from PySDM.physics.aqueous_chemistry.support import M, EquilibriumConsts
from PySDM.physics.constants import ROOM_TEMP, K_H2O
from PySDM.physics.formulae import Formulae
from PySDM.backends.numba.impl._chemistry_methods import ChemistryMethods
from PySDM.dynamics import aqueous_chemistry
from chempy import Equilibrium
from chempy.equilibria import EqSystem
from chempy.chemistry import Species
import numpy as np
import pytest
from collections import defaultdict
formulae = Formulae()
EQUILIBRIUM_CONST = EquilibriumConsts(formulae).EQUILIBRIUM_CONST
class Test_pH:
@staticmethod
def test_equilibrate_pH_pure_water():
# Arrange
eqs = {}
for key in EQUILIBRIUM_CONST.keys():
eqs[key] = np.full(1, EQUILIBRIUM_CONST[key].at(ROOM_TEMP))
# Act
result = np.empty(1)
ChemistryMethods.equilibrate_H_body(
within_tolerance=formulae.trivia.within_tolerance,
pH2H=formulae.trivia.pH2H,
H2pH=formulae.trivia.H2pH,
def __init__(self):
self.HENRY_CONST = HenryConsts(self.formulae)
self.KINETIC_CONST = KineticConsts(self.formulae)
self.EQUILIBRIUM_CONST = EquilibriumConsts(self.formulae)
from PySDM.physics.aqueous_chemistry.support import KineticConsts, EquilibriumConsts, \
DISSOCIATION_FACTORS, k4
from PySDM.physics.constants import T_STP, pi_4_3
import pytest
formulae = Formulae()
class SUT(ChemistryMethods):
def __init__(self):
self.formulae = formulae
super().__init__()
kinetic_consts = KineticConsts(formulae)
equilibrium_consts = EquilibriumConsts(formulae)
T = T_STP
k0 = Storage.from_ndarray(np.full(1, kinetic_consts.KINETIC_CONST['k0'].at(T)))
k1 = Storage.from_ndarray(np.full(1, kinetic_consts.KINETIC_CONST['k1'].at(T)))
k2 = Storage.from_ndarray(np.full(1, kinetic_consts.KINETIC_CONST['k2'].at(T)))
k3 = Storage.from_ndarray(np.full(1, kinetic_consts.KINETIC_CONST['k3'].at(T)))
K_SO2 = Storage.from_ndarray(
np.full(1, equilibrium_consts.EQUILIBRIUM_CONST['K_SO2'].at(T)))
K_HSO3 = Storage.from_ndarray(
np.full(1, equilibrium_consts.EQUILIBRIUM_CONST['K_HSO3'].at(T)))
volume = pi_4_3 * (1 * si.um)**3
pH = 5.
n_sd = 1
def test_calc_ionic_strength(nt, n_sd):
formulae = Formulae()
EQUILIBRIUM_CONST = EquilibriumConsts(formulae).EQUILIBRIUM_CONST
K_NH3 = EQUILIBRIUM_CONST["K_NH3"].at(ROOM_TEMP)
K_SO2 = EQUILIBRIUM_CONST["K_SO2"].at(ROOM_TEMP)
K_HSO3 = EQUILIBRIUM_CONST["K_HSO3"].at(ROOM_TEMP)
K_HSO4 = EQUILIBRIUM_CONST["K_HSO4"].at(ROOM_TEMP)
K_HCO3 = EQUILIBRIUM_CONST["K_HCO3"].at(ROOM_TEMP)
K_CO2 = EQUILIBRIUM_CONST["K_CO2"].at(ROOM_TEMP)
K_HNO3 = EQUILIBRIUM_CONST["K_HNO3"].at(ROOM_TEMP)
settings = Settings(dt=1, n_sd=n_sd, n_substep=5)
settings.t_max = nt * settings.dt
simulation = Simulation(settings)
simulation.run()
H = simulation.particulator.attributes['conc_N_mIII'].data
conc = {
'H+': H,
'N-3': simulation.particulator.attributes['conc_N_mIII'].data,
'N+5': simulation.particulator.attributes['conc_N_V'].data,
'S+4': simulation.particulator.attributes['conc_S_IV'].data,
'S+6': simulation.particulator.attributes['conc_S_VI'].data,
'C+4': simulation.particulator.attributes['conc_C_IV'].data,
}
alpha_C = (1 + K_CO2 / conc['H+'] + K_CO2 * K_HCO3 / conc['H+']**2)
alpha_S = (1 + K_SO2 / conc['H+'] + K_SO2 * K_HSO3 / conc['H+']**2)
alpha_N3 = (1 + conc['H+'] * K_NH3 / K_H2O)
alpha_N5 = (1 + K_HNO3 / conc['H+'])
actual = calc_ionic_strength(H=conc['H+'],
N_mIII=conc['N-3'],
N_V=conc['N+5'],
C_IV=conc['C+4'],
S_IV=conc['S+4'],
S_VI=conc['S+6'],
K_NH3=K_NH3,
K_SO2=K_SO2,
K_HSO3=K_HSO3,
K_HSO4=K_HSO4,
K_HCO3=K_HCO3,
K_CO2=K_CO2,
K_HNO3=K_HNO3)
expected = ionic_strength(
{
'H+':
conc['H+'] / rho_w,
'HCO3-':
K_CO2 / conc['H+'] * conc['C+4'] / alpha_C / rho_w,
'CO3-2':
K_CO2 / conc['H+'] * K_HCO3 / conc['H+'] * conc['C+4'] / alpha_C /
rho_w,
'HSO3-':
K_SO2 / conc['H+'] * conc['S+4'] / alpha_S / rho_w,
'SO3-2':
K_SO2 / conc['H+'] * K_HSO3 / conc['H+'] * conc['S+4'] / alpha_S /
rho_w,
'NH4+':
K_NH3 / K_H2O * conc['H+'] * conc['N-3'] / alpha_N3 / rho_w,
'NO3-':
K_HNO3 / conc['H+'] * conc['N+5'] / alpha_N5 / rho_w,
'HSO4-':
conc['H+'] * conc['S+6'] / (conc['H+'] + K_HSO4) / rho_w,
'SO4-2':
K_HSO4 * conc['S+6'] / (conc['H+'] + K_HSO4) / rho_w,
'OH-':
K_H2O / conc['H+'] / rho_w
},
warn=False) * rho_w
np.testing.assert_allclose(actual, expected, rtol=1e-15)