Merge branch 'dev' of https://github.com/QSD-Group/QSDsan into beta

qsdsan/_process.py

@@ -1041,8 +1041,8 @@ def load_from_file(cls, path='', components=None, data=None,
             stoichio = proc[cmp_IDs]
             if data.columns[-1] in cmp_IDs: rate_eq = None
             else:
-                if pd.isna(proc[-1]): rate_eq = None
-                else: rate_eq = proc[-1]
+                if pd.isna(proc.iloc[-1]): rate_eq = None
+                else: rate_eq = proc.iloc[-1]
             stoichio = stoichio[-pd.isna(stoichio)].to_dict()
             ref = None
             for k,v in stoichio.items():

qsdsan/_waste_stream.py

@@ -450,7 +450,7 @@ def _wastestream_info(self, details=True, concentrations=None, N=15):
             _ws_info += '\n'
             # Only non-zero properties are shown
             _ws_info += int(bool(self.pH))*f'  pH         : {self.pH:.1f}\n'
-            _ws_info += int(bool(self.SAlk))*f'  Alkalinity : {self.SAlk:.1f} mg/L\n'
+            _ws_info += int(bool(self.SAlk))*f'  Alkalinity : {self.SAlk:.1f} mmol/L\n'
             if details:
                 _ws_info += int(bool(self.COD))       *f'  COD        : {self.COD:.1f} mg/L\n'
                 _ws_info += int(bool(self.BOD))       *f'  BOD        : {self.BOD:.1f} mg/L\n'
@@ -1299,7 +1299,7 @@ def codstates_inf_model(cls, ID='', flow_tot=0., units = ('L/hr', 'mg/L'),
                      ...        9.96e+04
          WasteStream-specific properties:
           pH         : 7.0
-          Alkalinity : 10.0 mg/L
+          Alkalinity : 10.0 mmol/L
           COD        : 430.0 mg/L
           BOD        : 221.8 mg/L
           TC         : 265.0 mg/L
@@ -1522,7 +1522,7 @@ def codbased_inf_model(cls, ID='', flow_tot=0., units = ('L/hr', 'mg/L'),
                      ...        9.96e+04
          WasteStream-specific properties:
           pH         : 7.0
-          Alkalinity : 10.0 mg/L
+          Alkalinity : 10.0 mmol/L
           COD        : 430.0 mg/L
           BOD        : 249.4 mg/L
           TC         : 265.0 mg/L
@@ -1751,7 +1751,7 @@ def bodbased_inf_model(cls, ID='', flow_tot=0., units = ('L/hr', 'mg/L'),
                      ...        9.96e+04
          WasteStream-specific properties:
           pH         : 7.0
-          Alkalinity : 10.0 mg/L
+          Alkalinity : 10.0 mmol/L
           COD        : 431.0 mg/L
           BOD        : 250.0 mg/L
           TC         : 264.9 mg/L
@@ -1983,7 +1983,7 @@ def sludge_inf_model(cls, ID='', flow_tot=0., units = ('L/hr', 'mg/L'),
                      ...        9.88e+04
          WasteStream-specific properties:
           pH         : 7.0
-          Alkalinity : 10.0 mg/L
+          Alkalinity : 10.0 mmol/L
           COD        : 10814.4 mg/L
           BOD        : 1744.3 mg/L
           TC         : 4246.5 mg/L

qsdsan/processes/__init__.py

@@ -67,6 +67,7 @@ def __init__(self):
 from ._decay import *
 from ._kinetic_reaction import *
 from ._pm2 import *
+from ._aerobic_digestion_addon import *
 
 from . import (
     _aeration,
@@ -77,7 +78,8 @@ def __init__(self):
     # _madm1,
     _decay,
     _kinetic_reaction,
-    _pm2
+    _pm2,
+    _aerobic_digestion_addon,
     )
 
 __all__ = (
@@ -90,4 +92,5 @@ def __init__(self):
     *_decay.__all__,
     *_kinetic_reaction.__all__,
     *_pm2.__all__,
+    *_aerobic_digestion_addon.__all__,
     )

qsdsan/processes/_adm1_p_extension.py

@@ -1037,35 +1037,38 @@ def __new__(cls, components=None, path=None,
                                                #!!! new parameter
                                                KS_IP*P_mw, np.array(k_mmp), Ksp_mass, 
                                                np.array(K_dis), K_AlOH, K_FeOH]))
-        
-        def dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
+
+        def adm1p_dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
             state_arr[7] = S_h2
             Q = state_arr[45]
             rxn = _rhos_adm1p(state_arr, params, h=h)
             stoichio = f_stoichio(state_arr)  # should return the stoichiometric coefficients of S_h2 for all processes
             return Q/V_liq*(S_h2_in - S_h2) + np.dot(rxn, stoichio)
 
+
         grad_rhosp = np.zeros(5)
         X_biop = np.zeros(5)
-        def grad_dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
+        def adm1p_grad_dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
             state_arr[7] = S_h2
             ks = params['rate_constants'][[5,6,7,8,10]]
             Ks = params['half_sat_coeffs'][2:6]
             K_h2 = params['half_sat_coeffs'][7]
             pH_ULs = params['pH_ULs']
             pH_LLs = params['pH_LLs']
             KS_IN = params['KS_IN']
+            KS_IP = params['KS_IP']
             KIs_h2 = params['KIs_h2']
             kLa = params['kLa']
 
             X_biop[:] = state_arr[[18,19,19,20,22]]
             substrates = state_arr[2:6]
-            S_va, S_bu, S_IN = state_arr[[3,4,10]]
+            S_va, S_bu, S_IN, S_IP = state_arr[[3,4,10,11]]
             Iph = Hill_inhibit(h, pH_ULs, pH_LLs)[[2,3,4,5,7]]
             Iin = substr_inhibit(S_IN, KS_IN)
+            Iip = substr_inhibit(S_IP, KS_IP)
             grad_Ih2 = grad_non_compet_inhibit(S_h2, KIs_h2)
 
-            grad_rhosp[:] = ks * X_biop * Iph * Iin
+            grad_rhosp[:] = ks * X_biop * Iph * Iin * Iip
             grad_rhosp[:-1] *= substr_inhibit(substrates, Ks) * grad_Ih2
             if S_va > 0: grad_rhosp[1] *= 1/(1+S_bu/S_va)
             if S_bu > 0: grad_rhosp[2] *= 1/(1+S_va/S_bu)
@@ -1074,12 +1077,12 @@ def grad_dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
             stoichio = f_stoichio(state_arr)
 
             Q = state_arr[45]
-            return -Q/V_liq + np.dot(grad_rhos, stoichio[[5,6,7,8,10]]) + kLa*stoichio[-3]
+            return -Q/V_liq + np.dot(grad_rhosp, stoichio[[5,6,7,8,10]]) + kLa*stoichio[-3]
 
         dct['flex_rhos'] = _rhos_adm1p
         dct['solve_pH'] = adm1p_solve_pH
-        dct['dydt_Sh2_AD'] = dydt_Sh2_AD
-        dct['grad_dydt_Sh2_AD'] = grad_dydt_Sh2_AD
+        dct['dydt_Sh2_AD'] = adm1p_dydt_Sh2_AD
+        dct['grad_dydt_Sh2_AD'] = adm1p_grad_dydt_Sh2_AD
         return self
 
     def set_half_sat_K(self, K, process):

qsdsan/processes/_aerobic_digestion_addon.py

@@ -0,0 +1,107 @@
+# -*- coding: utf-8 -*-
+'''
+QSDsan: Quantitative Sustainable Design for sanitation and resource recovery systems
+
+This module is developed by:
+    Joy Zhang <[email protected]>
+
+This module is under the University of Illinois/NCSA Open Source License.
+Please refer to https://github.com/QSD-Group/QSDsan/blob/main/LICENSE.txt
+for license details.
+'''
+import numpy as np
+from qsdsan import Process
+from thermosteam import settings
+_load_components = settings.get_default_chemicals
+
+__all__ = ('ASM_AeDigAddOn',)
+
+class ASM_AeDigAddOn(Process):
+    '''
+    Creates a `Process` object representing the degradation of particulate
+    inert organic materials that typically occur in an aerobic digester. 
+    Stoichiometry is determined by rules of element conservation in corresponding
+    activated sludge models.
+
+    Parameters
+    ----------
+    k_dig : float, optional
+        The 1st-order degradation rate constant, in d^(-1). The default is 0.04.
+
+    See Also
+    --------
+    :class:`qsdsan.processes.ASM1`
+    :class:`qsdsan.processes.ASM2d`
+    :class:`qsdsan.processes.mASM2d`
+
+    Examples
+    --------
+    >>> import qsdsan.processes as pc
+    >>> cmps_asm1 = pc.create_asm1_cmps()
+    >>> dig_asm1 = pc.ASM_AeDigAddOn('dig_asm1')
+    >>> dig_asm1.show()
+    Process: dig_asm1
+    [stoichiometry]      X_I: -1
+                         X_S: 1
+                         S_NH: 0.06
+                         S_ALK: 0.0514
+    [reference]          X_I
+    [rate equation]      X_I*k_dig
+    [parameters]         k_dig: 0.04
+    [dynamic parameters] 
+    
+    >>> cmps_masm2d = pc.create_masm2d_cmps(set_thermo=False)
+    >>> dig_masm2d = pc.ASM_AeDigAddOn('dig_masm2d', components=cmps_masm2d)
+    >>> dig_masm2d.show()
+    Process: dig_masm2d
+    [stoichiometry]      S_NH4: 0.0265
+                         S_PO4: 0.0009
+                         S_IC: 0.0433
+                         X_I: -1
+                         X_S: 1
+    [reference]          X_I
+    [rate equation]      X_I*k_dig
+    [parameters]         k_dig: 0.04
+    [dynamic parameters]
+    
+    '''
+
+    def __init__(self, ID, k_dig=0.04, components=None):
+        cmps = _load_components(components)
+        rxn = 'X_I -> X_S'
+        consrv = []
+        if 'S_ALK' in cmps.IDs: 
+            consrv.append('charge')
+            rxn += ' + [?]S_ALK'
+        elif 'S_IC' in cmps.IDs:
+            consrv.append('C')
+            rxn += ' + [?]S_IC'
+
+        if 'S_NH' in cmps.IDs:
+            consrv.append('N')
+            rxn += ' + [?]S_NH'
+        elif 'S_NH4' in cmps.IDs:
+            consrv.append('N')
+            rxn += ' + [?]S_NH4'            
+
+        if 'S_PO4' in cmps.IDs:
+            consrv.append('P')
+            rxn += ' +[?]S_PO4'
+
+        super().__init__(ID=ID, reaction=rxn,
+                         rate_equation='k_dig*X_I',
+                         ref_component='X_I',
+                         components=cmps,
+                         conserved_for=consrv,
+                         parameters=('k_dig',))
+        self.k_dig=k_dig
+        self._stoichiometry = np.asarray(self._stoichiometry, dtype=float)
+
+    @property
+    def k_dig(self):
+        '''[float] Degradation rate constant, in d^(-1).'''
+        return self._k
+    @k_dig.setter
+    def k_dig(self, k):
+        self._k = k
+        self.set_parameters(k_dig=k)

qsdsan/processes/_asm2d.py

@@ -12,15 +12,16 @@
 import numpy as np
 from thermosteam.utils import chemicals_user
 from thermosteam import settings
-from qsdsan import Component, Components, Processes, CompiledProcesses
+from qsdsan import Component, Components, WasteStream, Processes, CompiledProcesses
 from ..utils import ospath, data_path, load_data
 from . import Monod, ion_speciation
 from scipy.optimize import brenth
 # from math import log10
 
 
 __all__ = ('create_asm2d_cmps', 'ASM2d',
-           'create_masm2d_cmps', 'mASM2d')
+           'create_masm2d_cmps', 'mASM2d', 
+           'create_masm2d_inf')
 
 _path = ospath.join(data_path, 'process_data/_asm2d.tsv')
 _load_components = settings.get_default_chemicals
@@ -990,3 +991,113 @@ def set_pKsps(self, ps):
                 K *= m2m**abs(v)
             Ksp_mass.append(K)
         self.rate_function._params['Ksp'] = np.array(Ksp_mass)
+
+#%%
+
+def create_masm2d_inf(
+        ID, Q, Q_unit='m3/d', T=298.15, 
+        COD=430, NH4_N=25.0, PO4_P=8.0, alkalinity=7.0, 
+        fr_SI=0.05, fr_SF=0.2, fr_SA=0.0, 
+        fr_XI=0.13, fr_XH=0.0, fr_XAUT=0.0, 
+        fr_XPAO=0.0, fr_XPHA=0.0, X_PP=0.0,
+        S_NO3=0.0, S_O2=0.0, S_N2=18, 
+        S_Ca=140, S_Mg=50, S_K=28, S_Na=87, S_Cl=425,
+        X_AlOH=0, X_AlPO4=0, X_FeOH=0, X_FePO4=0, 
+        X_CaCO3=0, X_ACP=0, X_MgCO3=0, X_newb=0, X_struv=0 
+        ):
+    '''
+    Convenient function to create an influent `WasteStream` object with `mASM2d`
+    state variables based on specified bulk properties.
+
+    Parameters
+    ----------
+    ID : str
+        Unique identification for the `WasteStream` object.
+    Q : float
+        Total volumetric flow rate.
+    Q_unit : str, optional
+        Unit of measurement for flow rate. The default is 'm3/d'.
+    T : float, optional
+        Temperature, in K. The default is 298.15.
+    COD : float, optional
+        Total chemical oxygen demand, not accounting for electron acceptors like 
+        dissvoled O2 or nitrate/nitrite, in mg-COD/L. The default is 430.
+    NH4_N : float, optional
+        Ammonium nitrogen, in mg-N/L. The default is 25.0.
+    PO4_P : float, optional
+        Ortho-phosphate, in mg-P/L. The default is 8.0.
+    alkalinity : float, optional
+        In mmol/L. The default is 7.0.
+    fr_SI : float, optional
+        Soluble inert fraction of total COD. The default is 0.05.
+    fr_SF : float, optional
+        Fermentable biodegradable fraction of total COD. The default is 0.2.
+    fr_SA : float, optional
+        VFA fraction of total COD. The default is 0.0.
+    fr_XI : float, optional
+        Particulate inert fraction of total COD. The default is 0.13.
+    fr_XH : float, optional
+        Heterotrophic biomass fraction of total COD. The default is 0.0.
+    fr_XAUT : float, optional
+        Autotrophic biomass fraction of total COD. The default is 0.0.
+    fr_XPAO : float, optional
+        Phosphorus accumulating biomass fraction of total COD. The default is 0.0.
+    fr_XPHA : float, optional
+        PHA fraction of total COD. The default is 0.0.
+    X_PP : float, optional
+        Poly-phosphate in mg-P/L. The default is 0.0.
+    S_NO3 : float, optional
+        Nitrate and nitrite in mg-N/L. The default is 0.0.
+    S_O2 : float, optional
+        Dissolved oxygen in mg-O2/L. The default is 0.0.
+    S_N2 : float, optional
+        Dissolved nitrogen gas in mg-N/L. The default is 18.
+    S_Ca : float, optional
+        Total soluble calcium in mg-Ca/L. The default is 140.
+    S_Mg : float, optional
+        Total soluble magnesium in mg-Mg/L. The default is 50.
+    S_K : float, optional
+        Total soluble potassium in mg-K/L. The default is 28.
+    S_Na : float, optional
+        Other cation, in mg-Na/L. The default is 87.
+    S_Cl : float, optional
+        Other anion, in mg-Cl/L. The default is 425.
+    X_AlOH : float, optional
+        Aluminum hydroxide [mg/L]. The default is 0.
+    X_AlPO4 : float, optional
+        Aluminum phosphate [mg/L]. The default is 0.
+    X_FeOH : float, optional
+        Iron hydroxide [mg/L]. The default is 0.
+    X_FePO4 : float, optional
+        Iron phosphate [mg/L]. The default is 0.
+    X_CaCO3 : float, optional
+        Calcium carbonate [mg/L]. The default is 0.
+    X_ACP : float, optional
+        Calcium phosphate [mg/L]. The default is 0.
+    X_MgCO3 : float, optional
+        Magnesium carbonate [mg/L]. The default is 0.
+    X_newb : float, optional
+        Newbryite [mg/L]. The default is 0.
+    X_struv : float, optional
+        Struvite [mg/L]. The default is 0.
+
+    '''
+
+    fr_xs = 1.0-fr_SI-fr_SF-fr_SA-fr_XI-fr_XH-fr_XAUT-fr_XPAO-fr_XPHA
+    if fr_xs < 0:
+        raise ValueError('The sum of all COD fractions of organic materials must '
+                         'not exceed 1.')
+
+    inf = WasteStream(ID, T=T, SAlk=alkalinity)
+    concs = dict(
+        S_NH4=NH4_N, S_PO4=PO4_P, S_IC=alkalinity*12,
+        S_I=COD*fr_SI, S_F=COD*fr_SF, S_A=COD*fr_SA, 
+        X_S=COD*fr_xs, X_I=COD*fr_XI, X_H=COD*fr_XH,
+        X_AUT=COD*fr_XAUT, X_PAO=COD*fr_XPAO, X_PHA=COD*fr_XPHA, 
+        X_PP=X_PP, S_NO3=S_NO3, S_O2=S_O2, S_N2=S_N2, 
+        S_Ca=S_Ca, S_Mg=S_Mg, S_K=S_K, S_Na=S_Na, S_Cl=S_Cl,
+        X_AlOH=X_AlOH, X_AlPO4=X_AlPO4, X_FeOH=X_FeOH, X_FePO4=X_FePO4, 
+        X_CaCO3=X_CaCO3, X_ACP=X_ACP, X_MgCO3=X_MgCO3, X_newb=X_newb, X_struv=X_struv
+        )
+    inf.set_flow_by_concentration(Q, concs, (Q_unit, 'mg/L'))
+    return inf