Recirculation calculation error in custom fermentor (parent CSTR)

[iilard]

Dear BioSTEAM Team & Community,

I am currently building a simulatin for a specific lactic acid production process, via anaerobic fermentation.
FYI:

• All my chemicals have Hf values set
• Reactions are properly set up (ParallelReaction Set)
• Parent class CSTR
• Tried defining reactions directly in class definition, so my separate _reactions.py won't be shared below... either way leads to same error.

I hope I didn't share too much code for you to understand the issue. Either way, as you can see from the error message, dH is somehow 0. That doesn't make sense as in a separate file I actually calculated the reaction enthalpies and found dH to not be 0. So the issue must somehow persist in the custom class itself.
Any help to solve this is much appreciated!

PS. this is my first post here, any tipps on structuring this better are welcome!

My _settings.py:

import thermosteam as tmo
import biosteam as bst
from _chemicals import chemicals 
from thermosteam import settings

#Activate chemicals list & register them in bio/thermosteam
tmo.settings.set_thermo(chemicals) 
bst.settings.set_thermo(chemicals)

My _chemicals.py:

import thermosteam as tmo
import biosteam as bst
from thermosteam import Chemicals, Chemical

def create_chemicals():
    chemicals = Chemicals([])
    def add_chemical(ID, ref=None, **data):
        chemical = Chemical(ID, **data) if ref is None else ref.copy(ID, **data)
        chemicals.append(chemical)
        return chemical
    
    Water = add_chemical('H2O')
    Glucose = add_chemical('Glucose', phase='l', rho=1560, Cp=1.213)
    CaCO3 = add_chemical('CaCO3', phase='s', rho=2710, Cp=0.834)
    CalciumLactate = add_chemical('CalciumLactate', phase='l', Hf=-1686100, rho=1494) # NOTE: phase=l because only in solution in process simulation; Cp value not available (yet), filler could be ca. 1.4
    lla = add_chemical('L-LacticAcid', phase='l', Hf=-686300, Cp=2.109, rho=1206)
    SulfuricAcid = add_chemical('H2SO4', phase='l', rho=1840, Cp=1.38)
    CarbonDioxide = add_chemical('CO2', phase='g')
    Gypsum = add_chemical('CaSO4_2H2O', phase='s', rho=2320, MW=172.18, Hf=-2023000, Cp=1.081, search_db=False)
    # Biomass_l density assumption similar to water, biomass_s filter cake density according to paper
    Biomass_l = add_chemical('Biomass_l', phase='l', formula='CH1.8O0.5N0.2', MW=24.626, rho=1050, Hf=-106800, Cp=1.25, search_db=False) # Same biomass, but once filtered it's rather a solid (cake), liquid version to simulate suspended in stream
    Biomass_s = add_chemical('Biomass_s', phase='s', formula='CH1.8O0.5N0.2', MW=24.626, rho=1093, Hf=-106800, Cp=1.25, search_db=False) # Cp value from bioindustrial park, as not found in lit.
    EthylAcetate = add_chemical('EthylAcetate', phase='l', Hf=-479860, Cp=1.924)
    Octanol = add_chemical('Octanol', phase='l', Hf=-426600, Cp=2.334)
    
    chemicals.compile()
    return chemicals

chemicals = create_chemicals()

My _units.py:

import biosteam as bst
import thermosteam as tmo
from biosteam import CSTR

# -----------------------------------CUSTOM CLASSES----------------------------------------

# Custom Fermentor based on CSTR for cont. ferm.
class Fermentor(bst.CSTR):
    _N_ins = 1
    _N_outs = 2
    
    def __init__(self, ID='Fermentor', ins=None, outs=(), thermo=None, *, T=313.15, **kwargs):
        if outs == ():
            outs = [None, None]  # liquid, gas
        super().__init__(ID, ins, outs, thermo=thermo, **kwargs)

        self.T=T
        
        # Define reactions here like bioindustrial park lactic example
        self.fermentation_rxns = tmo.ParallelReaction([
            # Reaction definition, Reactant, Conversion
            tmo.Reaction('Glucose -> 2 L-LacticAcid', 'Glucose', 0.92),
            tmo.Reaction('2 L-LacticAcid + CaCO3 -> CalciumLactate + CO2 + H2O', 'L-LacticAcid', 1.0),
            tmo.Reaction('Glucose -> 10.97 Biomass_l', 'Glucose', 0.08)
        ])

    def _run(self):
        feed = self.ins[0]
        liquid_effluent, gas_vent = self.outs

        # Copy feed to effluent
        liquid_effluent.copy_like(feed)

        # Apply reactions using the class-defined reactions
        self.fermentation_rxns(liquid_effluent.mol)

        # Handle gas separation - remove CO2 from liquid and send to gas vent
        gas_vent.copy_flow(liquid_effluent, 'CO2', remove=True)

        # Set temperature for both outlets
        liquid_effluent.T = gas_vent.T = self.T

My _system.py:

import biosteam as bst
from _units import Fermentor  # custom classes
from _reactions import fermentation_reactions, acidification_reaction  # reaction functions
from _settings import chemicals  # compiled thermo package

# -------------------- FEED STREAMS --------------------
glucose_feed = bst.Stream('glucose_feed', Glucose=100, Water=500, units='kg/hr')
CaCO3_feed = bst.Stream('CaCO3_feed', CaCO3=120, Water=100, units='kg/hr')
feedstock_mixer = bst.Mixer('feedstock_mixer', ins=[glucose_feed, CaCO3_feed])

# -------------------- SUBSYSTEM 1: CONVERSION --------------------
preheater = bst.HXutility('preheater', T=313.15) # NOTE: placeholder 40°C
fermentor = Fermentor('fermentor', T=313.15, tau=24, V_wf=0.8)    
# cooler = bst.HXutility('fermentor_cooler', T=313.15)

# Connect the Conversion section
preheater.ins[0] = feedstock_mixer.outs[0]
fermentor.ins[0] = preheater.outs[0]
# cooler.ins[0] = fermentor.outs[0]  # Liquid to cooler

# Create the Conversion subsystem
conversion_sys = bst.System('conversion_sys', path=[feedstock_mixer, preheater, fermentor])




# -------------------- MAIN SYSTEM --------------------
# Combine subsystems into the main system
lactic_acid_system = bst.System('lactic_acid_system',
                                path=[conversion_sys])

The error I get in my terminal:
Traceback (most recent call last):
File "c:\Users\ivano\Desktop\Masterarbeit\Code_system.py", line 34, in
lactic_acid_system.simulate()
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_system.py", line 3105, in simulate
with self.flowsheet:
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_flowsheet.py", line 120, in exit
if exception: raise exception
^^^^^^^^^^^^^^^
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_system.py", line 3166, in simulate
raise error
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_system.py", line 3154, in simulate
if design_and_cost: self._summary()
^^^^^^^^^^^^^^^
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_system.py", line 2862, in _summary
f(i, i._summary)
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 94, in try_method_with_object_stamp
raise_error_with_object_stamp(object, error)
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 84, in raise_error_with_object_stamp
raise error
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 88, in try_method_with_object_stamp
return method(*args)
^^^^^^^^^^^^^
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_system.py", line 2862, in _summary
f(i, i._summary)
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 94, in try_method_with_object_stamp
raise_error_with_object_stamp(object, error)
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 84, in raise_error_with_object_stamp
raise error
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 88, in try_method_with_object_stamp
return method(*args)
raise error
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 88, in try_method_with_object_stamp
return method(*args)
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\thermosteam\exceptions.py", line 88, in try_method_with_object_stamp
return method(*args)
^^^^^^^^^^^^^
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_unit.py", line 1191, in _summary
self._design(**design_kwargs) if design_kwargs else self._design()
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam_unit.py", line 1191, in _summary
self._design(**design_kwargs) if design_kwargs else self._design()
self._design(**design_kwargs) if design_kwargs else self._design()
^^^^^^^^^^^^^^
File "C:\Users\ivano\miniconda3\envs\glukose-env\Lib\site-packages\biosteam\units\stirred_tank_reactor.py", line 329, in _design
recirculation_ratio = reactor_duty / dH # Recirculated flow over net product flow
~~~~~~~~~~~~~^~~~
FloatingPointError: <System: conversion_sys> <Fermentor: fermentor> divide by zero encountered in scalar divide

[iilard]

Additional comment on issue:

• I require enthalpy calculations to work correctly, as the goal is a LCA study at the end
• My understanding as of now: The fermentor will calculate the enthalpy change and thus it should automatically calculate the heating/cooling duty to keep the temperature constant for the fermentation process (as it is usually exothermic)

[iilard]

UPDATE POST:

Tried different ways to solve the issue, this seems to have worked.
Would still appreciate any comments or suggestions, as it seems the power is a bit off for the pump and so on, and the overall process seems to be endothermic, although I expected it to be exothermic.... but will close this for now.

_units.py:

``import biosteam as bst
import thermosteam as tmo
from biosteam import CSTR
import numpy as np
from _reactions import fermentation_reactions, neutralization_reaction, acidification_reaction

# Custom Fermentor based on CSTR for cont. ferm.
class Fermentor(bst.CSTR):
    _N_ins = 1
    _N_outs = 2
    def __init__(self, ID='Fermentor', ins=None, outs=(), thermo=None, *, T=313.15, **kwargs):
        if outs == ():
            outs = [None, None]  # liquid, gas
        super().__init__(ID, ins, outs, thermo=thermo, **kwargs)
        self.T=T
        self.fermentation_rxns = fermentation_reactions()
        self.neutralization_rxn = neutralization_reaction()

    def _run(self):
        feed = self.ins[0]
        liquid_effluent, gas_vent = self.outs
        liquid_effluent.copy_like(feed)
        # Apply reactions using the class-defined reactions, first parallel fermentation, then neutralization
        self.fermentation_rxns(liquid_effluent.mol)
        self.neutralization_rxn(liquid_effluent.mol)
        # Handle gas separation - remove CO2 from liquid and send to gas vent
        gas_vent.copy_flow(liquid_effluent, 'CO2', remove=True)
        liquid_effluent.phase = 'l'
        gas_vent.phase = 'g'
        liquid_effluent.T = gas_vent.T = self.T``

_reactions.py:

import thermosteam as tmo

# Fermentor Unit Parallel Reactions
def fermentation_reactions():
    fermentation = tmo.Reaction(reaction='Glucose -> 2 L-LacticAcid', reactant='Glucose', X=0.92, basis='mol')
    BM_growth = tmo.Reaction(reaction='Glucose -> 10.97 Biomass_l', reactant='Glucose', X=0.08, basis='mol') # NOTE: Coefficient for biomass calculated from lit. yield and conversion eff.
    return tmo.ParallelReaction([fermentation, BM_growth])

# Separate Neutralization for correct mass balance
def neutralization_reaction():
    neutralization = tmo.Reaction(reaction='2 L-LacticAcid + CaCO3 -> CalciumLactate + CO2 + H2O', reactant='L-LacticAcid', X=1, basis='mol')
    return neutralization

# Acidification Tank Unit
def acidification_reaction():
    acidification = tmo.Reaction(reaction='CalciumLactate + H2SO4 -> 2 L-LacticAcid + CaSO4_2H2O', reactant='CalciumLactate', X=1, basis='mol')
    return acidification

_system.py:

import biosteam as bst
from _units import Fermentor  # custom classes
from _reactions import fermentation_reactions, acidification_reaction  # reaction functions
from _settings import chemicals  # compiled thermo package

# -------------------- FEED STREAMS --------------------
glucose_feed = bst.Stream('glucose_feed', Glucose=80, Water=920, units='kg/hr')
CaCO3_feed = bst.Stream('CaCO3_feed', CaCO3=44.5, Water=82.6, units='kg/hr')
feedstock_mixer = bst.Mixer('feedstock_mixer', ins=[glucose_feed, CaCO3_feed])

# -------------------- SUBSYSTEM 1: CONVERSION --------------------
preheater = bst.HXutility('preheater', T=313.15) # NOTE: placeholder 40°C
fermentor = Fermentor('fermentor', T=313.15, tau=24, V_wf=0.8)    
# cooler = bst.HXutility('fermentor_cooler', T=313.15)

# Connect the Conversion section
preheater.ins[0] = feedstock_mixer.outs[0]
fermentor.ins[0] = preheater.outs[0]
# cooler.ins[0] = fermentor.outs[0]  # Liquid to cooler

# Create the Conversion subsystem
conversion_sys = bst.System('conversion_sys', path=[feedstock_mixer, preheater, fermentor])




# -------------------- MAIN SYSTEM --------------------
# Combine subsystems into the main system
lactic_acid_system = bst.System('lactic_acid_system',
                                path=[conversion_sys])

# For simulation
if __name__ == '__main__':
    lactic_acid_system.simulate()
    print("Simulation completed!")
    # diagrams for subsystems:
    # conversion_sys.diagram()
    # lactic_acid_system.diagram()

# KPIs
fermentor.outs[0].show()  # Liquid
fermentor.outs[1].show()  # Gas
fermentor.power_utility.show()
fermentor.heat_utilities[0].show()

[yoelcortes]

@iilard,

Thanks for sharing the code and full details on the issue. I will have a look at this in detail tomorrowFriday (sorry for the delay) and provide you recommendations. Although it may not be a bug, let's leave this issue open until we address it 100%.

Thanks,

[yoelcortes]

@iilard,

The code and the structure is good. You had one issue in your code: the last stream of the fermenter should be the effluent (the first one can be the gas vent). So that is why you were getting that error.

Apart from that, here are are some recommendations:

• Use the _init method instead of __init__ to save you time. Here is another more detailed example: https://biosteam.readthedocs.io/en/latest/tutorial/Inheriting_from_Unit.html
• Let the System object take care of ordering the unit simulation order and partitioning recycle loops. The lactic acid biorefinery was made in 2020 when this feature did not exist yet. For more details, checkout https://biosteam.readthedocs.io/en/latest/tutorial/Creating_a_System.html
• You are correct that the fermentor should be exothermic. The issue probably has to do with ratio of CO2 to product that you are assuming. You might want to couple the production of cell mass with CO2 production within the Reaction object.
• You can pass correct_atomic_balance=True to reaction objects to take care of balancing the stoichiometry (not sure if you knew already).

Hope this helps!

import biosteam as bst

# %% Chemicals

chemicals = bst.Chemicals([
    'H2O',
    bst.Chemical('Glucose', phase='l', rho=1560, Cp=1.213),
    bst.Chemical('CaCO3', phase='s', rho=2710, Cp=0.834, default=True),
    bst.Chemical('CalciumLactate', phase='l', Hf=-1686100, rho=1494, default=True), # NOTE: phase=l because only in solution in process simulation; Cp value not available (yet), filler could be ca. 1.4
    bst.Chemical('L-LacticAcid', phase='l', Hf=-686300, Cp=2.109, rho=1206),
    bst.Chemical('H2SO4', phase='l', rho=1840, Cp=1.38),
    bst.Chemical('CO2', phase='g'),
    bst.Chemical('CaSO4_2H2O', phase='s', rho=2320, MW=172.18, Hf=-2023000, Cp=1.081, default=True, search_db=False),
    # Biomass_l density assumption similar to water, biomass_s filter cake density according to paper
    bst.Chemical('Biomass_l', phase='l', formula='CH1.8O0.5N0.2', MW=24.626, rho=1050, Hf=-106800, Cp=1.25, default=True, search_db=False), # Same biomass, but once filtered it's rather a solid (cake), liquid version to simulate suspended in stream
    bst.Chemical('Biomass_s', phase='s', formula='CH1.8O0.5N0.2', MW=24.626, rho=1093, Hf=-106800, Cp=1.25, default=True, search_db=False), # Cp value from bioindustrial park, as not found in lit.
    bst.Chemical('EthylAcetate', phase='l', Hf=-479860, Cp=1.924),
    bst.Chemical('Octanol', phase='l', Hf=-426600, Cp=2.334),
])
bst.settings.set_thermo(chemicals)
chemicals.set_alias('L-LacticAcid', 'lla')
chemicals.set_alias('CO2', 'CarbonDioxide')
chemicals.set_alias('CaSO4_2H2O', 'Gypsum')

# %% Reactions

# Fermentor Unit Parallel Reactions
def fermentation_reactions():
    fermentation = bst.Reaction(reaction='Glucose -> 2 L-LacticAcid', reactant='Glucose', X=0.92, basis='mol')
    BM_growth = bst.Reaction(reaction='Glucose -> 10.97 Biomass_l', reactant='Glucose', X=0.08, basis='mol') # NOTE: Coefficient for biomass calculated from lit. yield and conversion eff.
    return bst.ParallelReaction([fermentation, BM_growth])

# Separate Neutralization for correct mass balance
def neutralization_reaction():
    neutralization = bst.Reaction(reaction='2 L-LacticAcid + CaCO3 -> CalciumLactate + CO2 + H2O', reactant='L-LacticAcid', X=1, basis='mol')
    return neutralization

# Acidification Tank Unit
def acidification_reaction():
    acidification = bst.Reaction(reaction='CalciumLactate + H2SO4 -> 2 L-LacticAcid + CaSO4_2H2O', reactant='CalciumLactate', X=1, basis='mol')
    return acidification

# %% Unit operations

class Fermentor(bst.CSTR):
    # Custom Fermentor based on CSTR for cont. ferm.
    _N_ins = 1
    _N_outs = 2
    T_default = 313.15
    
    def _init(self):
        # Define reactions here like bioindustrial park lactic example
        self.fermentation_rxns = fermentation_reactions()
        self.neutralization_rxn = neutralization_reaction()

    def _run(self):
        feed = self.ins[0]
        gas_vent, liquid_effluent = self.outs # Last one is always the effluent

        # Copy feed to effluent
        liquid_effluent.copy_like(feed)

        # Apply reactions using the class-defined reactions
        self.fermentation_rxns(liquid_effluent)
        self.neutralization_rxn(liquid_effluent)

        # Handle gas separation - remove CO2 from liquid and send to gas vent
        gas_vent.copy_flow(liquid_effluent, 'CO2', remove=True)
        gas_vent.phase = 'g'

        # Set temperature for both outlets
        liquid_effluent.T = gas_vent.T = self.T
        
# %% System

# -------------------- FEED STREAMS --------------------
glucose_feed = bst.Stream('glucose_feed', Glucose=100, Water=500, units='kg/hr')
CaCO3_feed = bst.Stream('CaCO3_feed', CaCO3=120, Water=100, units='kg/hr')

# -------------------- SUBSYSTEM 1: CONVERSION --------------------

with bst.System('conversion_sys') as conversion_sys:
    feedstock_mixer = bst.Mixer('feedstock_mixer', ins=[glucose_feed, CaCO3_feed])
    preheater = bst.HXutility('preheater', feedstock_mixer.outs[0], T=313.15) # NOTE: placeholder 40°C
    fermentor = Fermentor('fermentor', preheater.outs[0], T=313.15, tau=24, V_wf=0.8)    

# Alternatively, you can also do: bst.System.from_units('conversion_sys', units=[feedstock_mixer, preheater, fermentor])

# -------------------- MAIN SYSTEM --------------------
# Combine subsystems into the main system
lactic_acid_system = bst.System('lactic_acid_system',
                                path=[conversion_sys])

lactic_acid_system.simulate()