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QSD-Group · Oct 16, 2024 · 75e083b · 75e083b
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diff --git a/docs/source/api/processes/ADM1p.rst b/docs/source/api/processes/ADM1p.rst
@@ -4,4 +4,4 @@ Anaerobic Digestion Model No.1 with P extension (ADM1 P/Extension)
    :members:
 
 .. autoclass:: qsdsan.processes.ADM1p
-:members:
+   :members:
diff --git a/qsdsan/processes/_adm1_p_extension.py b/qsdsan/processes/_adm1_p_extension.py
@@ -288,7 +288,7 @@ def grad_dydt_Sh2_AD(S_h2, state_arr, h, params, f_stoichio, V_liq, S_h2_in):
 @chemicals_user
 class ADM1_p_extension(ADM1):
     """
-    Anaerobic Digestion Model No.1 with P extension. [1]_, [2]_, [3]_.
+    Anaerobic Digestion Model No.1 with P extension.
     Compatible with the original `ASM2d`.
 
     Parameters
@@ -357,17 +357,19 @@ class ADM1_p_extension(ADM1):
     
     References
     ----------
-    .. [1] Batstone, D. J.; Keller, J.; Angelidaki, I.; Kalyuzhnyi, S. V; 
-        Pavlostathis, S. G.; Rozzi, A.; Sanders, W. T. M.; Siegrist, H.; 
-        Vavilin, V. A. The IWA Anaerobic Digestion Model No 1 (ADM1). 
-        Water Sci. Technol. 2002, 45 (10), 65–73.
-    .. [2] Rosen, C.; Jeppsson, U. Aspects on ADM1 Implementation within 
-        the BSM2 Framework; Lund, 2006.
-    .. [3] Flores-Alsina, X.; Solon, K.; Kazadi Mbamba, C.; Tait, S.; 
-        Gernaey, K. V.; Jeppsson, U.; Batstone, D. J. 
-        Modelling phosphorus (P), sulfur (S) and iron (FE) interactions for 
-        dynamic simulations of anaerobic digestion processes. Water Research. 2016,
-        95, 370–382.
+    [1] Batstone, D. J.; Keller, J.; Angelidaki, I.; Kalyuzhnyi, S. V; 
+    Pavlostathis, S. G.; Rozzi, A.; Sanders, W. T. M.; Siegrist, H.; 
+    Vavilin, V. A. The IWA Anaerobic Digestion Model No 1 (ADM1). 
+    Water Sci. Technol. 2002, 45 (10), 65–73.
+
+    [2] Rosen, C.; Jeppsson, U. Aspects on ADM1 Implementation within 
+    the BSM2 Framework; Lund, 2006.
+    
+    [3] Flores-Alsina, X.; Solon, K.; Kazadi Mbamba, C.; Tait, S.; 
+    Gernaey, K. V.; Jeppsson, U.; Batstone, D. J. 
+    Modelling phosphorus (P), sulfur (S) and iron (FE) interactions for 
+    dynamic simulations of anaerobic digestion processes. Water Research. 2016,
+    95, 370–382.
     """
 
     _stoichio_params = (*ADM1._stoichio_params[5:],
@@ -798,7 +800,7 @@ def _rhos_adm1p(state_arr, params, h=None):
 @chemicals_user
 class ADM1p(ADM1):
     """
-    Anaerobic Digestion Model No.1 with P extension. [1]_, [2]_.
+    Anaerobic Digestion Model No.1 with P extension. [1], [2].
     Compatible with `mASM2d`.
 
     Parameters
@@ -866,20 +868,20 @@ class ADM1p(ADM1):
     >>> adm.show()
     ADM1p([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, CaCO3_precipitation_dissolution, struvite_precipitation_dissolution, newberyite_precipitation_dissolution, ACP_precipitation_dissolution, MgCO3_precipitation_dissolution, AlPO4_precipitation_dissolution, FePO4_precipitation_dissolution, h2_transfer, ch4_transfer, IC_transfer])
     
-    
     References
     ----------
-    .. [1] Flores-Alsina, X., Solon, K., Kazadi Mbamba, C., Tait, S., 
-        Gernaey, K. V., Jeppsson, U., & Batstone, D. J. (2016).
-        Modelling phosphorus (P), sulfur (S) and iron (FE) interactions for 
-        dynamic simulations of anaerobic digestion processes. Water Research, 
-        95, 370–382.
-    .. [2] Solon, K., Flores-Alsina, X., Kazadi Mbamba, C., Ikumi, D., Volcke, 
-        E. I. P., Vaneeckhaute, C., Ekama, G., Vanrolleghem, P. A., Batstone, 
-        D. J., Gernaey, K. V., & Jeppsson, U. (2017). Plant-wide modelling 
-        of phosphorus transformations in wastewater treatment systems: 
-        Impacts of control and operational strategies. Water Research, 113, 
-        97–110.
+    [1] Flores-Alsina, X., Solon, K., Kazadi Mbamba, C., Tait, S., 
+    Gernaey, K. V., Jeppsson, U., & Batstone, D. J. (2016).
+    Modelling phosphorus (P), sulfur (S) and iron (FE) interactions for 
+    dynamic simulations of anaerobic digestion processes. Water Research, 
+    95, 370–382.
+
+    [2] Solon, K., Flores-Alsina, X., Kazadi Mbamba, C., Ikumi, D., Volcke, 
+    E. I. P., Vaneeckhaute, C., Ekama, G., Vanrolleghem, P. A., Batstone, 
+    D. J., Gernaey, K. V., & Jeppsson, U. (2017). Plant-wide modelling 
+    of phosphorus transformations in wastewater treatment systems: 
+    Impacts of control and operational strategies. Water Research, 113, 
+    97–110.
     """
 
     _stoichio_params = (*ADM1._stoichio_params[5:],

diff --git a/qsdsan/processes/_asm2d.py b/qsdsan/processes/_asm2d.py
@@ -253,7 +253,7 @@ def rhos_asm2d(state_arr, params):
 @chemicals_user
 class ASM2d(CompiledProcesses):
     '''
-    Activated Sludge Model No. 2d in original notation. [1]_, [2]_
+    Activated Sludge Model No. 2d in original notation.
 
     Parameters
     ----------
@@ -441,14 +441,15 @@ class ASM2d(CompiledProcesses):
 
     References
     ----------
-    .. [1] Henze, M.; Gujer, W.; Mino, T.; Loosdrecht, M. van. Activated Sludge
-        Models: ASM1, ASM2, ASM2d and ASM3; IWA task group on mathematical modelling
-        for design and operation of biological wastewater treatment, Ed.; IWA
-        Publishing: London, 2000.
-    .. [2] Rieger, L.; Gillot, S.; Langergraber, G.; Ohtsuki, T.; Shaw, A.; Takács,
-        I.; Winkler, S. Guidelines for Using Activated Sludge Models; IWA Publishing:
-        London, New York, 2012; Vol. 11.
-        https://doi.org/10.2166/9781780401164.
+    [1] Henze, M.; Gujer, W.; Mino, T.; Loosdrecht, M. van. Activated Sludge
+    Models: ASM1, ASM2, ASM2d and ASM3; IWA task group on mathematical modelling
+    for design and operation of biological wastewater treatment, Ed.; IWA
+    Publishing: London, 2000.
+    
+    [2] Rieger, L.; Gillot, S.; Langergraber, G.; Ohtsuki, T.; Shaw, A.; Takács,
+    I.; Winkler, S. Guidelines for Using Activated Sludge Models; IWA Publishing:
+    London, New York, 2012; Vol. 11.
+    https://doi.org/10.2166/9781780401164.
     '''
     _params = ('f_SI', 'Y_H', 'f_XI_H', 'Y_PAO', 'Y_PO4', 'Y_PHA', 'f_XI_PAO', 'Y_A', 'f_XI_AUT',
                'K_h', 'eta_NO3', 'eta_fe', 'K_O2', 'K_NO3', 'K_X',
@@ -701,7 +702,7 @@ def _rhos_masm2d(state_arr, params, acceptor_dependent_decay=True, h=None):
 @chemicals_user
 class mASM2d(CompiledProcesses):
     '''
-    Modified ASM2d. [1]_, [2]_ Compatible with `ADM1p` for plant-wide simulations.
+    Modified ASM2d. Compatible with `ADM1p` for plant-wide simulations.
     Includes an algebraic pH solver and precipitation/dissolution of common minerals.
 
     Parameters
@@ -768,18 +769,18 @@ class mASM2d(CompiledProcesses):
 
     References
     ----------
-    .. [1] Henze, M., Gujer, W., Mino, T., & van Loosdrecht, M. (2000). 
-        Activated Sludge Models: ASM1, ASM2, ASM2d and ASM3. In IWA task group 
-        on mathematical modelling for design and operation of biological 
-        wastewater treatment (Ed.), Scientific and Technical Report No. 9. 
-        IWA Publishing.
-    .. [2] Solon, K., Flores-Alsina, X., Kazadi Mbamba, C., Ikumi, D., Volcke, 
-        E. I. P., Vaneeckhaute, C., Ekama, G., Vanrolleghem, P. A., Batstone, 
-        D. J., Gernaey, K. V., & Jeppsson, U. (2017). Plant-wide modelling 
-        of phosphorus transformations in wastewater treatment systems: 
-        Impacts of control and operational strategies. Water Research, 113, 
-        97–110. https://doi.org/10.1016/j.watres.2017.02.007
-    
+    [1] Henze, M., Gujer, W., Mino, T., & van Loosdrecht, M. (2000). 
+    Activated Sludge Models: ASM1, ASM2, ASM2d and ASM3. In IWA task group 
+    on mathematical modelling for design and operation of biological 
+    wastewater treatment (Ed.), Scientific and Technical Report No. 9. 
+    IWA Publishing.
+    
+    [2] Solon, K., Flores-Alsina, X., Kazadi Mbamba, C., Ikumi, D., Volcke, 
+    E. I. P., Vaneeckhaute, C., Ekama, G., Vanrolleghem, P. A., Batstone, 
+    D. J., Gernaey, K. V., & Jeppsson, U. (2017). Plant-wide modelling 
+    of phosphorus transformations in wastewater treatment systems: 
+    Impacts of control and operational strategies. Water Research, 113, 
+    97–110. https://doi.org/10.1016/j.watres.2017.02.007
     '''
     _stoichio_params = ('f_SI', 'Y_H', 'Y_PAO', 'Y_PO4', 'Y_PHA', 'Y_A', 
                         'f_XI_H', 'f_XI_PAO', 'f_XI_AUT', 'COD_deN', 'K_XPP', 'Mg_XPP')

diff --git a/qsdsan/sanunits/_clarifier.py b/qsdsan/sanunits/_clarifier.py
@@ -71,7 +71,7 @@ def _settling_flux(X, v_max, v_max_practical, X_min, rh, rp, n0):
 class FlatBottomCircularClarifier(SanUnit):
     """
     A flat-bottom circular clarifier with a simple 1-dimensional
-    N-layer settling model. [1]_
+    N-layer settling model.
 
     Parameters
     ----------
@@ -123,15 +123,19 @@ class FlatBottomCircularClarifier(SanUnit):
     
     References
     ----------
-    .. [1] Takács, I.; Patry, G. G.; Nolasco, D. A Dynamic Model of the Clarification
-        -Thickening Process. Water Res. 1991, 25 (10), 1263–1271.
-        https://doi.org/10.1016/0043-1354(91)90066-Y.
-    .. [2] Chapter-12: Suspended-growth Treatment Processes. WEF Manual of Practice No. 8. 
-        6th Edition. Virginia: McGraw-Hill, 2018. 
-    .. [3] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
+    [1] Takács, I.; Patry, G. G.; Nolasco, D. A Dynamic Model of the Clarification
+    -Thickening Process. Water Res. 1991, 25 (10), 1263–1271.
+    https://doi.org/10.1016/0043-1354(91)90066-Y.
+    
+    [2] Chapter-12: Suspended-growth Treatment Processes. WEF Manual of Practice No. 8. 
+    6th Edition. Virginia: McGraw-Hill, 2018. 
+    
+    [3] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
     engineering: treatment, disposal, and reuse. Vol. 4. New York: McGraw-Hill, 1991.
-    .. [4] Introduction to Wastewater Clarifier Design by Nikolay Voutchkov, PE, BCEE.
-    .. [5] RECOMMENDED STANDARDS for WASTEWATER FACILITIES. 10 state standards. 2014 edition. 
+    
+    [4] Introduction to Wastewater Clarifier Design by Nikolay Voutchkov, PE, BCEE.
+    
+    [5] RECOMMENDED STANDARDS for WASTEWATER FACILITIES. 10 state standards. 2014 edition. 
     """
 
     _N_ins = 1
@@ -1092,6 +1096,7 @@ class PrimaryClarifierBSM2(SanUnit):
     ----------
     [1] Otterpohl R. and Freund M. (1992). Dynamic Models for clarifiers of activated sludge 
     plants with dry and wet weather flows. Water Sci. Technol., 26(5-6), 1391-1400. 
+    
     [2] Gernaey, Krist V., Ulf Jeppsson, Peter A. Vanrolleghem, and John B. Copp.
     Benchmarking of control strategies for wastewater treatment plants. IWA publishing, 2014.
     """
@@ -1312,8 +1317,10 @@ class PrimaryClarifier(IdealClarifier):
     ----------
     [1] Chapter-10: Primary Treatment. Design of water resource recovery facilities. 
     WEF Manual of Practice No. 8. 6th Edition. Virginia: McGraw-Hill, 2018. 
+    
     [2] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
     engineering: treatment, disposal, and reuse. Vol. 4. New York: McGraw-Hill, 1991.
+    
     [3] Introduction to Wastewater Clarifier Design by Nikolay Voutchkov, PE, BCEE.
     """
 

diff --git a/qsdsan/sanunits/_junction.py b/qsdsan/sanunits/_junction.py
@@ -1643,7 +1643,6 @@ class mADM1toASM2d(mADMjunction):
     [1] Nopens, I.; Batstone, D. J.; Copp, J. B.; Jeppsson, U.; Volcke, E.; 
     Alex, J.; Vanrolleghem, P. A. An ASM/ADM Model Interface for Dynamic 
     Plant-Wide Simulation. Water Res. 2009, 43, 1913–1923.
-    
     [2] Flores-Alsina, X., Solon, K., Kazadi Mbamba, C., Tait, S., Gernaey, K. V., 
     Jeppsson, U., & Batstone, D. J. (2016). Modelling phosphorus (P), sulfur (S) 
     and iron (FE) interactions for dynamic simulations of anaerobic digestion processes. 
@@ -2479,7 +2478,7 @@ def check_component_properties(self, cmps_asm, cmps_adm):
 class ADM1ptomASM2d(A1junction):
     '''
     Interface unit to convert ADM1 state variables
-    to ASM2d components, following the A1 algorithm in [1]_.
+    to ASM2d components, following the A1 algorithm in [1].
     
     Parameters
     ----------
@@ -2727,7 +2726,7 @@ def adm1p2masm2d(adm_vals):
 class mASM2dtoADM1p(A1junction):
     '''
     Interface unit to convert ASM2d state variables
-    to ADM1 components, following the A1 scenario in [1]_.
+    to ADM1 components, following the A1 scenario in [1].
     
     Parameters
     ----------

diff --git a/qsdsan/sanunits/_sludge_treatment.py b/qsdsan/sanunits/_sludge_treatment.py
@@ -64,7 +64,9 @@ def calc_f_Qu_thin(TSS_removal_perc, thickener_factor):
 class Thickener(SanUnit):
 
     """
-    Thickener based on BSM2 Layout. [1]
+    Thickener based on BSM2 Layout.
+    
+    Parameters
     ----------
     ID : str
         ID for the Thickener. The default is ''.
@@ -160,12 +162,15 @@ class Thickener(SanUnit):
 
     References
     ----------
-    .. [1] Gernaey, Krist V., Ulf Jeppsson, Peter A. Vanrolleghem, and John B. Copp.
+    [1] Gernaey, Krist V., Ulf Jeppsson, Peter A. Vanrolleghem, and John B. Copp.
     Benchmarking of control strategies for wastewater treatment plants. IWA publishing, 2014.
-    .. [2] Chapter-21: Solids Thicknening (Table 21.3). WEF Manual of Practice No. 8. 
+
+    [2] Chapter-21: Solids Thicknening (Table 21.3). WEF Manual of Practice No. 8. 
     6th Edition. Virginia: McGraw-Hill, 2018. 
-    .. [3] Introduction to Wastewater Clarifier Design by Nikolay Voutchkov, PE, BCEE.
-    .. [4] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
+    
+    [3] Introduction to Wastewater Clarifier Design by Nikolay Voutchkov, PE, BCEE.
+    
+    [4] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
     engineering: treatment, disposal, and reuse. Vol. 4. New York: McGraw-Hill, 1991.
     """
 
@@ -370,7 +375,7 @@ def yt(t, QC_ins, dQC_ins):
 class Centrifuge(Thickener):
 
     """
-    Centrifuge based on BSM2 Layout. [1]
+    Centrifuge based on BSM2 Layout.
     
     Parameters
     ----------
@@ -409,12 +414,17 @@ class Centrifuge(Thickener):
     ----------
     [1] Gernaey, Krist V., Ulf Jeppsson, Peter A. Vanrolleghem, and John B. Copp.
     Benchmarking of control strategies for wastewater treatment plants. IWA publishing, 2014.
+
     [2] Metcalf, Leonard, Harrison P. Eddy, and Georg Tchobanoglous. Wastewater 
     engineering: treatment, disposal, and reuse. Vol. 4. New York: McGraw-Hill, 1991.
+    
     [3] Design of Municipal Wastewater Treatment Plants: WEF Manual of Practice 
     No. 8 ASCE Manuals and Reports on Engineering Practice No. 76, Fifth Edition. 
+    
     [4] https://www.alibaba.com/product-detail/Multifunctional-Sludge-Dewatering-Decanter-Centrifuge_1600285055254.html?spm=a2700.galleryofferlist.normal_offer.d_title.1cd75229sPf1UW&s=p
+    
     [5] United States Environmental Protection Agency (EPA) 'Biosolids Technology Fact Sheet Centrifuge Thickening and Dewatering'  
+    
     [6] San Diego (.gov) Chapter - 3 'Solids Treatment Facility' 
     (https://www.sandiego.gov/sites/default/files/legacy/mwwd/pdf/mbc/chapterthree.pdf)
     """
@@ -531,11 +541,12 @@ class Incinerator(SanUnit):
     flow (g/hr): X_Ig_ISS  2.37e+05
         WasteStream-specific properties: None for non-liquid waste streams
     
-    References: 
+    References
     ----------
-    .. [1] Khuriati, A., P. Purwanto, H. S. Huboyo, Suryono Sumariyah, S. Suryono, and A. B. Putranto. 
+    [1] Khuriati, A., P. Purwanto, H. S. Huboyo, Suryono Sumariyah, S. Suryono, and A. B. Putranto. 
     "Numerical calculation based on mass and energy balance of waste incineration in the fixed bed reactor." 
     In Journal of Physics: Conference Series, vol. 1524, no. 1, p. 012002. IOP Publishing, 2020.
+    
     [2] Omari, Arthur, Karoli N. Njau, Geoffrey R. John, Joseph H. Kihedu, and Peter L. Mtui. 
     "Mass And Energy Balance For Fixed Bed Incinerators A case of a locally designed incinerator in Tanzania."
     """