From f226608916c6ab882d3e7e70ba982930689c4c31 Mon Sep 17 00:00:00 2001 From: Joy Zhang Date: Fri, 6 Oct 2023 17:12:07 -0700 Subject: [PATCH] mADM1 kinetic rate equations --- qsdsan/processes/_madm1.py | 156 ++++++++++++++++++++++++++++++++++--- 1 file changed, 147 insertions(+), 9 deletions(-) diff --git a/qsdsan/processes/_madm1.py b/qsdsan/processes/_madm1.py index 9d3218d3..b8f83db6 100644 --- a/qsdsan/processes/_madm1.py +++ b/qsdsan/processes/_madm1.py @@ -16,6 +16,16 @@ from qsdsan import Component, Components, Process, Processes, CompiledProcesses import numpy as np, qsdsan.processes as pc, qsdsan as qs from qsdsan.utils import ospath, data_path +from qsdsan.processes._adm1 import ( + R, + create_adm1_cmps, + ADM1, + mass2mol_conversion, + T_correction_factor, + substr_inhibit, + non_compet_inhibit, + Hill_inhibit + ) # from scipy.optimize import brenth # from warnings import warn @@ -24,7 +34,6 @@ _path = ospath.join(data_path, 'process_data/_madm1.tsv') - #%% components # C_mw = get_mw({'C':1}) N_mw = get_mw({'N':1}) @@ -37,7 +46,7 @@ def create_madm1_cmps(set_thermo=True): # Components from the original ADM1 # ********************************* - _cmps = pc.create_adm1_cmps(False) + _cmps = create_adm1_cmps(False) S_aa = _cmps.S_aa X_pr = _cmps.X_pr S_aa.i_C = X_pr.i_C = 0.36890 @@ -161,10 +170,138 @@ def create_madm1_cmps(set_thermo=True): return cmps_madm1 #%% rate functions +{'S_su': 0, + 'S_aa': 1, + 'S_fa': 2, + 'S_va': 3, + 'S_bu': 4, + 'S_pro': 5, + 'S_ac': 6, + 'S_h2': 7, + 'S_ch4': 8, + 'S_IC': 9, + 'S_IN': 10, + 'S_IP': 11, + 'S_I': 12, + 'X_ch': 13, + 'X_pr': 14, + 'X_li': 15, + 'X_su': 16, + 'X_aa': 17, + 'X_fa': 18, + 'X_c4': 19, + 'X_pro': 20, + 'X_ac': 21, + 'X_h2': 22, + 'X_I': 23, + 'X_PHA': 24, + 'X_PP': 25, + 'X_PAO': 26, + 'S_K': 27, + 'S_Mg': 28, + 'S_SO4': 29, + 'S_IS': 30, + 'X_hSRB': 31, + 'X_aSRB': 32, + 'X_pSRB': 33, + 'X_c4SRB': 34, + 'S_S0': 35, + 'S_Fe3': 36, + 'S_Fe2': 37, + 'H2O': 38} + +def calc_pH(): + pass -def rhos_madm1(): +def calc_biogas(): pass +rhos = np.zeros(40) # 36 biochemical processes + 4 gas transfer processes +Cs = np.empty(36) + +def rhos_madm1(state_arr, params): + ks = params['rate_constants'] + Ks = params['half_sat_coeffs'] + K_PP = params['K_PP'] + K_so4 = params['K_so4'] + cmps = params['components'] + # n = len(cmps) + pH_LLs, pH_ULs = params['pH_limits'] + KS_IN = params['KS_IN'] + KS_IP = params['KS_IP'] + KI_nh3 = params['KI_nh3'] + KIs_h2 = params['KIs_h2'] + KIs_h2s = params['KIs_h2s'] + KHb = params['K_H_base'] + Kab = params['Ka_base'] + KH_dH = params['K_H_dH'] + Ka_dH = params['Ka_dH'] + kLa = params['kLa'] + T_base = params['T_base'] + + Cs[:7] = state_arr[13:20] # original ADM1 processes + Cs[7:11] = state_arr[19:23] + Cs[11:18] = state_arr[16:23] + Cs[18:23] = X_PAO = state_arr[26] # P extension processes + Cs[23:25] = X_PP, X_PHA = state_arr[[25,24]] + Cs[25:27] = state_arr[31] # S extension processes + Cs[27:29] = state_arr[32] + Cs[29:31] = state_arr[33] + Cs[31:34] = state_arr[34] + Cs[34:36] = state_arr[36] # Fe extension processes + + rhos[:-4] = ks * Cs + primary_substrates = state_arr[:8] + + rhos[3:11] *= substr_inhibit(primary_substrates, Ks[:8]) + c4 = primary_substrates[[3,4]] + if sum(c4) > 0: rhos[[6,7]] *= c4/sum(c4) + + vfas = primary_substrates[3:7] + rhos[18:22] *= substr_inhibit(vfas, Ks[8]) + if sum(vfas) > 0: rhos[18:22] *= vfas/sum(vfas) + if X_PAO > 0: rhos[18:22] *= substr_inhibit(X_PP/X_PAO, K_PP) + + srb_subs = np.flip(primary_substrates[3:]) + S_SO4, S_IS = state_arr[29:31] + rhos[[25,27,29,31,32]] *= substr_inhibit(srb_subs, Ks[-4:]) * substr_inhibit(S_SO4, K_so4) + if sum(srb_subs[-2:]) > 0: rhos[[31,32]] *= srb_subs[-2:]/sum(srb_subs[-2:]) + + #!!! why divide by 16 or 64? + S_h2 = primary_substrates[-1] + rhos[34] *= S_h2 / 16 + rhos[35] *= S_IS / 64 + +# ============================================================================= +# inhibition factors +# ============================================================================= + + S_IN, S_IP = state_arr[[10,11]] + I_nutrients = substr_inhibit(S_IN, KS_IN) * substr_inhibit(S_IP, KS_IP) + rhos[3:11] *= I_nutrients + rhos[[25,27,29,31,32]] *= I_nutrients + +# ============================================================================= +# #!!! place holder for pH +# ============================================================================= + pH, nh3 = calc_pH(state_arr, params) + Is_pH = Hill_inhibit(10**(-pH), pH_ULs, pH_LLs) + rhos[3:9] *= Is_pH[0] + rhos[9:11] *= Is_pH[1:3] + rhos[[25,27]] *= Is_pH[3:5] + rhos[[29,31,32]] *= Is_pH[-1] + + Is_h2 = non_compet_inhibit(S_h2, KIs_h2) + rhos[5:9] *= Is_h2 + Inh3 = non_compet_inhibit(nh3, KI_nh3) + rhos[9] *= Inh3 + + Z_h2s = calc_biogas() + Is_h2s = non_compet_inhibit(Z_h2s, KIs_h2s) + rhos[6:11] *= Is_h2s[:5] + rhos[[25,27,29,31,32]] *= Is_h2s[5:] + + #%% modified ADM1 class _load_components = settings.get_default_chemicals @@ -323,7 +460,7 @@ class ModifiedADM1(CompiledProcesses): _cmp_dependent_stoichio = ('K_XPP', 'Mg_XPP', 'MW_S0', 'MW_IS', 'i_mass_S0', 'i_mass_IS', 'i_mass_Fe2') - _stoichio_params = (*pc.ADM1._stoichio_params[5:], + _stoichio_params = (*ADM1._stoichio_params[5:], 'f_ch_xb', 'f_pr_xb', 'f_li_xb', 'f_xI_xb', 'f_sI_xb', 'f_va_pha', 'f_bu_pha', 'f_pro_pha', 'f_ac_pha', 'f_is_pro', 'f_is_bu', 'f_is_va', @@ -331,13 +468,14 @@ class ModifiedADM1(CompiledProcesses): *_cmp_dependent_stoichio ) _kinetic_params = ('rate_constants', 'half_sat_coeffs', 'K_PP', 'K_so4', - 'pH_limits', 'KS_IN', 'KI_nh3', 'KIs_h2', + 'pH_limits', 'KS_IN', 'KS_IP', 'KI_nh3', 'KIs_h2', 'KIs_h2s' 'Ka_base', 'Ka_dH', 'K_H_base', 'K_H_dH', 'kLa', - 'T_base', 'components', 'root', + 'T_base', 'components', + # 'root' ) - _acid_base_pairs = pc.ADM1._acid_base_pairs - _biogas_IDs = (*pc.ADM1._biogas_IDs, 'S_IS') - _biomass_IDs = (*pc.ADM1._biomass_IDs, 'X_PAO', 'X_hSRB', 'X_aSRB', 'X_pSRB', 'X_c4SRB') + _acid_base_pairs = ADM1._acid_base_pairs + _biogas_IDs = (*ADM1._biogas_IDs, 'S_IS') + _biomass_IDs = (*ADM1._biomass_IDs, 'X_PAO', 'X_hSRB', 'X_aSRB', 'X_pSRB', 'X_c4SRB') _T_base = 298.15 _K_H_base = [7.8e-4, 1.4e-3, 3.5e-2, 0.105] # biogas species Henry's Law constant [M/bar] _K_H_dH = [-4180, -14240, -19410, -19180] # Heat of reaction of liquid-gas transfer of biogas species [J/mol]