Merge pull request #38 from QSD-Group/metab

merge updates on `metab` branch
QSD-Group · Oct 5, 2023 · a80a98c · a80a98c
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diff --git a/exposan/metab/README.rst b/exposan/metab/README.rst
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+=================================================================
+metab: Modular Encapsulated Two-stage Anaerobic Biological system
+=================================================================
+
+Summary
+-------
+This module serves as a process simulator for the Modular Encapsulated Two-stage Anaerobic Biological (METAB) system and its design variants,
+as described in Zhang et al. [1]_
+
+This module include a "flexible" version of the Anaerobic Digestion Model no.1 (ADM1) [2]_, which enables ideal control of pH and estimation
+of the required acid/base dosing by directly setting a target pH.
+
+Multiple reactor types for the METAB system are included in the ``units.py`` file in this module:
+
+  - upflow sludge blanket reactor (``UASB``)
+  - fluidized bed reactor (``METAB_FluidizedBed``)
+  - packed bed reactor (``METAB_PackedBed``)
+  - batch experiment reactor (``METAB_BatchExp``)
+
+Among them, ``METAB_FluidizedBed``, ``METAB_PackedBed``, and ``METAB_BatchExp`` include a micro-scale mechanistic model of mass transfer through
+encapsulation matrix in reactor mass balance.
+
+.. figure:: ./readme_figures/example_system.png
+
+    *An example METAB system layout: two packed bed reactors in series with sidestream membrane gas extraction at the 1st stage and effluent degassing.*
+
+To reproduce the results and figures included in Zhang et al. [1]_, run corresponding functions in ``analyses.py``. You can find a full list of the
+packages in the environment used to generate the results in `qsdsan.yml <https://github.com/QSD-Group/EXPOsan/blob/main/exposan/metab/qsdsan.yml>`_.
+
+Getting Started
+---------------
+.. code-block:: python
+
+    >>> # create a METAB system by specifying reactor type, gas extraction method, design HRT etc.
+    >>> from exposan.metab import create_system
+    >>> sys = create_system(
+    ...     n_stages=2,         # number of stages
+    ...     reactor_type='PB',  # PB for packed bed, FB for fluidized bed, or UASB
+    ...     gas_extraction='M', # M for membrane gas extraction, V for vacuum extraction, P for passive venting
+    ...     Q=5,                # influent flowrate in m3/d
+    ...     T=22,               # reactor temperature in degree C
+    ...     tot_HRT=12,         # total HRT in d
+    ...     )
+
+    >>> # Simulate the system for 200 days
+    >>> sys.simulate(state_reset_hook='reset_cache', t_span=(0,200), method='BDF')
+    System: PB2M_edg
+    Highest convergence error among components in recycle
+    streams {DMs-1} after 3 loops:
+    - flow rate   1.82e-12 kmol/hr (4e-14%)
+    - temperature 0.00e+00 K (0%)
+    ins...
+    [0] inf
+        phase: 'l', T: 295.15 K, P: 101325 Pa
+        flow (kmol/hr): S_su   0.00347
+                        S_aa   0.125
+                        S_fa   0.000325
+                        S_va   0.000816
+                        S_bu   0.000957
+                        S_pro  0.00114
+                        S_ac   0.00141
+                        ...    11.6
+    outs...
+    [0] bg1
+        phase: 'g', T: 295.15 K, P: 101325 Pa
+        flow: 0
+    [1] bg2
+        phase: 'g', T: 295.15 K, P: 101325 Pa
+        flow (kmol/hr): S_h2   1.49e-07
+                        S_ch4  0.0589
+                        S_IC   0.000946
+                        H2O    0.000489
+    [2] bge
+        phase: 'g', T: 295.15 K, P: 101325 Pa
+        flow (kmol/hr): S_h2   3.76e-10
+                        S_ch4  0.000449
+                        S_IC   0.000413
+    [3] eff_dg
+        phase: 'l', T: 295.15 K, P: 101325 Pa
+        flow (kmol/hr): S_su   2.28e-07
+                        S_aa   4.9e-05
+                        S_fa   7.64e-06
+                        S_va   5.64e-07
+                        S_bu   8.55e-07
+                        S_pro  8.7e-07
+                        S_ac   7.4e-06
+                        ...    11.7
+    [4] bgs
+        phase: 'g', T: 295.15 K, P: 101325 Pa
+        flow (kmol/hr): S_h2   1.01e-05
+                        S_ch4  0.0213
+                        S_IC   0.00291
+
+    >>> # You can look at TEA and LCA results after simulation
+    >>> sys.TEA
+    TEA: PB2M_edg
+    NPV  : -1,413,755 USD at 10.0% discount rate
+
+    >>> sys.LCA
+    LCA: PB2M_edg (lifetime 30 yr)
+    Impacts:
+                        Construction  Transportation    Stream   Others    Total
+    ODP (kg CFC-11-Eq)        0.0196               0   -0.0322   0.0252   0.0126
+    HTNC (CTUh)                 0.18               0   -0.0046    0.121    0.296
+    EP (kg N-Eq)            1.65e+03               0     -27.6 3.24e+03 4.87e+03
+    PMFP (PM2.5-Eq)              467               0     -16.3 1.27e+03 1.72e+03
+    MIR (kg O3-Eq)          2.92e+04               0 -2.32e+03  1.4e+04 4.09e+04
+    EF (CTUe)               1.25e+07               0 -2.33e+05 5.11e+06 1.74e+07
+    GWP100 (kg CO2-Eq)       5.6e+05               0 -3.78e+04 4.45e+05 9.67e+05
+    HTC (CTUh)                 0.061               0  -0.00259   0.0375   0.0959
+    AP (kg SO2-Eq)          2.52e+03               0      -205      946 3.26e+03
+
+
+References
+----------
+.. [1] Zhang et al., Pathway toward sustainable distributed treatment of high strength food industry wastewater with encapsulated anaerobic technology. 2023, *In preparation*
+.. [2] IWA Task Group for Mathematical Modelling of Anaerobic Digestion Processes. Anaerobic Digestion Model No.1 (ADM1); IWA Publishing, 2005. `<https://doi.org/10.2166/9781780403052>`_