def test_get_odesys__Expr_as_param__unique_as_param():
def _eyring_pe_coupled(args, T, S, backend=math, **kwargs):
freq, = args
return freq*T/S
EyringPreExpCoupled = Expr.from_callback(_eyring_pe_coupled, argument_names=('freq',),
parameter_keys=('temperature', 'S_u'))
def _k(args, T, backend=math, **kwargs):
A, H, S = args
return A*backend.exp(-(H - T*S)/(8.314511*T))
EyringMA = MassAction.from_callback(_k, parameter_keys=('temperature',),
argument_names=('Aa', 'Ha', 'Sa'))
kb_h = 2.08e10
rxn = Reaction({'A'}, {'B'}, EyringMA(unique_keys=('A_u', 'H_u', 'S_u')))
rsys = ReactionSystem([rxn], ['A', 'B'])
odesys2, extra2 = get_odesys(rsys, include_params=False,
substitutions={'A_u': EyringPreExpCoupled(kb_h)})
y0 = defaultdict(float, {'A': 7.0})
rt = 293.15
xout2, yout2, info2 = odesys2.integrate(5, y0, {'H_u': 107e3, 'S_u': 150, 'temperature': rt},
integrator='cvode', atol=1e-12, rtol=1e-10, nsteps=1000)
kref2 = kb_h*rt*np.exp(-(107e3 - rt*150)/(8.314511*rt))/150
ref2 = y0['A']*np.exp(-kref2*xout2)
assert np.allclose(yout2[:, 0], ref2)
assert np.allclose(yout2[:, 1], y0['A'] - ref2)
def test_get_odesys__Expr_as_param__unique_as_param():
def _eyring_pe_coupled(args, T, S, backend=math, **kwargs):
freq, = args
return freq*T/S
EyringPreExpCoupled = Expr.from_callback(_eyring_pe_coupled, argument_names=('freq',),
parameter_keys=('temperature', 'S_u'))
def _k(args, T, backend=math, **kwargs):
A, H, S = args
return A*backend.exp(-(H - T*S)/(8.314511*T))
EyringMA = MassAction.from_callback(_k, parameter_keys=('temperature',),
argument_names=('Aa', 'Ha', 'Sa'))
kb_h = 2.08e10
rxn = Reaction({'A'}, {'B'}, EyringMA(unique_keys=('A_u', 'H_u', 'S_u')))
rsys = ReactionSystem([rxn], ['A', 'B'])
odesys2, extra2 = get_odesys(rsys, include_params=False,
substitutions={'A_u': EyringPreExpCoupled(kb_h)})
y0 = defaultdict(float, {'A': 7.0})
rt = 293.15
xout2, yout2, info2 = odesys2.integrate(5, y0, {'H_u': 107e3, 'S_u': 150, 'temperature': rt},
integrator='cvode', atol=1e-12, rtol=1e-10, nsteps=1000)
kref2 = kb_h*rt*np.exp(-(107e3 - rt*150)/(8.314511*rt))/150
ref2 = y0['A']*np.exp(-kref2*xout2)
assert np.allclose(yout2[:, 0], ref2)
assert np.allclose(yout2[:, 1], y0['A'] - ref2)
def test_Expr__from_callback():
def rate_coeff(args, T, reaction, backend=math):
return args[0]*backend.exp(args[1]/T)
RateExpr = Expr.from_callback(rate_coeff, parameter_keys=('Tem',), nargs=2)
k1 = RateExpr([2.1e10, -5132.2])
rxn = Reaction({'H2': 2, 'O2': 1}, {'H2O': 2}, MassAction(k1))
ma = rxn.rate_expr()
res = ma({'Tem': 273.15, 'H2': 7, 'O2': 13}, reaction=rxn)
ref = 7*7*13*2.1e10*math.exp(-5132.2/273.15)
assert abs((res-ref)/ref) < 1e-14
def test_Expr__from_callback():
def rate_coeff(args, T, reaction, backend=math):
return args[0] * backend.exp(args[1] / T)
RateExpr = Expr.from_callback(rate_coeff,
parameter_keys=("Tem", ),
nargs=2)
k1 = RateExpr([2.1e10, -5132.2])
rxn = Reaction({"H2": 2, "O2": 1}, {"H2O": 2}, MassAction(k1))
ma = rxn.rate_expr()
res = ma({"Tem": 273.15, "H2": 7, "O2": 13}, reaction=rxn)
ref = 7 * 7 * 13 * 2.1e10 * math.exp(-5132.2 / 273.15)
assert abs((res - ref) / ref) < 1e-14
def test_get_odesys__Expr_as_param__unique_as_param():
def _eyring_pe_coupled(args, T, S, backend=math, **kwargs):
(freq,) = args
return freq * T / S
EyringPreExpCoupled = Expr.from_callback(
_eyring_pe_coupled,
argument_names=("freq",),
parameter_keys=("temperature", "S_u"),
)
def _k(args, T, backend=math, **kwargs):
A, H, S = args
return A * backend.exp(-(H - T * S) / (8.314511 * T))
EyringMA = MassAction.from_callback(
_k, parameter_keys=("temperature",), argument_names=("Aa", "Ha", "Sa")
)
kb_h = 2.08e10
rxn = Reaction({"A"}, {"B"}, EyringMA(unique_keys=("A_u", "H_u", "S_u")))
rsys = ReactionSystem([rxn], ["A", "B"])
odesys2, extra2 = get_odesys(
rsys, include_params=False, substitutions={"A_u": EyringPreExpCoupled(kb_h)}
)
y0 = defaultdict(float, {"A": 7.0})
rt = 293.15
xout2, yout2, info2 = odesys2.integrate(
5,
y0,
{"H_u": 107e3, "S_u": 150, "temperature": rt},
integrator="cvode",
atol=1e-12,
rtol=1e-10,
nsteps=1000,
)
kref2 = kb_h * rt * np.exp(-(107e3 - rt * 150) / (8.314511 * rt)) / 150
ref2 = y0["A"] * np.exp(-kref2 * xout2)
assert np.allclose(yout2[:, 0], ref2)
assert np.allclose(yout2[:, 1], y0["A"] - ref2)