Merge pull request #127 from QSD-Group/beta

Merge in recent updates; release new version

docs/source/conf.py

@@ -31,7 +31,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.4.0'
+version = '1.4.1'
 # The full version, including alpha/beta/rc tags.
 release = version
 

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/_sanunit.py

@@ -217,6 +217,7 @@ def __init__(self, ID='', ins=None, outs=(), thermo=None, init_with='WasteStream
             self._assert_compatible_property_package()
 
         self._utility_cost = None
+        self._recycle_system = None
 
         ##### qsdsan-specific #####
         for i in (*construction, *transportation, *equipment):

qsdsan/_waste_stream.py

@@ -154,7 +154,11 @@ def __init__(self, dct, F_vol, MW, phase, phase_container):
     def output(self, index, value):
         '''Concentration flows, in mg/L (g/m3).'''
         f_mass = value * self.MW[index]
-        phase = self.phase or self.phase_container.phase
+        if self.phase:
+            phase = self.phase
+        else:
+            try: phase = self.phase_container._phase
+            except: phase = self.phase_container
         if phase != 'l':
             raise AttributeError('Concentration only valid for liquid phase.')
         V_sum = self.F_vol
@@ -186,7 +190,7 @@ def by_conc(self, TP):
         check_data=False,
         )
     return conc
-indexer.ChemicalMolarFlowIndexer.by_conc = by_conc
+ChemicalMolarFlowIndexer.by_conc = by_conc
 del by_conc
 
 
@@ -450,7 +454,7 @@ 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 +1303,7 @@ 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 +1526,7 @@ 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 +1755,7 @@ 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 +1987,7 @@ 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/data/process_data/_pm2asm2d.tsv

@@ -0,0 +1,39 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+photoadaptation	1																			
+ammonium_uptake									-1			1								
+phosphorus_uptake											-1		1							
+growth_pho		1			?			1				?	?							
+carbohydrate_storage_pho			1		?			1												
+lipid_storage_pho				1	?			1												
+carbohydrate_growth_pho		1	(-Y_CH_PHO/Y_X_ALG_PHO)		?			?				?	?							
+lipid_growth_pho		1		(-Y_LI_PHO/Y_X_ALG_PHO)	?			?				?	?							
+carbohydrate_maintenance_pho			-1		?			-1												
+lipid_maintenance_pho				-1	?			-1												
+endogenous_respiration_pho		-1			?			-1				?	?							
+growth_ace		1			?	(-1)/Y_X_ALG_HET_ACE		?				?	?							
+carbohydrate_storage_ace			1		?	(-1)/Y_CH_ND_HET_ACE		?												
+lipid_storage_ace				1	?	(-1)/Y_LI_ND_HET_ACE		?												
+carbohydrate_growth_ace		1	(-Y_CH_NR_HET_ACE/Y_X_ALG_HET_ACE)		?			?				?	?							
+lipid_growth_ace		1		(-Y_LI_NR_HET_ACE/Y_X_ALG_HET_ACE)	?			?				?	?							
+carbohydrate_maintenance_ace			-1		?			-1												
+lipid_maintenance_ace				-1	?			-1												
+endogenous_respiration_ace		-1			?			-1				?	?							
+growth_glu		1			?		(-1)/Y_X_ALG_HET_GLU	?				?	?							
+carbohydrate_storage_glu			1		?		(-1)/Y_CH_ND_HET_GLU	?												
+lipid_storage_glu				1	?		(-1)/Y_LI_ND_HET_GLU	?												
+carbohydrate_growth_glu		1	(-Y_CH_NR_HET_GLU/Y_X_ALG_HET_GLU)		?			?				?	?							
+lipid_growth_glu		1		(-Y_LI_NR_HET_GLU/Y_X_ALG_HET_GLU)	?			?				?	?							
+carbohydrate_maintenance_glu			-1		?			-1												
+lipid_maintenance_glu				-1	?			-1												
+endogenous_respiration_glu		-1			?			-1				?	?							
+aero_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anox_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anae_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+hetero_growth_S_F							(-1)/Y_H	1-1/Y_H	?		?				?				1	
+hetero_growth_S_A						(-1)/Y_H		1-1/Y_H	?		?				?				1	
+denitri_S_F							(-1)/Y_H		?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+denitri_S_A						(-1)/Y_H			?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+ferment						1	-1		?		?				?					
+hetero_lysis									?		?				?		f_XI_H	1-f_XI_H	-1	
+auto_aero_growth								(Y_A-32/7)/Y_A	?	1/Y_A	?				?					1
+auto_lysis									?		?				?		f_XI_AUT	1-f_XI_AUT		-1

qsdsan/data/process_data/_pm2asm2d_1.tsv

@@ -0,0 +1,28 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+photoadaptation	1																			
+ammonium_uptake									-1			1								
+phosphorus_uptake											-1		1							
+growth_pho		1			?			1				?	?							
+carbohydrate_storage_pho			1		?			1												
+lipid_storage_pho				1	?			1												
+carbohydrate_growth_pho		1	(-Y_CH_PHO/Y_X_ALG_PHO)		?			?				?	?							
+lipid_growth_pho		1		(-Y_LI_PHO/Y_X_ALG_PHO)	?			?				?	?							
+carbohydrate_maintenance_pho			-1		?			-1												
+lipid_maintenance_pho				-1	?			-1												
+endogenous_respiration_pho		-1			?			-1				?	?							
+growth_ace		1			?	(-1)/Y_X_ALG_HET_ACE		?				?	?							
+carbohydrate_storage_ace			1		?	(-1)/Y_CH_ND_HET_ACE		?												
+lipid_storage_ace				1	?	(-1)/Y_LI_ND_HET_ACE		?												
+carbohydrate_growth_ace		1	(-Y_CH_NR_HET_ACE/Y_X_ALG_HET_ACE)		?			?				?	?							
+lipid_growth_ace		1		(-Y_LI_NR_HET_ACE/Y_X_ALG_HET_ACE)	?			?				?	?							
+carbohydrate_maintenance_ace			-1		?			-1												
+lipid_maintenance_ace				-1	?			-1												
+endogenous_respiration_ace		-1			?			-1				?	?							
+growth_glu		1			?		(-1)/Y_X_ALG_HET_GLU	?				?	?							
+carbohydrate_storage_glu			1		?		(-1)/Y_CH_ND_HET_GLU	?												
+lipid_storage_glu				1	?		(-1)/Y_LI_ND_HET_GLU	?												
+carbohydrate_growth_glu		1	(-Y_CH_NR_HET_GLU/Y_X_ALG_HET_GLU)		?			?				?	?							
+lipid_growth_glu		1		(-Y_LI_NR_HET_GLU/Y_X_ALG_HET_GLU)	?			?				?	?							
+carbohydrate_maintenance_glu			-1		?			-1												
+lipid_maintenance_glu				-1	?			-1												
+endogenous_respiration_glu		-1			?			-1				?	?							

qsdsan/data/process_data/_pm2asm2d_2.tsv

@@ -0,0 +1,12 @@
+	X_CHL	X_ALG	X_CH	X_LI	S_CO2	S_A	S_F	S_O2	S_NH	S_NO	S_P	X_N_ALG	X_P_ALG	S_N2	S_ALK	S_I	X_I	X_S	X_H	X_AUT
+aero_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anox_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+anae_hydrolysis							1-f_SI		?		?				?	f_SI		-1		
+hetero_growth_S_F							(-1)/Y_H	1-1/Y_H	?		?				?				1	
+hetero_growth_S_A						(-1)/Y_H		1-1/Y_H	?		?				?				1	
+denitri_S_F							(-1)/Y_H		?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+denitri_S_A						(-1)/Y_H			?	(Y_H-1)/(20/7*Y_H)	?			(1-Y_H)/(20/7*Y_H)	?				1	
+ferment						1	-1		?		?				?					
+hetero_lysis									?		?				?		f_XI_H	1-f_XI_H	-1	
+auto_aero_growth								(Y_A-32/7)/Y_A	?	1/Y_A	?				?					1
+auto_lysis									?		?				?		f_XI_AUT	1-f_XI_AUT		-1

qsdsan/processes/__init__.py

@@ -10,6 +10,8 @@
     
     Joy Zhang <[email protected]>
 
+    Ga-Yeong Kim <[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.
@@ -59,6 +61,7 @@ def __init__(self):
 
 #%%
 from ._aeration import *
+from ._aerobic_digestion_addon import *
 from ._asm1 import *
 from ._asm2d import *
 from ._adm1 import *
@@ -67,21 +70,25 @@ def __init__(self):
 from ._decay import *
 from ._kinetic_reaction import *
 from ._pm2 import *
+from ._pm2asm2d import *
 
 from . import (
     _aeration,
+    _aerobic_digestion_addon,
     _asm1,
     _asm2d,
     _adm1,
     _adm1_p_extension,
     # _madm1,
     _decay,
     _kinetic_reaction,
-    _pm2
+    _pm2,
+    _pm2asm2d,
     )
 
 __all__ = (
     *_aeration.__all__,
+    *_aerobic_digestion_addon.__all__,
     *_asm1.__all__,
     *_asm2d.__all__,
     *_adm1.__all__,
@@ -90,4 +97,5 @@ def __init__(self):
     *_decay.__all__,
     *_kinetic_reaction.__all__,
     *_pm2.__all__,
-    )
+    *_pm2asm2d.__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)