def test_from_ReactionSystem__g_values__multiple_types():
from chempy import Reaction, ReactionSystem as RS
from chempy.kinetics.rates import mk_Radiolytic
RABG = mk_Radiolytic('alpha', 'beta', 'gamma')
dens, yields_k, yields_v = .7, 'ya yb yg'.split(), [3, 5, 7]
rxn = Reaction({}, {'H': 2}, RABG(yields_k))
doserates = {'doserate_alpha': 11, 'doserate_beta': 13, 'doserate_gamma': 17}
yields = dict(zip(yields_k, yields_v))
params = dict(doserates)
params.update(yields)
params['density'] = dens
ref = .7*2*(3*11 + 5*13 + 7*17)
rat = rxn.rate(params)
assert abs(rat['H'] - ref) < 1e-13
assert RABG.parameter_keys == ('density', 'doserate_alpha', 'doserate_beta', 'doserate_gamma')
assert RABG.argument_names == tuple('radiolytic_yield_%s' % k for k in 'alpha beta gamma'.split())
rs = RS([rxn], checks=())
rd = ReactionDiffusion.from_ReactionSystem(rs, variables=params)
gv = rd.g_values
assert len(gv) == 3
assert np.allclose(sorted(gv), [[v*2] for v in sorted(yields_v)])
assert len(rd.fields) == 3
assert len(rd.fields[0]) == 1
assert np.allclose(sorted(np.array(rd.fields).squeeze()), sorted([drat*dens for drat in doserates.values()]))
fout = rd.alloc_fout()
rd.f(0, np.array([0.0]), fout)
assert np.allclose(fout, ref)
def test_integrate_nondimensionalisation__g_values(from_rsys):
from chempy import Reaction, ReactionSystem
from chempy.units import allclose, default_units as u
rstr = "-> H + OH; Radiolytic({'radiolytic_yield': 2.1e-7*mol/J})"
if from_rsys:
rxn = Reaction.from_string(rstr, None)
rsys = ReactionSystem([rxn], 'H OH')
rd = ReactionDiffusion.from_ReactionSystem(
rsys, unit_registry=SI_base_registry,
variables=dict(doserate=0.15*u.Gy/u.s, density=0.998*u.kg/u.dm3))
assert rd.g_value_parents == [-1]
assert rd.g_values == [[2.1e-7]*2]
assert abs(rd.fields[0][0] - 0.15*998) < 1e-14
else:
rd = ReactionDiffusion.nondimensionalisation(
2, [[]], [[0, 1]], [2.1e-7*0.15*0.998*u.molar/u.second],
unit_registry=SI_base_registry)
C0 = [3*molar, 4*molar]
tout = np.linspace(0, 1)*day
integr = Integration(rd, C0, tout, integrator='scipy')
k_m3_p_mol_p_sec = 0.15*998*2.1e-7
t_sec = np.linspace(0, 24*3600)
C0_mol_p_m3 = [3000, 4000]
Cref_mol_p_m3 = np.empty(integr.Cout.squeeze().shape)
Cref_mol_p_m3[:, 0] = C0_mol_p_m3[0] + k_m3_p_mol_p_sec*t_sec
Cref_mol_p_m3[:, 1] = C0_mol_p_m3[1] + k_m3_p_mol_p_sec*t_sec
print(integr.with_units('Cout').squeeze())
print(integr.with_units('Cout').squeeze() - Cref_mol_p_m3*u.mole/u.metre**3)
assert allclose(integr.with_units('tout'), t_sec*u.s)
assert allclose(integr.with_units('Cout').squeeze(),
Cref_mol_p_m3*u.mole/u.metre**3)
def test_integrate_nondimensionalisation(from_rsys):
from chempy import Reaction, ReactionSystem
from chempy.units import allclose, default_units as u
# 2A -> B
if from_rsys:
rxn = Reaction.from_string('2 A -> B; 2e-3*metre**3/mol/hour', None)
rsys = ReactionSystem([rxn], 'A B')
rd = ReactionDiffusion.from_ReactionSystem(rsys, unit_registry=SI_base_registry)
else:
rd = ReactionDiffusion.nondimensionalisation(
2, [[0, 0]], [[1]], [2e-9/(umol/metre**3)/hour],
unit_registry=SI_base_registry)
C0 = [3*molar, 4*molar]
tout = np.linspace(0, 1)*day
integr = Integration(rd, C0, tout, integrator='scipy')
k_m3_p_mol_p_sec = 2e-3/3600
t_sec = np.linspace(0, 24*3600)
C0_mol_p_m3 = [3000, 4000]
Cref_mol_p_m3 = np.empty(integr.Cout.squeeze().shape)
Cref_mol_p_m3[:, 0] = 1/(C0_mol_p_m3[0]**-1 + 2*k_m3_p_mol_p_sec*t_sec)
missing_A = (C0_mol_p_m3[0] - Cref_mol_p_m3[:, 0])
Cref_mol_p_m3[:, 1] = C0_mol_p_m3[1] + missing_A/2
assert allclose(integr.with_units('tout'), t_sec*u.s)
assert allclose(integr.with_units('Cout').squeeze(),
Cref_mol_p_m3*u.mol/u.metre**3, rtol=1e-6)
