def test_get_odesys__with_units():
a = Substance('A')
b = Substance('B')
molar = u.molar
second = u.second
r = Reaction({'A': 2}, {'B': 1}, param=1e-3/molar/second)
rsys = ReactionSystem([r], [a, b])
odesys = get_odesys(rsys, include_params=True,
unit_registry=SI_base_registry)[0]
c0 = {
'A': 13*u.mol / u.metre**3,
'B': .2 * u.molar
}
conc_unit = get_derived_unit(SI_base_registry, 'concentration')
t = np.linspace(0, 10)*u.hour
xout, yout, info = odesys.integrate(
t, rsys.as_per_substance_array(c0, unit=conc_unit),
atol=1e-10, rtol=1e-12)
t_unitless = to_unitless(xout, u.second)
Aref = dimerization_irrev(t_unitless, 1e-6, 13.0)
# Aref = 1/(1/13 + 2*1e-6*t_unitless)
yref = np.zeros((xout.size, 2))
yref[:, 0] = Aref
yref[:, 1] = 200 + (13-Aref)/2
assert allclose(yout, yref*conc_unit)
def test_get_odesys_3():
M = u.molar
s = u.second
mol = u.mol
m = u.metre
substances = list(map(Substance, 'H2O H+ OH-'.split()))
dissociation = Reaction({'H2O': 1}, {'H+': 1, 'OH-': 1}, 2.47e-5/s)
recombination = Reaction({'H+': 1, 'OH-': 1}, {'H2O': 1}, 1.37e11/M/s)
rsys = ReactionSystem([dissociation, recombination], substances)
odesys = get_odesys(
rsys, include_params=True, unit_registry=SI_base_registry,
output_conc_unit=M)[0]
c0 = {'H2O': 55.4*M, 'H+': 1e-7*M, 'OH-': 1e-4*mol/m**3}
x, y, p = odesys.to_arrays(-42*u.second,
rsys.as_per_substance_array(c0, unit=M), ())
fout = odesys.f_cb(x, y, p)
time_unit = get_derived_unit(SI_base_registry, 'time')
conc_unit = get_derived_unit(SI_base_registry, 'concentration')
r1 = to_unitless(55.4*2.47e-5*M/s, conc_unit/time_unit)
r2 = to_unitless(1e-14*1.37e11*M/s, conc_unit/time_unit)
assert np.all(abs(fout[:, 0] - r2 + r1)) < 1e-10
assert np.all(abs(fout[:, 1] - r1 + r2)) < 1e-10
assert np.all(abs(fout[:, 2] - r1 + r2)) < 1e-10
def test_get_odesys_3():
M = u.molar
s = u.second
mol = u.mol
m = u.metre
substances = list(map(Substance, 'H2O H+ OH-'.split()))
dissociation = Reaction({'H2O': 1}, {'H+': 1, 'OH-': 1}, 2.47e-5/s)
recombination = Reaction({'H+': 1, 'OH-': 1}, {'H2O': 1}, 1.37e11/M/s)
rsys = ReactionSystem([dissociation, recombination], substances)
odesys = get_odesys(
rsys, include_params=True, unit_registry=SI_base_registry,
output_conc_unit=M)[0]
c0 = {'H2O': 55.4*M, 'H+': 1e-7*M, 'OH-': 1e-4*mol/m**3}
x, y, p = odesys.to_arrays(-42*u.second,
rsys.as_per_substance_array(c0, unit=M), ())
fout = odesys.f_cb(x, y, p)
time_unit = get_derived_unit(SI_base_registry, 'time')
conc_unit = get_derived_unit(SI_base_registry, 'concentration')
r1 = to_unitless(55.4*2.47e-5*M/s, conc_unit/time_unit)
r2 = to_unitless(1e-14*1.37e11*M/s, conc_unit/time_unit)
assert np.all(abs(fout[:, 0] - r2 + r1)) < 1e-10
assert np.all(abs(fout[:, 1] - r1 + r2)) < 1e-10
assert np.all(abs(fout[:, 2] - r1 + r2)) < 1e-10
def test_get_odesys__with_units():
a = Substance('A')
b = Substance('B')
molar = u.molar
second = u.second
r = Reaction({'A': 2}, {'B': 1}, param=1e-3/molar/second)
rsys = ReactionSystem([r], [a, b])
odesys = get_odesys(rsys, include_params=True,
unit_registry=SI_base_registry)[0]
c0 = {
'A': 13*u.mol / u.metre**3,
'B': .2 * u.molar
}
conc_unit = get_derived_unit(SI_base_registry, 'concentration')
t = np.linspace(0, 10)*u.hour
xout, yout, info = odesys.integrate(
t, rsys.as_per_substance_array(c0, unit=conc_unit),
atol=1e-10, rtol=1e-12)
t_unitless = to_unitless(xout, u.second)
Aref = dimerization_irrev(t_unitless, 1e-6, 13.0)
# Aref = 1/(1/13 + 2*1e-6*t_unitless)
yref = np.zeros((xout.size, 2))
yref[:, 0] = Aref
yref[:, 1] = 200 + (13-Aref)/2
assert allclose(yout, yref*conc_unit)
def test_get_odesys_2():
g = Radiolytic([3.14])
a = Substance('A')
b = Substance('B')
r = Reaction({'A': 1}, {'B': 1}, param=g)
rsys = ReactionSystem([r], [a, b])
odesys = get_odesys(rsys, include_params=True)[0]
c0 = {
'A': 1.0,
'B': 3.0,
}
t = np.linspace(0.0, .1)
xout, yout, info = odesys.integrate(t, rsys.as_per_substance_array(c0),
{'doserate': 2.72, 'density': .998})
yref = np.zeros((t.size, 2))
k = 3.14*2.72*.998
yref[:, 0] = 1 - k*t
yref[:, 1] = 3 + k*t
assert np.allclose(yout, yref)
def test_get_odesys_2():
g = Radiolytic([3.14])
a = Substance('A')
b = Substance('B')
r = Reaction({'A': 1}, {'B': 1}, param=g)
rsys = ReactionSystem([r], [a, b])
odesys = get_odesys(rsys, include_params=True)[0]
c0 = {
'A': 1.0,
'B': 3.0,
}
t = np.linspace(0.0, .1)
xout, yout, info = odesys.integrate(t, rsys.as_per_substance_array(c0),
{'doserate': 2.72, 'density': .998})
yref = np.zeros((t.size, 2))
k = 3.14*2.72*.998
yref[:, 0] = 1 - k*t
yref[:, 1] = 3 + k*t
assert np.allclose(yout, yref)
def test_get_odesys_2():
g = Radiolytic([3.14])
a = Substance("A")
b = Substance("B")
r = Reaction({"A": 1}, {"B": 1}, param=g)
rsys = ReactionSystem([r], [a, b])
odesys = get_odesys(rsys, include_params=True)[0]
c0 = {
"A": 1.0,
"B": 3.0,
}
t = np.linspace(0.0, 0.1)
xout, yout, info = odesys.integrate(
t, rsys.as_per_substance_array(c0), {"doserate": 2.72, "density": 0.998}
)
yref = np.zeros((t.size, 2))
k = 3.14 * 2.72 * 0.998
yref[:, 0] = 1 - k * t
yref[:, 1] = 3 + k * t
assert np.allclose(yout, yref)
