nasa(name='H2O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'H': 2,
'O': 1
},
a_low=[
4.19864056E+00, -2.03643410E-03,
6.52040211E-06, -5.48797062E-09,
1.77197817E-12, -3.02937267E+04,
-8.49032208E-01
],
a_high=[
3.03399249E+00, 2.17691804E-03,
-1.64072518E-07, -9.70419870E-11,
1.68200992E-14, -3.00042971E+04,
4.96677010E+00
])
self.H2_nasa = Nasa(name='H2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 2},
a_low=[
2.34433112E+00, 7.98052075E-03,
-1.94781510E-05, 2.01572094E-08,
-7.37611761E-12, -9.17935173E+02,
6.83010238E-01
],
a_high=[
3.33727920E+00, -4.94024731E-05,
4.99456778E-07, -1.79566394E-10,
2.00255376E-14, -9.50158922E+02,
-3.20502331E+00
])
self.O2_nasa = Nasa(name='O2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 2},
a_low=[
3.78245636E+00, -2.99673416E-03,
9.84730201E-06, -9.68129509E-09,
3.24372837E-12, -1.06394356E+03, 3.65767573E+00
],
a_high=[
3.28253784E+00, 1.48308754E-03,
-7.57966669E-07, 2.09470555E-10,
-2.16717794E-14, -1.08845772E+03,
5.45323129E+00
])
self.rxn_nasa = rxn.Reaction(reactants=[self.H2_nasa, self.O2_nasa],
reactants_stoich=[1., 0.5],
products=[self.H2O_nasa],
products_stoich=[1.])
self.rxn_nasa_dict = {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07, -9.7041987e-11,
1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06, -5.48797062e-09,
1.77197817e-12, -30293.7267, -0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922, -3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05, 2.01572094e-08,
-7.37611761e-12, -917.935173, 0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.28253784, 0.00148308754, -7.57966669e-07, 2.09470555e-10,
-2.16717794e-14, -1088.45772, 5.45323129
],
'a_low': [
3.78245636, -0.00299673416, 9.84730201e-06,
-9.68129509e-09, 3.24372837e-12, -1063.94356, 3.65767573
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 2
},
'name':
'O2',
'notes':
None,
'phase':
None,
'model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 0.5],
'transition_state':
None,
'transition_state_stoich':
None,
'reaction_str':
'H2+0.50O2=H2O',
}
'''Reactions using StatMech'''
ideal_gas_param = presets['idealgas']
self.H2O_sm = StatMech(name='H2O',
atoms=molecule('H2O'),
symmetrynumber=2,
vib_wavenumbers=[3825.434, 3710.2642, 1582.432],
potentialenergy=-6.7598,
spin=0.,
**ideal_gas_param)
self.H2_sm = StatMech(name='H2',
atoms=molecule('H2'),
symmetrynumber=2,
vib_wavenumbers=[4306.1793],
potentialenergy=-14.2209,
spin=0.,
**ideal_gas_param)
self.O2_sm = StatMech(name='O2',
atoms=molecule('O2'),
symmetrynumber=2,
vib_wavenumbers=[1556.],
potentialenergy=-9.862407,
spin=1.,
**ideal_gas_param)
# This is an arbitrary transition state for testing
self.H2O_TS_sm = StatMech(name='H2O_TS',
atoms=molecule('H2O'),
symmetrynumber=1.,
vib_wavenumbers=[4000., 3900., 1600.],
potentialenergy=-5.7598,
spin=0.,
**ideal_gas_param)
self.rxn_sm = rxn.Reaction(reactants=[self.H2_sm, self.O2_sm],
reactants_stoich=[1., 0.5],
products=[self.H2O_sm],
products_stoich=[1.],
transition_state=[self.H2O_TS_sm],
transition_state_stoich=[1.])
self.species_dict = {
'H2O': self.H2O_sm,
'H2': self.H2_sm,
'O2': self.O2_sm,
'H2O_TS': self.H2O_TS_sm
}
self.maxDiff = None
def test_compare_element_balance(self):
self.assertIsNone(self.rxn_nasa.check_element_balance())
def test_get_species(self):
self.assertDictEqual(self.rxn_sm.get_species(key='name'),
self.species_dict)
def test_get_q_state(self):
exp_q_react = self.H2_sm.get_q(T=c.T0('K')) \
* self.O2_sm.get_q(T=c.T0('K'))**0.5
exp_q_prod = self.H2O_sm.get_q(T=c.T0('K'))
exp_q_TS = self.H2O_TS_sm.get_q(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_q_state(state='reactants', T=c.T0('K')),
exp_q_react)
self.assertAlmostEqual(
self.rxn_sm.get_q_state(state='products', T=c.T0('K')), exp_q_prod)
self.assertAlmostEqual(
self.rxn_sm.get_q_state(state='transition state', T=c.T0('K')),
exp_q_TS)
def test_get_CvoR_state(self):
exp_CvoR_react = self.H2_sm.get_CvoR(T=c.T0('K')) \
+ self.O2_sm.get_CvoR(T=c.T0('K'))*0.5
exp_CvoR_prod = self.H2O_sm.get_CvoR(T=c.T0('K'))
exp_CvoR_TS = self.H2O_TS_sm.get_CvoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_CvoR_state(state='reactants', T=c.T0('K')),
exp_CvoR_react)
self.assertAlmostEqual(
self.rxn_sm.get_CvoR_state(state='products', T=c.T0('K')),
exp_CvoR_prod)
self.assertAlmostEqual(
self.rxn_sm.get_CvoR_state(state='transition state', T=c.T0('K')),
exp_CvoR_TS)
def test_get_Cv_state(self):
units = 'J/mol/K'
exp_Cv_react = self.H2_sm.get_Cv(T=c.T0('K'), units=units) \
+ self.O2_sm.get_Cv(T=c.T0('K'), units=units)*0.5
exp_Cv_prod = self.H2O_sm.get_Cv(T=c.T0('K'), units=units)
exp_Cv_TS = self.H2O_TS_sm.get_Cv(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_Cv_state(state='reactants',
T=c.T0('K'),
units=units), exp_Cv_react)
self.assertAlmostEqual(
self.rxn_sm.get_Cv_state(state='products',
T=c.T0('K'),
units=units), exp_Cv_prod)
self.assertAlmostEqual(
self.rxn_sm.get_Cv_state(state='transition state',
T=c.T0('K'),
units=units), exp_Cv_TS)
def test_get_CpoR_state(self):
exp_CpoR_react = self.H2_sm.get_CpoR(T=c.T0('K')) \
+ self.O2_sm.get_CpoR(T=c.T0('K'))*0.5
exp_CpoR_prod = self.H2O_sm.get_CpoR(T=c.T0('K'))
exp_CpoR_TS = self.H2O_TS_sm.get_CpoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_CpoR_state(state='reactants', T=c.T0('K')),
exp_CpoR_react)
self.assertAlmostEqual(
self.rxn_sm.get_CpoR_state(state='products', T=c.T0('K')),
exp_CpoR_prod)
self.assertAlmostEqual(
self.rxn_sm.get_CpoR_state(state='transition state', T=c.T0('K')),
exp_CpoR_TS)
def test_get_Cp_state(self):
units = 'J/mol/K'
exp_Cp_react = self.H2_sm.get_Cp(T=c.T0('K'), units=units) \
+ self.O2_sm.get_Cp(T=c.T0('K'), units=units)*0.5
exp_Cp_prod = self.H2O_sm.get_Cp(T=c.T0('K'), units=units)
exp_Cp_TS = self.H2O_TS_sm.get_Cp(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_Cp_state(state='reactants',
T=c.T0('K'),
units=units), exp_Cp_react)
self.assertAlmostEqual(
self.rxn_sm.get_Cp_state(state='products',
T=c.T0('K'),
units=units), exp_Cp_prod)
self.assertAlmostEqual(
self.rxn_sm.get_Cp_state(state='transition state',
T=c.T0('K'),
units=units), exp_Cp_TS)
def test_get_EoRT_state(self):
exp_EoRT_react = self.H2_sm.get_EoRT(T=c.T0('K')) \
+ self.O2_sm.get_EoRT(T=c.T0('K'))*0.5
exp_EoRT_prod = self.H2O_sm.get_EoRT(T=c.T0('K'))
exp_EoRT_TS = self.H2O_TS_sm.get_EoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_EoRT_state(state='reactants', T=c.T0('K')),
exp_EoRT_react)
self.assertAlmostEqual(
self.rxn_sm.get_EoRT_state(state='products', T=c.T0('K')),
exp_EoRT_prod)
self.assertAlmostEqual(
self.rxn_sm.get_EoRT_state(state='transition state', T=c.T0('K')),
exp_EoRT_TS)
def test_get_E_state(self):
units = 'J/mol'
exp_E_react = self.H2_sm.get_E(T=c.T0('K'), units=units) \
+ self.O2_sm.get_E(T=c.T0('K'), units=units)*0.5
exp_E_prod = self.H2O_sm.get_E(T=c.T0('K'), units=units)
exp_E_TS = self.H2O_TS_sm.get_E(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_E_state(state='reactants',
T=c.T0('K'),
units=units), exp_E_react)
self.assertAlmostEqual(
self.rxn_sm.get_E_state(state='products', T=c.T0('K'),
units=units), exp_E_prod)
self.assertAlmostEqual(
self.rxn_sm.get_E_state(state='transition state',
T=c.T0('K'),
units=units), exp_E_TS)
def test_get_UoRT_state(self):
exp_UoRT_react = self.H2_sm.get_UoRT(T=c.T0('K')) \
+ self.O2_sm.get_UoRT(T=c.T0('K'))*0.5
exp_UoRT_prod = self.H2O_sm.get_UoRT(T=c.T0('K'))
exp_UoRT_TS = self.H2O_TS_sm.get_UoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_UoRT_state(state='reactants', T=c.T0('K')),
exp_UoRT_react)
self.assertAlmostEqual(
self.rxn_sm.get_UoRT_state(state='products', T=c.T0('K')),
exp_UoRT_prod)
self.assertAlmostEqual(
self.rxn_sm.get_UoRT_state(state='transition state', T=c.T0('K')),
exp_UoRT_TS)
def test_get_U_state(self):
units = 'J/mol'
exp_U_react = self.H2_sm.get_U(T=c.T0('K'), units=units) \
+ self.O2_sm.get_U(T=c.T0('K'), units=units)*0.5
exp_U_prod = self.H2O_sm.get_U(T=c.T0('K'), units=units)
exp_U_TS = self.H2O_TS_sm.get_U(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_U_state(state='reactants',
T=c.T0('K'),
units=units), exp_U_react)
self.assertAlmostEqual(
self.rxn_sm.get_U_state(state='products', T=c.T0('K'),
units=units), exp_U_prod)
self.assertAlmostEqual(
self.rxn_sm.get_U_state(state='transition state',
T=c.T0('K'),
units=units), exp_U_TS)
def test_get_HoRT_state(self):
exp_HoRT_react = self.H2_sm.get_HoRT(T=c.T0('K')) \
+ self.O2_sm.get_HoRT(T=c.T0('K'))*0.5
exp_HoRT_prod = self.H2O_sm.get_HoRT(T=c.T0('K'))
exp_HoRT_TS = self.H2O_TS_sm.get_HoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_HoRT_state(state='reactants', T=c.T0('K')),
exp_HoRT_react)
self.assertAlmostEqual(
self.rxn_sm.get_HoRT_state(state='products', T=c.T0('K')),
exp_HoRT_prod)
self.assertAlmostEqual(
self.rxn_sm.get_HoRT_state(state='transition state', T=c.T0('K')),
exp_HoRT_TS)
def test_get_H_state(self):
units = 'J/mol'
exp_H_react = self.H2_sm.get_H(T=c.T0('K'), units=units) \
+ self.O2_sm.get_H(T=c.T0('K'), units=units)*0.5
exp_H_prod = self.H2O_sm.get_H(T=c.T0('K'), units=units)
exp_H_TS = self.H2O_TS_sm.get_H(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_H_state(state='reactants',
T=c.T0('K'),
units=units), exp_H_react)
self.assertAlmostEqual(
self.rxn_sm.get_H_state(state='products', T=c.T0('K'),
units=units), exp_H_prod)
self.assertAlmostEqual(
self.rxn_sm.get_H_state(state='transition state',
T=c.T0('K'),
units=units), exp_H_TS)
def test_get_SoR_state(self):
exp_SoR_react = self.H2_sm.get_SoR(T=c.T0('K')) \
+ self.O2_sm.get_SoR(T=c.T0('K'))*0.5
exp_SoR_prod = self.H2O_sm.get_SoR(T=c.T0('K'))
exp_SoR_TS = self.H2O_TS_sm.get_SoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_SoR_state(state='reactants', T=c.T0('K')),
exp_SoR_react)
self.assertAlmostEqual(
self.rxn_sm.get_SoR_state(state='products', T=c.T0('K')),
exp_SoR_prod)
self.assertAlmostEqual(
self.rxn_sm.get_SoR_state(state='transition state', T=c.T0('K')),
exp_SoR_TS)
def test_get_S_state(self):
units = 'J/mol/K'
exp_S_react = self.H2_sm.get_S(T=c.T0('K'), units=units) \
+ self.O2_sm.get_S(T=c.T0('K'), units=units)*0.5
exp_S_prod = self.H2O_sm.get_S(T=c.T0('K'), units=units)
exp_S_TS = self.H2O_TS_sm.get_S(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_S_state(state='reactants',
T=c.T0('K'),
units=units), exp_S_react)
self.assertAlmostEqual(
self.rxn_sm.get_S_state(state='products', T=c.T0('K'),
units=units), exp_S_prod)
self.assertAlmostEqual(
self.rxn_sm.get_S_state(state='transition state',
T=c.T0('K'),
units=units), exp_S_TS)
def test_get_FoRT_state(self):
exp_FoRT_react = self.H2_sm.get_FoRT(T=c.T0('K')) \
+ self.O2_sm.get_FoRT(T=c.T0('K'))*0.5
exp_FoRT_prod = self.H2O_sm.get_FoRT(T=c.T0('K'))
exp_FoRT_TS = self.H2O_TS_sm.get_FoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_FoRT_state(state='reactants', T=c.T0('K')),
exp_FoRT_react)
self.assertAlmostEqual(
self.rxn_sm.get_FoRT_state(state='products', T=c.T0('K')),
exp_FoRT_prod)
self.assertAlmostEqual(
self.rxn_sm.get_FoRT_state(state='transition state', T=c.T0('K')),
exp_FoRT_TS)
def test_get_F_state(self):
units = 'J/mol'
exp_F_react = self.H2_sm.get_F(T=c.T0('K'), units=units) \
+ self.O2_sm.get_F(T=c.T0('K'), units=units)*0.5
exp_F_prod = self.H2O_sm.get_F(T=c.T0('K'), units=units)
exp_F_TS = self.H2O_TS_sm.get_F(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_F_state(state='reactants',
T=c.T0('K'),
units=units), exp_F_react)
self.assertAlmostEqual(
self.rxn_sm.get_F_state(state='products', T=c.T0('K'),
units=units), exp_F_prod)
self.assertAlmostEqual(
self.rxn_sm.get_F_state(state='transition state',
T=c.T0('K'),
units=units), exp_F_TS)
def test_get_GoRT_state(self):
exp_GoRT_react = self.H2_sm.get_GoRT(T=c.T0('K')) \
+ self.O2_sm.get_GoRT(T=c.T0('K'))*0.5
exp_GoRT_prod = self.H2O_sm.get_GoRT(T=c.T0('K'))
exp_GoRT_TS = self.H2O_TS_sm.get_GoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_GoRT_state(state='reactants', T=c.T0('K')),
exp_GoRT_react)
self.assertAlmostEqual(
self.rxn_sm.get_GoRT_state(state='products', T=c.T0('K')),
exp_GoRT_prod)
self.assertAlmostEqual(
self.rxn_sm.get_GoRT_state(state='transition state', T=c.T0('K')),
exp_GoRT_TS)
def test_get_G_state(self):
units = 'J/mol'
exp_G_react = self.H2_sm.get_G(T=c.T0('K'), units=units) \
+ self.O2_sm.get_G(T=c.T0('K'), units=units)*0.5
exp_G_prod = self.H2O_sm.get_G(T=c.T0('K'), units=units)
exp_G_TS = self.H2O_TS_sm.get_G(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_G_state(state='reactants',
T=c.T0('K'),
units=units), exp_G_react)
self.assertAlmostEqual(
self.rxn_sm.get_G_state(state='products', T=c.T0('K'),
units=units), exp_G_prod)
self.assertAlmostEqual(
self.rxn_sm.get_G_state(state='transition state',
T=c.T0('K'),
units=units), exp_G_TS)
def test_get_delta_CvoR(self):
exp_sm_CvoR = self.H2O_sm.get_CvoR(T=c.T0('K')) \
- self.H2_sm.get_CvoR(T=c.T0('K')) \
- self.O2_sm.get_CvoR(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_sm.get_delta_CvoR(T=c.T0('K')),
exp_sm_CvoR)
self.assertAlmostEqual(
self.rxn_sm.get_delta_CvoR(T=c.T0('K'), rev=True), -exp_sm_CvoR)
exp_sm_CvoR_TS = self.H2O_TS_sm.get_CvoR(T=c.T0('K')) \
- self.H2_sm.get_CvoR(T=c.T0('K')) \
- self.O2_sm.get_CvoR(T=c.T0('K'))*0.5
exp_sm_CvoR_rev_TS = self.H2O_TS_sm.get_CvoR(T=c.T0('K')) \
- self.H2O_sm.get_CvoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_CvoR(T=c.T0('K'), act=True), exp_sm_CvoR_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_CvoR(T=c.T0('K'), rev=True, act=True),
exp_sm_CvoR_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_CvoR_act(T=c.T0('K'), rev=True),
exp_sm_CvoR_rev_TS)
def test_get_delta_Cv(self):
units = 'J/mol/K'
exp_sm_Cv = self.H2O_sm.get_Cv(T=c.T0('K'), units=units) \
- self.H2_sm.get_Cv(T=c.T0('K'), units=units) \
- self.O2_sm.get_Cv(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cv(T=c.T0('K'), units=units), exp_sm_Cv)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cv(T=c.T0('K'), units=units, rev=True),
-exp_sm_Cv)
exp_sm_Cv_TS = self.H2O_TS_sm.get_Cv(T=c.T0('K'), units=units) \
- self.H2_sm.get_Cv(T=c.T0('K'), units=units) \
- self.O2_sm.get_Cv(T=c.T0('K'), units=units)*0.5
exp_sm_Cv_rev_TS = self.H2O_TS_sm.get_Cv(T=c.T0('K'), units=units) \
- self.H2O_sm.get_Cv(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cv(T=c.T0('K'), act=True, units=units),
exp_sm_Cv_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cv(T=c.T0('K'),
rev=True,
units=units,
act=True), exp_sm_Cv_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_Cv_act(T=c.T0('K'), rev=True, units=units),
exp_sm_Cv_rev_TS)
def test_get_delta_CpoR(self):
exp_nasa_CpoR = self.H2O_nasa.get_CpoR(T=c.T0('K')) \
- self.H2_nasa.get_CpoR(T=c.T0('K')) \
- self.O2_nasa.get_CpoR(T=c.T0('K'))*0.5
exp_sm_CpoR = self.H2O_sm.get_CpoR(T=c.T0('K')) \
- self.H2_sm.get_CpoR(T=c.T0('K')) \
- self.O2_sm.get_CpoR(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_nasa.get_delta_CpoR(T=c.T0('K')),
exp_nasa_CpoR)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_CpoR(T=c.T0('K'), rev=True),
-exp_nasa_CpoR)
self.assertAlmostEqual(self.rxn_sm.get_delta_CpoR(T=c.T0('K')),
exp_sm_CpoR)
self.assertAlmostEqual(
self.rxn_sm.get_delta_CpoR(T=c.T0('K'), rev=True), -exp_sm_CpoR)
exp_sm_CpoR_TS = self.H2O_TS_sm.get_CpoR(T=c.T0('K')) \
- self.H2_sm.get_CpoR(T=c.T0('K')) \
- self.O2_sm.get_CpoR(T=c.T0('K'))*0.5
exp_sm_CpoR_rev_TS = self.H2O_TS_sm.get_CpoR(T=c.T0('K')) \
- self.H2O_sm.get_CpoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_CpoR(T=c.T0('K'), act=True), exp_sm_CpoR_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_CpoR(T=c.T0('K'), rev=True, act=True),
exp_sm_CpoR_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_CpoR_act(T=c.T0('K'), rev=True),
exp_sm_CpoR_rev_TS)
def test_get_delta_Cp(self):
units = 'J/mol/K'
exp_nasa_Cp = self.H2O_nasa.get_Cp(T=c.T0('K'), units=units) \
- self.H2_nasa.get_Cp(T=c.T0('K'), units=units) \
- self.O2_nasa.get_Cp(T=c.T0('K'), units=units)*0.5
exp_sm_Cp = self.H2O_sm.get_Cp(T=c.T0('K'), units=units) \
- self.H2_sm.get_Cp(T=c.T0('K'), units=units) \
- self.O2_sm.get_Cp(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_nasa.get_delta_Cp(T=c.T0('K'), units=units), exp_nasa_Cp)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_Cp(T=c.T0('K'), units=units, rev=True),
-exp_nasa_Cp)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cp(T=c.T0('K'), units=units), exp_sm_Cp)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cp(T=c.T0('K'), units=units, rev=True),
-exp_sm_Cp)
exp_sm_Cp_TS = self.H2O_TS_sm.get_Cp(T=c.T0('K'), units=units) \
- self.H2_sm.get_Cp(T=c.T0('K'), units=units) \
- self.O2_sm.get_Cp(T=c.T0('K'), units=units)*0.5
exp_sm_Cp_rev_TS = self.H2O_TS_sm.get_Cp(T=c.T0('K'), units=units) \
- self.H2O_sm.get_Cp(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cp(T=c.T0('K'), act=True, units=units),
exp_sm_Cp_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_Cp(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_Cp_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_Cp_act(T=c.T0('K'), rev=True, units=units),
exp_sm_Cp_rev_TS)
def test_get_delta_EoRT(self):
exp_sm_EoRT = self.H2O_sm.get_EoRT(T=c.T0('K')) \
- self.H2_sm.get_EoRT(T=c.T0('K')) \
- self.O2_sm.get_EoRT(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_sm.get_delta_EoRT(T=c.T0('K')),
exp_sm_EoRT)
self.assertAlmostEqual(
self.rxn_sm.get_delta_EoRT(T=c.T0('K'), rev=True), -exp_sm_EoRT)
exp_sm_EoRT_TS = self.H2O_TS_sm.get_EoRT(T=c.T0('K')) \
- self.H2_sm.get_EoRT(T=c.T0('K')) \
- self.O2_sm.get_EoRT(T=c.T0('K'))*0.5
exp_sm_EoRT_rev_TS = self.H2O_TS_sm.get_EoRT(T=c.T0('K')) \
- self.H2O_sm.get_EoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_EoRT(T=c.T0('K'), act=True), exp_sm_EoRT_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_EoRT(T=c.T0('K'), rev=True, act=True),
exp_sm_EoRT_rev_TS)
def test_get_delta_E(self):
units = 'J/mol'
exp_sm_E = self.H2O_sm.get_E(T=c.T0('K'), units=units) \
- self.H2_sm.get_E(T=c.T0('K'), units=units) \
- self.O2_sm.get_E(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_sm.get_delta_E(T=c.T0('K'), units=units), exp_sm_E)
self.assertAlmostEqual(
self.rxn_sm.get_delta_E(T=c.T0('K'), rev=True, units=units),
-exp_sm_E)
exp_sm_E_TS = self.H2O_TS_sm.get_E(T=c.T0('K'), units=units) \
- self.H2_sm.get_E(T=c.T0('K'), units=units) \
- self.O2_sm.get_E(T=c.T0('K'), units=units)*0.5
exp_sm_E_rev_TS = self.H2O_TS_sm.get_E(T=c.T0('K'), units=units) \
- self.H2O_sm.get_E(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_E(T=c.T0('K'), act=True, units=units),
exp_sm_E_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_E(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_E_rev_TS)
def test_get_delta_UoRT(self):
exp_sm_UoRT = self.H2O_sm.get_UoRT(T=c.T0('K')) \
- self.H2_sm.get_UoRT(T=c.T0('K')) \
- self.O2_sm.get_UoRT(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_sm.get_delta_UoRT(T=c.T0('K')),
exp_sm_UoRT)
self.assertAlmostEqual(
self.rxn_sm.get_delta_UoRT(T=c.T0('K'), rev=True), -exp_sm_UoRT)
exp_sm_UoRT_TS = self.H2O_TS_sm.get_UoRT(T=c.T0('K')) \
- self.H2_sm.get_UoRT(T=c.T0('K')) \
- self.O2_sm.get_UoRT(T=c.T0('K'))*0.5
exp_sm_UoRT_rev_TS = self.H2O_TS_sm.get_UoRT(T=c.T0('K')) \
- self.H2O_sm.get_UoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_UoRT(T=c.T0('K'), act=True), exp_sm_UoRT_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_UoRT(T=c.T0('K'), rev=True, act=True),
exp_sm_UoRT_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_UoRT_act(T=c.T0('K'), rev=True),
exp_sm_UoRT_rev_TS)
def test_get_delta_U(self):
units = 'J/mol'
exp_sm_U = self.H2O_sm.get_U(T=c.T0('K'), units=units) \
- self.H2_sm.get_U(T=c.T0('K'), units=units) \
- self.O2_sm.get_U(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_sm.get_delta_U(T=c.T0('K'), units=units), exp_sm_U)
self.assertAlmostEqual(
self.rxn_sm.get_delta_U(T=c.T0('K'), rev=True, units=units),
-exp_sm_U)
exp_sm_U_TS = self.H2O_TS_sm.get_U(T=c.T0('K'), units=units) \
- self.H2_sm.get_U(T=c.T0('K'), units=units) \
- self.O2_sm.get_U(T=c.T0('K'), units=units)*0.5
exp_sm_U_rev_TS = self.H2O_TS_sm.get_U(T=c.T0('K'), units=units) \
- self.H2O_sm.get_U(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_U(T=c.T0('K'), act=True, units=units),
exp_sm_U_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_U(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_U_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_U_act(T=c.T0('K'), rev=True, units=units),
exp_sm_U_rev_TS)
def test_get_delta_HoRT(self):
exp_nasa_HoRT = self.H2O_nasa.get_HoRT(T=c.T0('K')) \
- self.H2_nasa.get_HoRT(T=c.T0('K')) \
- self.O2_nasa.get_HoRT(T=c.T0('K'))*0.5
exp_sm_HoRT = self.H2O_sm.get_HoRT(T=c.T0('K')) \
- self.H2_sm.get_HoRT(T=c.T0('K')) \
- self.O2_sm.get_HoRT(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_nasa.get_delta_HoRT(T=c.T0('K')),
exp_nasa_HoRT)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_HoRT(T=c.T0('K'), rev=True),
-exp_nasa_HoRT)
self.assertAlmostEqual(self.rxn_sm.get_delta_HoRT(T=c.T0('K')),
exp_sm_HoRT)
self.assertAlmostEqual(
self.rxn_sm.get_delta_HoRT(T=c.T0('K'), rev=True), -exp_sm_HoRT)
exp_sm_HoRT_TS = self.H2O_TS_sm.get_HoRT(T=c.T0('K')) \
- self.H2_sm.get_HoRT(T=c.T0('K')) \
- self.O2_sm.get_HoRT(T=c.T0('K'))*0.5
exp_sm_HoRT_rev_TS = self.H2O_TS_sm.get_HoRT(T=c.T0('K')) \
- self.H2O_sm.get_HoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_HoRT(T=c.T0('K'), act=True), exp_sm_HoRT_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_HoRT(T=c.T0('K'), rev=True, act=True),
exp_sm_HoRT_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_HoRT_act(T=c.T0('K'), rev=True),
exp_sm_HoRT_rev_TS)
def test_get_delta_H(self):
units = 'J/mol'
exp_nasa_H = self.H2O_nasa.get_H(T=c.T0('K'), units=units) \
- self.H2_nasa.get_H(T=c.T0('K'), units=units) \
- self.O2_nasa.get_H(T=c.T0('K'), units=units)*0.5
exp_sm_H = self.H2O_sm.get_H(T=c.T0('K'), units=units) \
- self.H2_sm.get_H(T=c.T0('K'), units=units) \
- self.O2_sm.get_H(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_nasa.get_delta_H(T=c.T0('K'), units=units), exp_nasa_H)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_H(T=c.T0('K'), units=units, rev=True),
-exp_nasa_H)
self.assertAlmostEqual(
self.rxn_sm.get_delta_H(T=c.T0('K'), units=units), exp_sm_H)
self.assertAlmostEqual(
self.rxn_sm.get_delta_H(T=c.T0('K'), units=units, rev=True),
-exp_sm_H)
exp_sm_H_TS = self.H2O_TS_sm.get_H(T=c.T0('K'), units=units) \
- self.H2_sm.get_H(T=c.T0('K'), units=units) \
- self.O2_sm.get_H(T=c.T0('K'), units=units)*0.5
exp_sm_H_rev_TS = self.H2O_TS_sm.get_H(T=c.T0('K'), units=units) \
- self.H2O_sm.get_H(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_H(T=c.T0('K'), act=True, units=units),
exp_sm_H_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_H(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_H_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_H_act(T=c.T0('K'), rev=True, units=units),
exp_sm_H_rev_TS)
def test_get_delta_SoR(self):
exp_nasa_SoR = self.H2O_nasa.get_SoR(T=c.T0('K')) \
- self.H2_nasa.get_SoR(T=c.T0('K')) \
- self.O2_nasa.get_SoR(T=c.T0('K'))*0.5
exp_sm_SoR = self.H2O_sm.get_SoR(T=c.T0('K')) \
- self.H2_sm.get_SoR(T=c.T0('K')) \
- self.O2_sm.get_SoR(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_nasa.get_delta_SoR(T=c.T0('K')),
exp_nasa_SoR)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_SoR(T=c.T0('K'), rev=True), -exp_nasa_SoR)
self.assertAlmostEqual(self.rxn_sm.get_delta_SoR(T=c.T0('K')),
exp_sm_SoR)
self.assertAlmostEqual(
self.rxn_sm.get_delta_SoR(T=c.T0('K'), rev=True), -exp_sm_SoR)
exp_sm_SoR_TS = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2_sm.get_SoR(T=c.T0('K')) \
- self.O2_sm.get_SoR(T=c.T0('K'))*0.5
exp_sm_SoR_rev_TS = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2O_sm.get_SoR(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_SoR(T=c.T0('K'), act=True), exp_sm_SoR_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_SoR(T=c.T0('K'), rev=True, act=True),
exp_sm_SoR_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_SoR_act(T=c.T0('K'), rev=True),
exp_sm_SoR_rev_TS)
def test_get_delta_S(self):
units = 'J/mol/K'
exp_nasa_S = self.H2O_nasa.get_S(T=c.T0('K'), units=units) \
- self.H2_nasa.get_S(T=c.T0('K'), units=units) \
- self.O2_nasa.get_S(T=c.T0('K'), units=units)*0.5
exp_sm_S = self.H2O_sm.get_S(T=c.T0('K'), units=units) \
- self.H2_sm.get_S(T=c.T0('K'), units=units) \
- self.O2_sm.get_S(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_nasa.get_delta_S(T=c.T0('K'), units=units), exp_nasa_S)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_S(T=c.T0('K'), units=units, rev=True),
-exp_nasa_S)
self.assertAlmostEqual(
self.rxn_sm.get_delta_S(T=c.T0('K'), units=units), exp_sm_S)
self.assertAlmostEqual(
self.rxn_sm.get_delta_S(T=c.T0('K'), rev=True, units=units),
-exp_sm_S)
exp_sm_S_TS = self.H2O_TS_sm.get_S(T=c.T0('K'), units=units) \
- self.H2_sm.get_S(T=c.T0('K'), units=units) \
- self.O2_sm.get_S(T=c.T0('K'), units=units)*0.5
exp_sm_S_rev_TS = self.H2O_TS_sm.get_S(T=c.T0('K'), units=units) \
- self.H2O_sm.get_S(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_S(T=c.T0('K'), act=True, units=units),
exp_sm_S_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_S(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_S_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_S_act(T=c.T0('K'), rev=True, units=units),
exp_sm_S_rev_TS)
def test_get_delta_FoRT(self):
exp_sm_FoRT = self.H2O_sm.get_FoRT(T=c.T0('K')) \
- self.H2_sm.get_FoRT(T=c.T0('K')) \
- self.O2_sm.get_FoRT(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_sm.get_delta_FoRT(T=c.T0('K')),
exp_sm_FoRT)
self.assertAlmostEqual(
self.rxn_sm.get_delta_FoRT(T=c.T0('K'), rev=True), -exp_sm_FoRT)
exp_sm_FoRT_TS = self.H2O_TS_sm.get_FoRT(T=c.T0('K')) \
- self.H2_sm.get_FoRT(T=c.T0('K')) \
- self.O2_sm.get_FoRT(T=c.T0('K'))*0.5
exp_sm_FoRT_rev_TS = self.H2O_TS_sm.get_FoRT(T=c.T0('K')) \
- self.H2O_sm.get_FoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_FoRT(T=c.T0('K'), act=True), exp_sm_FoRT_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_FoRT(T=c.T0('K'), rev=True, act=True),
exp_sm_FoRT_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_FoRT_act(T=c.T0('K'), rev=True),
exp_sm_FoRT_rev_TS)
def test_get_delta_F(self):
units = 'J/mol'
exp_sm_F = self.H2O_sm.get_F(T=c.T0('K'), units=units) \
- self.H2_sm.get_F(T=c.T0('K'), units=units) \
- self.O2_sm.get_F(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_sm.get_delta_F(T=c.T0('K'), units=units), exp_sm_F)
self.assertAlmostEqual(
self.rxn_sm.get_delta_F(T=c.T0('K'), units=units, rev=True),
-exp_sm_F)
exp_sm_F_TS = self.H2O_TS_sm.get_F(T=c.T0('K'), units=units) \
- self.H2_sm.get_F(T=c.T0('K'), units=units) \
- self.O2_sm.get_F(T=c.T0('K'), units=units)*0.5
exp_sm_F_rev_TS = self.H2O_TS_sm.get_F(T=c.T0('K'), units=units) \
- self.H2O_sm.get_F(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_F(T=c.T0('K'), act=True, units=units),
exp_sm_F_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_F(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_F_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_F_act(T=c.T0('K'), rev=True, units=units),
exp_sm_F_rev_TS)
def test_get_delta_GoRT(self):
exp_nasa_GoRT = self.H2O_nasa.get_GoRT(T=c.T0('K')) \
- self.H2_nasa.get_GoRT(T=c.T0('K')) \
- self.O2_nasa.get_GoRT(T=c.T0('K'))*0.5
exp_sm_GoRT = self.H2O_sm.get_GoRT(T=c.T0('K')) \
- self.H2_sm.get_GoRT(T=c.T0('K')) \
- self.O2_sm.get_GoRT(T=c.T0('K'))*0.5
self.assertAlmostEqual(self.rxn_nasa.get_delta_GoRT(T=c.T0('K')),
exp_nasa_GoRT)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_GoRT(T=c.T0('K'), rev=True),
-exp_nasa_GoRT)
self.assertAlmostEqual(self.rxn_sm.get_delta_GoRT(T=c.T0('K')),
exp_sm_GoRT)
self.assertAlmostEqual(
self.rxn_sm.get_delta_GoRT(T=c.T0('K'), rev=True), -exp_sm_GoRT)
exp_sm_GoRT_TS = self.H2O_TS_sm.get_GoRT(T=c.T0('K')) \
- self.H2_sm.get_GoRT(T=c.T0('K')) \
- self.O2_sm.get_GoRT(T=c.T0('K'))*0.5
exp_sm_GoRT_rev_TS = self.H2O_TS_sm.get_GoRT(T=c.T0('K')) \
- self.H2O_sm.get_GoRT(T=c.T0('K'))
self.assertAlmostEqual(
self.rxn_sm.get_delta_GoRT(T=c.T0('K'), act=True), exp_sm_GoRT_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_GoRT(T=c.T0('K'), rev=True, act=True),
exp_sm_GoRT_rev_TS)
self.assertAlmostEqual(self.rxn_sm.get_GoRT_act(T=c.T0('K'), rev=True),
exp_sm_GoRT_rev_TS)
def test_get_delta_G(self):
units = 'J/mol'
exp_nasa_G = self.H2O_nasa.get_G(T=c.T0('K'), units=units) \
- self.H2_nasa.get_G(T=c.T0('K'), units=units) \
- self.O2_nasa.get_G(T=c.T0('K'), units=units)*0.5
exp_sm_G = self.H2O_sm.get_G(T=c.T0('K'), units=units) \
- self.H2_sm.get_G(T=c.T0('K'), units=units) \
- self.O2_sm.get_G(T=c.T0('K'), units=units)*0.5
self.assertAlmostEqual(
self.rxn_nasa.get_delta_G(T=c.T0('K'), units=units), exp_nasa_G)
self.assertAlmostEqual(
self.rxn_nasa.get_delta_G(T=c.T0('K'), rev=True, units=units),
-exp_nasa_G)
self.assertAlmostEqual(
self.rxn_sm.get_delta_G(T=c.T0('K'), units=units), exp_sm_G)
self.assertAlmostEqual(
self.rxn_sm.get_delta_G(T=c.T0('K'), rev=True, units=units),
-exp_sm_G)
exp_sm_G_TS = self.H2O_TS_sm.get_G(T=c.T0('K'), units=units) \
- self.H2_sm.get_G(T=c.T0('K'), units=units) \
- self.O2_sm.get_G(T=c.T0('K'), units=units)*0.5
exp_sm_G_rev_TS = self.H2O_TS_sm.get_G(T=c.T0('K'), units=units) \
- self.H2O_sm.get_G(T=c.T0('K'), units=units)
self.assertAlmostEqual(
self.rxn_sm.get_delta_G(T=c.T0('K'), act=True, units=units),
exp_sm_G_TS)
self.assertAlmostEqual(
self.rxn_sm.get_delta_G(T=c.T0('K'),
rev=True,
act=True,
units=units), exp_sm_G_rev_TS)
self.assertAlmostEqual(
self.rxn_sm.get_G_act(T=c.T0('K'), rev=True, units=units),
exp_sm_G_rev_TS)
def test_get_EoRT_act(self):
exp_sm_EoRT = self.H2O_TS_sm.get_HoRT(T=c.T0('K')) \
- self.H2_sm.get_HoRT(T=c.T0('K')) \
- self.O2_sm.get_HoRT(T=c.T0('K'))*0.5
exp_sm_EoRT_rev = self.H2O_TS_sm.get_HoRT(T=c.T0('K')) \
- self.H2O_sm.get_HoRT(T=c.T0('K'))
self.assertAlmostEqual(self.rxn_sm.get_EoRT_act(T=c.T0('K')),
exp_sm_EoRT)
self.assertAlmostEqual(self.rxn_sm.get_EoRT_act(T=c.T0('K'), rev=True),
exp_sm_EoRT_rev)
def test_get_E_act(self):
units = 'J/mol'
exp_sm_E = self.H2O_TS_sm.get_H(T=c.T0('K'), units=units) \
- self.H2_sm.get_H(T=c.T0('K'), units=units) \
- self.O2_sm.get_H(T=c.T0('K'), units=units)*0.5
exp_sm_E_rev = self.H2O_TS_sm.get_H(T=c.T0('K'), units=units) \
- self.H2O_sm.get_H(T=c.T0('K'), units=units)
self.assertAlmostEqual(self.rxn_sm.get_E_act(T=c.T0('K'), units=units),
exp_sm_E)
self.assertAlmostEqual(
self.rxn_sm.get_E_act(T=c.T0('K'), rev=True, units=units),
exp_sm_E_rev)
def test_get_A(self):
# Testing partition function method
exp_sm_q = self.H2O_TS_sm.get_q(T=c.T0('K'), include_ZPE=False) \
/ self.H2_sm.get_q(T=c.T0('K'), include_ZPE=False) \
/ self.O2_sm.get_q(T=c.T0('K'), include_ZPE=False)**0.5
exp_sm_A = c.kb('J/K') * c.T0('K') / c.h('J s') * exp_sm_q
exp_sm_q_rev = self.H2O_TS_sm.get_q(T=c.T0('K'), include_ZPE=False) \
/ self.H2O_sm.get_q(T=c.T0('K'), include_ZPE=False)
exp_sm_A_rev = c.kb('J/K') * c.T0('K') / c.h('J s') * exp_sm_q_rev
np.testing.assert_almost_equal(self.rxn_sm.get_A(T=c.T0('K')),
exp_sm_A,
decimal=0)
np.testing.assert_almost_equal(self.rxn_sm.get_A(T=c.T0('K'),
rev=True),
exp_sm_A_rev,
decimal=0)
# Testing entropy method
exp_sm_SoR = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2_sm.get_SoR(T=c.T0('K')) \
- self.O2_sm.get_SoR(T=c.T0('K'))*0.5
exp_sm_A = c.kb('J/K') * c.T0('K') / c.h('J s') * np.exp(exp_sm_SoR)
exp_sm_SoR_rev = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2O_sm.get_SoR(T=c.T0('K'))
exp_sm_A_rev = c.kb('J/K')*c.T0('K')/c.h('J s') \
* np.exp(exp_sm_SoR_rev)
np.testing.assert_almost_equal(self.rxn_sm.get_A(T=c.T0('K'),
use_q=False),
exp_sm_A,
decimal=0)
np.testing.assert_almost_equal(self.rxn_sm.get_A(T=c.T0('K'),
rev=True,
use_q=False),
exp_sm_A_rev,
decimal=0)
def test_from_string(self):
reaction_str = 'H2+0.5O2=H2O_TS=H2O'
self.assertEqual(
rxn.Reaction.from_string(reaction_str=reaction_str,
species=self.species_dict), self.rxn_sm)
def test_to_dict(self):
self.assertEqual(self.rxn_nasa.to_dict(), self.rxn_nasa_dict)
def test_from_dict(self):
self.assertEqual(rxn.Reaction.from_dict(self.rxn_nasa_dict),
self.rxn_nasa)
#
# <img src="images/configurations.png" width=600>
#
# First, we initialize the species as a dictionary to enable easy `Reaction` initialization.
# In[1]:
from ase.build import molecule
from pmutt.statmech import StatMech, presets
species = {
'CO':
StatMech(name='CO',
atoms=molecule('CO'),
potentialenergy=-14.8021,
vib_wavenumbers=[2121.2],
symmetrynumber=1,
**presets['idealgas']),
'Pt':
StatMech(name='Pt', potentialenergy=-383.161235, **presets['electronic']),
'CO(S) 1/16ML fcc':
StatMech(name='CO(S) 1/16ML fcc',
potentialenergy=-399.48282843,
vib_wavenumbers=[
1731.942697, 349.970617, 322.15111, 319.114152, 161.45669
],
**presets['harmonic']),
'CO(S) 1/16ML br':
StatMech(name='CO(S) 1/16ML br',
potentialenergy=-399.464095,
vib_wavenumbers=[
# In[2]:
from pmutt.statmech import StatMech, trans, vib, rot, elec
'''Translational'''
H2_trans = trans.FreeTrans(n_degrees=3, atoms=H2_atoms)
'''Vibrational'''
H2_vib = vib.HarmonicVib(vib_wavenumbers=[4342.]) # vib_wavenumbers in cm-1
'''Rotational'''
H2_rot = rot.RigidRotor(symmetrynumber=2, atoms=H2_atoms)
'''Electronic'''
H2_elec = elec.GroundStateElec(potentialenergy=-6.77,
spin=0) # potentialenergy in eV
'''StatMech Initialization'''
H2_statmech = StatMech(name='H2',
trans_model=H2_trans,
vib_model=H2_vib,
rot_model=H2_rot,
elec_model=H2_elec)
'''Calculate thermodynamic properties per mole basis'''
H_statmech = H2_statmech.get_H(T=298., units='kJ/mol')
S_statmech = H2_statmech.get_S(T=298., units='J/mol/K')
print('H_H2(T=298 K) = {:.1f} kJ/mol'.format(H_statmech))
print('S_H2(T=298 K) = {:.2f} J/mol/K'.format(S_statmech))
# If you specify the composition of your species, you can calculate per mass quantities too.
# In[3]:
'''Input composition'''
H2_statmech.elements = {'H': 2}
'''Calculate thermodynamic properties per mass basis'''
H_statmech = H2_statmech.get_H(T=298., units='kJ/g')
def setUp(self):
self.species_dict = {
'H2O':
Nasa(name='H2O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'H': 2,
'O': 1
},
a_low=[
4.19864056E+00, -2.03643410E-03, 6.52040211E-06,
-5.48797062E-09, 1.77197817E-12, -3.02937267E+04,
-8.49032208E-01
],
a_high=[
3.03399249E+00, 2.17691804E-03, -1.64072518E-07,
-9.70419870E-11, 1.68200992E-14, -3.00042971E+04,
4.96677010E+00
]),
'H2':
Nasa(name='H2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 2},
a_low=[
2.34433112E+00, 7.98052075E-03, -1.94781510E-05,
2.01572094E-08, -7.37611761E-12, -9.17935173E+02,
6.83010238E-01
],
a_high=[
3.33727920E+00, -4.94024731E-05, 4.99456778E-07,
-1.79566394E-10, 2.00255376E-14, -9.50158922E+02,
-3.20502331E+00
]),
'O2':
Nasa(name='O2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 2},
a_low=[
3.78245636E+00, -2.99673416E-03, 9.84730201E-06,
-9.68129509E-09, 3.24372837E-12, -1.06394356E+03,
3.65767573E+00
],
a_high=[
3.28253784E+00, 1.48308754E-03, -7.57966669E-07,
2.09470555E-10, -2.16717794E-14, -1.08845772E+03,
5.45323129E+00
]),
'O':
Nasa(name='O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 1},
a_low=[
3.16826710E+00, -3.27931884E-03, 6.64306396E-06,
-6.12806624E-09, 2.11265971E-12, 2.91222592E+04,
2.05193346E+00
],
a_high=[
2.56942078E+00, -8.59741137E-05, 4.19484589E-08,
-1.00177799E-11, 1.22833691E-15, 2.92175791E+04,
4.78433864E+00
]),
'H':
Nasa(name='H',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 1},
a_low=[
2.50000000E+00, 7.05332819E-13, -1.99591964E-15,
2.30081632E-18, -9.27732332E-22, 2.54736599E+04,
-4.46682853E-01
],
a_high=[
2.50000001E+00, -2.30842973E-11, 1.61561948E-14,
-4.73515235E-18, 4.98197357E-22, 2.54736599E+04,
-4.46682914E-01
]),
'OH':
Nasa(name='OH',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'O': 1,
'H': 1
},
a_high=[
3.09288767E+00, 5.48429716E-04, 1.26505228E-07,
-8.79461556E-11, 1.17412376E-14, 3.85865700E+03,
4.47669610E+00
],
a_low=[
3.99201543E+00, -2.40131752E-03, 4.61793841E-06,
-3.88113333E-09, 1.36411470E-12, 3.61508056E+03,
-1.03925458E-01
])
}
self.reactions = Reactions(reactions=[
Reaction.from_string('O+2H=H2O', self.species_dict),
Reaction.from_string('O+H2=H2O', self.species_dict),
Reaction.from_string('OH+H=H2O', self.species_dict),
Reaction.from_string('OH+0.5H2=H2O', self.species_dict),
Reaction.from_string('0.5O+2H=H2O', self.species_dict),
Reaction.from_string('0.5O2+H2=H2O', self.species_dict)
])
self.reactions_dict = {
'class':
"<class 'pmutt.reaction.Reactions'>",
'reactions': [{
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 2.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.09288767, 0.000548429716, 1.26505228e-07,
-8.79461556e-11, 1.17412376e-14, 3858.657, 4.4766961
],
'a_low': [
3.99201543, -0.00240131752, 4.61793841e-06,
-3.88113333e-09, 1.3641147e-12, 3615.08056,
-0.103925458
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1,
'O': 1
},
'name':
'OH',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [1.0, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.09288767, 0.000548429716, 1.26505228e-07,
-8.79461556e-11, 1.17412376e-14, 3858.657, 4.4766961
],
'a_low': [
3.99201543, -0.00240131752, 4.61793841e-06,
-3.88113333e-09, 1.3641147e-12, 3615.08056,
-0.103925458
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1,
'O': 1
},
'name':
'OH',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [1.0, 0.5],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [0.5, 2.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.28253784, 0.00148308754, -7.57966669e-07,
2.09470555e-10, -2.16717794e-14, -1088.45772,
5.45323129
],
'a_low': [
3.78245636, -0.00299673416, 9.84730201e-06,
-9.68129509e-09, 3.24372837e-12, -1063.94356,
3.65767573
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 2
},
'name':
'O2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [0.5, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}]
}
species_pathway = {
'A': StatMech(G=1., **presets['constant']),
'A_TS1': StatMech(G=3., **presets['constant']),
'A_TS2': StatMech(G=2., **presets['constant']),
'B': StatMech(G=-1., **presets['constant']),
'C': StatMech(G=2., **presets['constant']),
'C_TS': StatMech(G=2.5, **presets['constant']),
'D': StatMech(G=0., **presets['constant']),
}
self.rxn_pathway1 = Reactions(reactions=[
Reaction.from_string('A = A_TS1 = B', species_pathway),
Reaction.from_string('B = C', species_pathway),
Reaction.from_string('C = C_TS = D', species_pathway)
])
self.rxn_pathway2 = Reactions(reactions=[
Reaction.from_string('A = A_TS2 = B', species_pathway),
Reaction.from_string('B = C', species_pathway),
Reaction.from_string('C = C_TS = D', species_pathway)
])
O2_nasa = Nasa(name='O2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 2},
a_low=np.array([
3.78245636E+00, -2.99673416E-03, 9.84730201E-06,
-9.68129509E-09, 3.24372837E-12, -1.06394356E+03,
3.65767573E+00
]),
a_high=np.array([
3.28253784E+00, 1.48308754E-03, -7.57966669E-07,
2.09470555E-10, -2.16717794E-14, -1.08845772E+03,
5.45323129E+00
]))
H2_shomate = Shomate(name='H2',
T_low=298.,
T_high=1000.,
a=np.array([
33.066178, -11.363417, 11.432816, -2.772874,
-0.158558, -9.980797, 172.707974, 0.
]))
H2O_statmech = StatMech(atoms=molecule('H2O'),
potentialenergy=-6.7598,
symmetrynumber=2,
spin=0,
vib_wavenumbers=[3825.434, 3710.264, 1582.432],
**presets['idealgas'])