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updated Fe extension with HFO
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@joyxyz1994
joyxyz1994 committed Oct 11, 2023
1 parent ff6045a commit 6731162
Showing 1 changed file with 52 additions and 55 deletions.
107 changes: 52 additions & 55 deletions qsdsan/processes/_madm1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,23 @@
O_mw = get_mw({'O':1})

def create_madm1_cmps(set_thermo=True, ASF_L=0.31, ASF_H=1.2):
'''
Create a set of components for the modified ADM1.
Parameters
----------
set_thermo : bool, optional
Whether to set thermo with the returned set of components. The default is True.
ASF_L : float, optional
Active site factor for X_HFO_L [mol P sites/mol Fe]. The default is 0.31.
ASF_H : float, optional
Active site factor for X_HFO_H [mol P sites/mol Fe]. The default is 1.2.
Returns
-------
cmps_madm1 : class:`CompiledComponents`
'''

# Components from the original ADM1
# *********************************
Expand Down Expand Up @@ -210,54 +227,32 @@ def create_madm1_cmps(set_thermo=True, ASF_L=0.31, ASF_H=1.2):
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}

"https://wiki.dynamita.com/en/biokinetic_process_models#chemical-phosphorus-removal-with-metal-salts-addition-iron-or-aluminium"

{'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,
'X_HFO_H': 38, 'X_HFO_L': 39, 'X_HFO_old': 40, 'X_HFO_HP': 41, 'X_HFO_LP': 42, 'X_HFO_HP_old': 43, 'X_HFO_LP_old': 44,
'S_Ca': 45, 'S_Al': 46,
'X_CCM': 47, 'X_ACC': 48, 'X_ACP': 49, 'X_HAP': 50, 'X_DCPD': 51, 'X_OCP': 52,
'X_struv': 53, 'X_newb': 54, 'X_magn': 55, 'X_kstruv': 56,
'X_FeS': 57, 'X_Fe3PO42': 58,
'X_AlPO4': 59,
'S_Na': 60, 'S_Cl': 61, 'H2O': 62}

def calc_pH():
pass

def calc_biogas():
pass

rhos = np.zeros(40) # 36 biochemical processes + 4 gas transfer processes
Cs = np.empty(36)
rhos = np.zeros(38+8+13+4) # 38 biological + 8 chemical P removal by HFO + 13 MMP + 4 gas transfer
Cs = np.empty(38)

def rhos_madm1(state_arr, params):
ks = params['rate_constants']
Expand Down Expand Up @@ -288,9 +283,9 @@ def rhos_madm1(state_arr, params):
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
Cs[34:36] = Cs[36:38] = state_arr[38:40] # Fe extension processes

rhos[:-4] = ks * Cs
rhos[:38] = ks * Cs
primary_substrates = state_arr[:8]

rhos[3:11] *= substr_inhibit(primary_substrates, Ks[:8])
Expand All @@ -309,20 +304,19 @@ def rhos_madm1(state_arr, params):

#!!! why divide by 16 or 64?
S_h2 = primary_substrates[-1]
rhos[34] *= S_h2 / 16
rhos[35] *= S_IS / 64
rhos[34:36] *= S_h2 / 16
rhos[36:38] *= S_IS / 64

# =============================================================================
# inhibition factors
# =============================================================================
# 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
# !!! place holder for pH
# =============================================================================
pH, nh3 = calc_pH(state_arr, params)
Is_pH = Hill_inhibit(10**(-pH), pH_ULs, pH_LLs)
Expand All @@ -339,7 +333,7 @@ def rhos_madm1(state_arr, params):
# =============================================================================
# !!! place holder for gas-liquid transfer
# =============================================================================
Z_h2s = calc_biogas() # should be a function of pH
Z_h2s = calc_biogas() # should be a function of pH, like co2 and nh3
Is_h2s = non_compet_inhibit(Z_h2s, KIs_h2s)
rhos[6:11] *= Is_h2s[:5]
rhos[[25,27,29,31,32]] *= Is_h2s[5:]
Expand Down Expand Up @@ -442,9 +436,12 @@ class ModifiedADM1(CompiledProcesses):
K_so4_c4SRB : float, optional
Sulfate half saturation coefficient of SRB uptaking butyrate or valerate
[kg S/m3]. The default is 6.413e-3.
k_Fe3t2 : float, optional
Fe(3+) reduction rate constant [m3∙kg^(-1) Fe(III)∙d^(-1)].
The default is 1.79e7.
k_Fe3t2_h2 : float, optional
Fe(3+) reduction rate constant [m3∙kg^(-1) Fe(III)∙d^(-1)] using hydrogen
as electron donor. The default is 1.79e7.
k_Fe3t2_is : float, optional
Fe(3+) reduction rate constant [m3∙kg^(-1) Fe(III)∙d^(-1)] using sulfide
as electron donor. The default is 1.79e7.
KS_IP : float, optional
Inorganic phosphorus (nutrient) inhibition coefficient for soluble
substrate uptake [M]. The default is 2e-5.
Expand Down Expand Up @@ -552,7 +549,7 @@ def __new__(cls, components=None, path=None,
b_hSRB=0.02, b_aSRB=0.02, b_pSRB=0.02, b_c4SRB=0.02,
K_hSRB=5.96e-6, K_aSRB=0.176, K_pSRB=0.088, K_c4SRB=0.1739,
K_so4_hSRB=1.04e-4*S_mw, K_so4_aSRB=2e-4*S_mw, K_so4_pSRB=2e-4*S_mw, K_so4_c4SRB=2e-4*S_mw,
k_Fe3t2=1e9/Fe_mw,
k_Fe3t2_h2=1e9/Fe_mw, k_Fe3t2_is=1e9/Fe_mw,
KI_h2_fa=5e-6, KI_h2_c4=1e-5, KI_h2_pro=3.5e-6, KI_nh3=1.8e-3, KS_IN=1e-4, KS_IP=2e-5,
KI_h2s_c4=0.481, KI_h2s_pro=0.481, KI_h2s_ac=0.460, KI_h2s_h2=0.400,
KI_h2s_c4SRB=0.520, KI_h2s_pSRB=0.520, KI_h2s_aSRB=0.499, KI_h2s_hSRB=0.499,
Expand Down Expand Up @@ -643,7 +640,7 @@ def __new__(cls, components=None, path=None,
b_su, b_aa, b_fa, b_c4, b_pro, b_ac, b_h2, # original ADM1
q_pha, q_pha, q_pha, q_pha, b_pao, b_pp, b_pha, # P extension
k_hSRB, b_hSRB, k_aSRB, b_aSRB, k_pSRB, b_pSRB, k_c4SRB, k_c4SRB, b_c4SRB, # S extension
k_Fe3t2, k_Fe3t2)) # Fe extension
k_Fe3t2_h2, k_Fe3t2_h2, k_Fe3t2_is, k_Fe3t2_is)) # Fe extension + HFO

Ks = np.array((K_su, K_aa, K_fa, K_c4, K_c4, K_pro, K_ac, K_h2, # original ADM1
K_A, # P extension
Expand Down

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