def test_EyringMassAction():
args = kB_h_times_exp_dS_R, dH_over_R, c0 = 1.2e11 / 273.15, 40e3 / 8, 1
ama = MassAction(Eyring(args, ("Sfreq", "Hact")))
rxn1 = Reaction({"A": 2, "B": 1}, {"C": 1}, ama, {"B": 1})
T_ = "temperature"
def ref(v):
return (v.get("Sfreq", 1.2e11 / 273.15) * v[T_] *
math.exp(-v.get("Hact", 40e3 / 8) / v[T_]) * v["B"] *
v["A"]**2)
for params in [(11.0, 13.0, 17.0, 311.2), (12, 8, 5, 270)]:
var = dict(zip(["A", "B", "C", T_], params))
ref_val = ref(var)
assert abs((ama(var, reaction=rxn1) - ref_val) / ref_val) < 1e-14
with pytest.raises(ValueError):
MassAction(Eyring([1, 1, 1, 1, 1]))
# assert ama.as_mass_action({T_: 273.15}).args[0] == 1.2e11*math.exp(-40e3/8/273.15)
ama2 = MassAction(
Eyring4([1.2e11 / 273, 40e3 / 8, 1.2, 1e3],
("Sfreq", "Hact", "Sref", "Href")))
rxn2 = Reaction({"C": 1}, {"A": 2, "B": 2}, ama2)
var2 = {"C": 29, "temperature": 273}
def ref2(var):
return (var["C"] * var.get("temperature", 273) *
var.get("Sfreq", 1.2e11 / 273) / var.get("Sref", 1.2) *
math.exp((var.get("Href", 1e3) - var.get("Hact", 5e3)) /
var.get("temperature", 273)))
r2 = ref2(var2)
assert abs((ama2(var2, reaction=rxn2) - r2) / r2) < 1e-14
rsys = ReactionSystem([rxn1, rxn2])
var3 = {
"A": 11,
"B": 13,
"C": 17,
"temperature": 298,
"Sfreq": 1.2e11 / 298
}
rates = rsys.rates(var3)
rf3 = ref(var3)
rb3 = ref2(var3)
ref_rates = {"A": 2 * (rb3 - rf3), "B": 2 * (rb3 - rf3), "C": rf3 - rb3}
for k, v in ref_rates.items():
assert abs((rates[k] - v) / v) < 1e-14
def test_EyringMassAction():
args = kB_h_times_exp_dS_R, dH_over_R, c0 = 1.2e11 / 273.15, 40e3 / 8, 1
ama = MassAction(Eyring(args, ('Sfreq', 'Hact')))
rxn1 = Reaction({'A': 2, 'B': 1}, {'C': 1}, ama, {'B': 1})
T_ = 'temperature'
def ref(v):
return v.get('Sfreq', 1.2e11 / 273.15) * v[T_] * math.exp(
-v.get('Hact', 40e3 / 8) / v[T_]) * v['B'] * v['A']**2
for params in [(11., 13., 17., 311.2), (12, 8, 5, 270)]:
var = dict(zip(['A', 'B', 'C', T_], params))
ref_val = ref(var)
assert abs((ama(var, reaction=rxn1) - ref_val) / ref_val) < 1e-14
with pytest.raises(ValueError):
MassAction(Eyring([1, 1, 1, 1, 1]))
# assert ama.as_mass_action({T_: 273.15}).args[0] == 1.2e11*math.exp(-40e3/8/273.15)
ama2 = MassAction(
Eyring4([1.2e11 / 273, 40e3 / 8, 1.2, 1e3],
('Sfreq', 'Hact', 'Sref', 'Href')))
rxn2 = Reaction({'C': 1}, {'A': 2, 'B': 2}, ama2)
var2 = {'C': 29, 'temperature': 273}
def ref2(var):
return var['C'] * var.get('temperature', 273) * var.get(
'Sfreq', 1.2e11 / 273) / var.get('Sref', 1.2) * math.exp(
(var.get('Href', 1e3) - var.get('Hact', 5e3)) /
var.get('temperature', 273))
r2 = ref2(var2)
assert abs((ama2(var2, reaction=rxn2) - r2) / r2) < 1e-14
rsys = ReactionSystem([rxn1, rxn2])
var3 = {
'A': 11,
'B': 13,
'C': 17,
'temperature': 298,
'Sfreq': 1.2e11 / 298
}
rates = rsys.rates(var3)
rf3 = ref(var3)
rb3 = ref2(var3)
ref_rates = {'A': 2 * (rb3 - rf3), 'B': 2 * (rb3 - rf3), 'C': rf3 - rb3}
for k, v in ref_rates.items():
assert abs((rates[k] - v) / v) < 1e-14
def test_EyringMassAction():
args = kB_h_times_exp_dS_R, dH_over_R, c0 = 1.2e11/273.15, 40e3/8, 1
ama = MassAction(Eyring(args, ('Sfreq', 'Hact')))
rxn1 = Reaction({'A': 2, 'B': 1}, {'C': 1}, ama, {'B': 1})
T_ = 'temperature'
def ref(v):
return v.get('Sfreq', 1.2e11/273.15)*v[T_]*math.exp(-v.get('Hact', 40e3/8)/v[T_])*v['B']*v['A']**2
for params in [(11., 13., 17., 311.2),
(12, 8, 5, 270)]:
var = dict(zip(['A', 'B', 'C', T_], params))
ref_val = ref(var)
assert abs((ama(var, reaction=rxn1) - ref_val)/ref_val) < 1e-14
with pytest.raises(ValueError):
MassAction(Eyring([1, 1, 1, 1, 1]))
# assert ama.as_mass_action({T_: 273.15}).args[0] == 1.2e11*math.exp(-40e3/8/273.15)
ama2 = MassAction(Eyring4([1.2e11/273, 40e3/8, 1.2, 1e3], ('Sfreq', 'Hact', 'Sref', 'Href')))
rxn2 = Reaction({'C': 1}, {'A': 2, 'B': 2}, ama2)
var2 = {'C': 29, 'temperature': 273}
def ref2(var):
return var['C']*var.get('temperature', 273)*var.get('Sfreq', 1.2e11/273)/var.get('Sref', 1.2)*math.exp(
(var.get('Href', 1e3) - var.get('Hact', 5e3))/var.get('temperature', 273))
r2 = ref2(var2)
assert abs((ama2(var2, reaction=rxn2) - r2)/r2) < 1e-14
rsys = ReactionSystem([rxn1, rxn2])
var3 = {'A': 11, 'B': 13, 'C': 17, 'temperature': 298, 'Sfreq': 1.2e11/298}
rates = rsys.rates(var3)
rf3 = ref(var3)
rb3 = ref2(var3)
ref_rates = {'A': 2*(rb3 - rf3), 'B': 2*(rb3 - rf3), 'C': rf3 - rb3}
for k, v in ref_rates.items():
assert abs((rates[k] - v)/v) < 1e-14
