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)