merge changes from main

docs/source/conf.py

@@ -31,7 +31,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.1'
+version = '1.4.0'
 # The full version, including alpha/beta/rc tags.
 release = version
 

qsdsan/processes/__init__.py

@@ -63,7 +63,7 @@ def __init__(self):
 from ._asm2d import *
 from ._adm1 import *
 from ._adm1_p_extension import *
-from ._madm1 import *
+# from ._madm1 import *
 from ._decay import *
 from ._kinetic_reaction import *
 from ._pm2 import *
@@ -74,7 +74,7 @@ def __init__(self):
     _asm2d,
     _adm1,
     _adm1_p_extension,
-    _madm1,
+    # _madm1,
     _decay,
     _kinetic_reaction,
     _pm2
@@ -86,7 +86,7 @@ def __init__(self):
     *_asm2d.__all__,
     *_adm1.__all__,
     *_adm1_p_extension.__all__,
-    *_madm1.__all__,
+    # *_madm1.__all__,
     *_decay.__all__,
     *_kinetic_reaction.__all__,
     *_pm2.__all__,

qsdsan/processes/_adm1_p_extension.py

@@ -94,15 +94,6 @@ def acid_base_rxn(h_ion, weak_acids_tot, Kas):
     nh3, hpo4, hco3, ac, pro, bu, va = Kas[1:] * weak_acids_tot[4:] / (Kas[1:] + h_ion)
     return S_cat + S_K + 2*S_Mg + h_ion + (S_IN - nh3) - S_an - oh_ion - hco3 - ac - pro - bu - va - 2*hpo4 - (S_IP - hpo4)
 
-# The function 'fprime_abr' is not used in the code
-def fprime_abr(h_ion, weak_acids_tot, Kas):
-    # S_cat, S_K, S_Mg, S_an, S_IN, S_IP = weak_acids_tot[:6]
-    Kw = Kas[0]
-    doh_ion = - Kw / h_ion ** 2
-    dnh3, dhpo4, dhco3, dac, dpro, dbu, dva = - Kas[1:] * weak_acids_tot[4:] / (Kas[1:] + h_ion)**2
-    return 1 + (-dnh3) - doh_ion - dhco3 - dac - dpro - dbu - dva - dhpo4
-
-
 rhos = np.zeros(28) # 28 kinetic processes (25 as defined in modified ADM1 + 3 for gases)
 Cs = np.empty(25) # 25 processes as defined in modified ADM1
 
@@ -239,7 +230,6 @@ def _rhos_adm1_p_extension(state_arr, params, h=None):
     rhos[9] *= Inh3
     rhos[-3:] = kLa * (biogas_S - KH * biogas_p)
 
-    # print(rhos)
     return rhos
 
 def dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
@@ -355,6 +345,42 @@ class ADM1_p_extension(ADM1):
     >>> adm1_p.show()
     ADM1_p_extension([hydrolysis_carbs, hydrolysis_proteins, hydrolysis_lipids, uptake_sugars, uptake_amino_acids, uptake_LCFA, uptake_valerate, uptake_butyrate, uptake_propionate, uptake_acetate, uptake_h2, decay_Xsu, decay_Xaa, decay_Xfa, decay_Xc4, decay_Xpro, decay_Xac, decay_Xh2, storage_Sva_in_XPHA, storage_Sbu_in_XPHA, storage_Spro_in_XPHA, storage_Sac_in_XPHA, lysis_XPAO, lysis_XPP, lysis_XPHA, h2_transfer, ch4_transfer, IC_transfer])
     
+    >>> import numpy as np
+    >>> state_arr = np.ones(cmps.size + len(adm1_p._biogas_IDs) + 2)   # liquid-phase concentrations, gas-phase concentrations, liquid flowrate, and temperature
+    >>> state_arr[-1] = 273.15+35  # Temperature
+    >>> rhos = adm1_p.rate_function(state_arr)  # reaction rate for each process
+    >>> for i,j in zip(adm1_p.IDs, rhos):
+    ...     print(f'{i}{(40-len(i))*" "}{j:.3g}')
+    hydrolysis_carbs                        10
+    hydrolysis_proteins                     10
+    hydrolysis_lipids                       10
+    uptake_sugars                           20
+    uptake_amino_acids                      38.4
+    uptake_LCFA                             2.14e-05
+    uptake_valerate                         8.32e-05
+    uptake_butyrate                         8.32e-05
+    uptake_propionate                       4.13e-05
+    uptake_acetate                          1.93
+    uptake_h2                               34.9
+    decay_Xsu                               0.02
+    decay_Xaa                               0.02
+    decay_Xfa                               0.02
+    decay_Xc4                               0.02
+    decay_Xpro                              0.02
+    decay_Xac                               0.02
+    decay_Xh2                               0.02
+    storage_Sva_in_XPHA                     0.747
+    storage_Sbu_in_XPHA                     0.747
+    storage_Spro_in_XPHA                    0.747
+    storage_Sac_in_XPHA                     0.747
+    lysis_XPAO                              0.2
+    lysis_XPP                               0.2
+    lysis_XPHA                              0.2
+    h2_transfer                             139
+    ch4_transfer                            -181
+    IC_transfer                             -1.66e+03
+    
+    
     References
     ----------
     [1] Batstone, D. J.; Keller, J.; Angelidaki, I.; Kalyuzhnyi, S. V; 

qsdsan/processes/_aeration.py

@@ -80,6 +80,25 @@ class DiffusedAeration(Process):
     [parameters]         KLa: 240
                          DOsat: 8
     [dynamic parameters]
+
+    >>> aer2 = pc.DiffusedAeration('aer2', 'S_O', KLa_20=100, V=1000, d_submergence=3.7)
+    >>> aer2.show()
+    Process: aer2
+    [stoichiometry]      S_O: 1
+    [reference]          S_O
+    [rate equation]      KLa*(DOsat - S_O)
+    [parameters]         KLa: 60
+                         DOsat: 9.87
+    [dynamic parameters] 
+
+    >>> aer2.Q_air   # doctest: +ELLIPSIS
+    12470.65...
+    >>> round(aer2.SOTR / 1000)
+    1039
+    
+    >>> aer3 = pc.DiffusedAeration('aer3', 'S_O', Q_air=7600, V=1000, d_submergence=3.7)
+    >>> aer3.kLa     # doctest: +ELLIPSIS
+    36.56...
     """
 
 
@@ -357,5 +376,7 @@ def DOsat(self):
         return self._DOsat
     @DOsat.setter
     def DOsat(self, DOsat):
+        if DOsat is not None: 
+            self._DOsat_s20 = DOsat / (self.tau * self._beta * self.Omega * self.delta)
         self._DOsat = DOsat or self._calc_DOsat()
         self.set_parameters(DOsat = self._DOsat)

qsdsan/processes/_asm2d.py

@@ -73,8 +73,6 @@ def create_asm2d_cmps(set_thermo=True):
 
     return cmps_asm2d
 
-# create_asm2d_cmps()
-
 def create_masm2d_cmps(set_thermo=True):
     c2d = create_asm2d_cmps(False)
     ion_kwargs = dict(particle_size='Soluble',
@@ -433,7 +431,7 @@ class ASM2d(CompiledProcesses):
 
     Examples
     --------
-    >>> from qsdsan import processes as pc, set_thermo
+    >>> from qsdsan import processes as pc
     >>> cmps = pc.create_asm2d_cmps()
     >>> asm2d = pc.ASM2d()
     >>> asm2d.show()
@@ -714,6 +712,8 @@ class mASM2d(CompiledProcesses):
     electron_acceptor_dependent_decay : bool, optional
         Whether biomass decay kinetics is dependent on concentrations of 
         electron acceptors. The default is True.
+    pH_ctrl : float or None, optional
+        Whether to fix pH at a specific value or solve for pH (`None`). The default is 7.0.
     k_h : float, optional
         Hydrolysis rate constant, in [d^(-1)]. The default is 3.0.
     eta_NO3_Hl : float, optional
@@ -766,6 +766,46 @@ class mASM2d(CompiledProcesses):
     >>> asm.show()
     mASM2d([aero_hydrolysis, anox_hydrolysis, anae_hydrolysis, hetero_growth_S_F, hetero_growth_S_A, denitri_S_F, denitri_S_A, ferment, hetero_lysis, storage_PHA, aero_storage_PP, anox_storage_PP, PAO_aero_growth_PHA, PAO_anox_growth, PAO_lysis, PP_lysis, PHA_lysis, auto_aero_growth, auto_lysis, CaCO3_precipitation_dissolution, struvite_precipitation_dissolution, newberyite_precipitation_dissolution, ACP_precipitation_dissolution, MgCO3_precipitation_dissolution, AlPO4_precipitation_dissolution, FePO4_precipitation_dissolution])
 
+    >>> # Calculate process rate given state variable values and fixed pH.
+    >>> import numpy as np
+    >>> state_arr = np.ones(len(cmps))
+    >>> rhos = asm.rate_function(state_arr)  # reaction rate for each process
+    >>> for i,j in zip(asm.IDs, rhos): 
+    ...     print(f'{i}{(40-len(i))*" "}{j:.3g}')
+    aero_hydrolysis                         2.27
+    anox_hydrolysis                         0.182
+    anae_hydrolysis                         0.0606
+    hetero_growth_S_F                       0.471
+    hetero_growth_S_A                       0.471
+    denitri_S_F                             0.0503
+    denitri_S_A                             0.0503
+    ferment                                 0.0333
+    hetero_lysis                            0.356
+    storage_PHA                             0.594
+    aero_storage_PP                         1.06
+    anox_storage_PP                         0.0851
+    PAO_aero_growth_PHA                     0.778
+    PAO_anox_growth                         0.0622
+    PAO_lysis                               0.174
+    PP_lysis                                0.174
+    PHA_lysis                               0.174
+    auto_aero_growth                        0.33
+    auto_lysis                              0.111
+    CaCO3_precipitation_dissolution         0
+    struvite_precipitation_dissolution      0
+    newberyite_precipitation_dissolution    0
+    ACP_precipitation_dissolution           0
+    MgCO3_precipitation_dissolution         0
+    AlPO4_precipitation_dissolution         1.82e-11
+    FePO4_precipitation_dissolution         1.82e-11
+
+    >>> # Estimate pH given state variable values.
+    >>> Ka = asm.rate_function.params['Ka']
+    >>> unit_conversion = asm.rate_function.params['mass2mol']
+    >>> h_ion = asm.solve_pH(state_arr, Ka, unit_conversion)
+    >>> pH = -np.log10(h_ion)
+    >>> print(f'{pH:.2f}')
+    8.40
 
     References
     ----------