Error Consultation on Fermentation Code.

[om11kar]

I have been working on the Fermentation of Lactic Acid and tried to use the Fermentation code given in the Bioindustrial-Park/biorefineries. The code is as follows: -

import numpy as np import pandas as pd import biosteam as bst from warnings import warn from biosteam.utils import TicToc from biorefineries.lactic import _load_system, SSCF_flowsheet, SSCF_funcs, SHF_flowsheet, SHF_funcs from biorefineries.lactic._chemicals import sugars from biorefineries.lactic.utils import set_yield

_load_system('SSCF') _load_system('SHF')

Initiate a timer

timer = TicToc('timer') timer.tic() run_number = 0 sugar_concs = [[], []] lactics ={'target yield': [], 'target titer': [], 'actual yield': [], 'actual titer': []} MPSPs = {0.89: [], 0.18: [], 1.92: []} NPVs = {0.89: [], 0.18: [], 1.92: []} GWPs = {0.89: [], 0.18: [], 1.92: []} FECs = {0.89: [], 0.18: [], 1.92: []}

def compute_sugar_conc(stream): return stream.imass[sugars].sum()/stream.F_vol

def solve_TEA(lactic_acid, lactic_tea): lactic_acid.price = 0 for i in range(3): MPSP = lactic_acid.price = lactic_tea.solve_price(lactic_acid) return MPSP

def update_productivity(R301,R302,productivity): R301.productivity = productivity R302.productivity = productivity * R302.ferm_ratio for unit in (R301, R302): unit._design() unit._cost()

def simulate_log_results(kind): kind = kind.upper() if 'SSCF' in kind: flowsheet = SSCF_flowsheet funcs = SHF_funcs bst.main_flowsheet.set_flowsheet(flowsheet) _load_system(kind)

R301 = flowsheet.unit.R301
R302 = flowsheet.unit.R302
lactic_acid = flowsheet.stream.lactic_acid
lactic_sys = flowsheet.system.lactic_sys
lactic_tea = lactic_sys.TEA

try:
    lactic_sys.simulate()
    for productivity in (0.89, 0.18, 1.92):
        update_productivity(R301, R302, productivity)
        MPSP = solve_TEA(lactic_acid, lactic_tea)
        GWP = funcs['get_GWP']()
        FEC = funcs['get_FEC']()
        MPSPs[productivity].append(MPSP)
        GWPs[productivity].append(GWP)
        FECs[productivity].append(FEC)
        NPVs[productivity].append(lactic_tea.NPV)
    lactics['actual yield'].append(R301.lactic_yield)
    lactics['actual titer'].append(R301.effluent_titer)
except:
    warn(f'Simulation failed at target yield {round(R301.target_yield,2)},'\
         f'target titer {R301.target_titer}.')
    lactic_sys.empty_recycles()
    lactic_sys.reset_cache()
    lactics['actual yield'].append(np.nan)
    lactics['actual titer'].append(np.nan)
    for m in (MPSPs, NPVs, GWPs, FECs):
        for n in m.keys():
            m[n].append(np.nan)

global run_number
run_number += 1
print(f'Target yield is {round(R301.target_yield, 2)}, actual yield is {round(R301.cofermentation_rxns.X[0], 2)}; ' \
      f'target titer is {R301.target_titer}, actual titer is {round(R301.effluent_titer)}.')

def save_data_clear(): df = pd.DataFrame({ ('Lactic acid','Target Yield [g/g]'): lactics['target yield'], ('Lactic acid','Target Titer [g/L]'): lactics['target titer'], ('Lactic acid','Actual Yield [g/g]'): lactics['actual yield'], ('Lactic acid','Actual Titer [g/L]'): lactics['actual titer'], ('0.89 [g/L/hr]','MPSP [$/kg]'): MPSPs[0.89], ('0.89 [g/L/hr]','NPV [$]'): NPVs[0.89], ('0.89 [g/L/hr]', 'GWP [kg CO2-eq/kg]'): GWPs[0.89], ('0.89 [g/L/hr]', 'FEC [MJ/kg]'): FECs[0.89], ('0.18 [g/L/hr]', 'MPSP [$/kg]'): MPSPs[0.18], ('0.18 [g/L/hr]', 'NPV [$]'): NPVs[0.18], ('0.18 [g/L/hr]', 'GWP [kg CO2-eq/kg]'): GWPs[0.18], ('0.18 [g/L/hr]', 'FEC [MJ/kg]'): FECs[0.18], ('1.92 [g/L/hr]', 'MPSP [$/kg]'): MPSPs[1.92], ('1.92 [g/L/hr]', 'NPV [$]'): NPVs[1.92], ('1.92 [g/L/hr]', 'GWP [kg CO2-eq/kg]'): GWPs[1.92], ('1.92 [g/L/hr]', 'FEC [MJ/kg]'): FECs[1.92] }) for i in (lactics, MPSPs, NPVs, GWPs, FECs): for j in i.keys(): i[j] = [] return df

def run_TRY(yield_range, kind, mode, feed_freq, if_resistant, titer_range): bst.speed_up() if 'SSCF' in str(kind).upper(): flowsheet = SSCF_flowsheet elif 'SHF' in str(kind).upper(): flowsheet = SHF_flowsheet bst.main_flowsheet.set_flowsheet(flowsheet)

u = flowsheet.unit
R301 = u.R301
R302 = u.R302
R401 = u.R401
S402 = u.S402
R301.mode = mode
R301.feed_freq = feed_freq
R301.allow_dilution = True
if hasattr(R301, 'allow_concentration'):
    R301.allow_concentration = True
R401.bypass = if_resistant
S402.bypass = if_resistant
for i in yield_range:
    for j in titer_range:
        lactics['target yield'].append(i)
        lactics['target titer'].append(j)
        R301.target_yield = i
        R301.target_titer = j
        set_yield(i,R301,R302)
        simulate_log_results(kind)
        if R301.effluent_titer + 2<j:
            n_remained = len(titer_range) - titer_range.index(j) - 1
            lactics['target yield'].extend([i]*n_remained)
            lactics['target titer'].extend(titer_range[titer_range.index(j)+1:])
            lactics['actual yield'].extend([i]*n_remained)
            lactics['actual titer'].extend([''] * n_remained)
            for p in (0.89,0.18,1.92):
                for m in (MPSPs,NPVs,GWPs,FECs):
                    m[p].extend(['']*n_remained)
            break
print(f'\nSimulation time is {timer.elapsed_time / 60:.1f} min for {run_number} runs.')

yield_range = np.arange(0.3,1.01,0.2) - 1e-6 yield_range = yield_range.tolist()

titer_range = np.arange(50,220,50) titer_range = titer_range.tolist()

print('\n---------- SSCF Regular Strain Batch Mode ----------') run_TRY(yield_range=yield_range, kind='SSCF', mode='batch', feed_freq=1, if_resistant=False, titer_range=titer_range) SSCF_reg_b = save_data_clear() SSCF_reg_b.to_excel('SSCF_reg_batch.xlsx')

for i in (1,): print(f'\n---------- SHF Regular Strain Batch Feed {i + 1} Times ----------') run_TRY(yield_range=yield_range, kind='SHF', mode='batch', feed_freq=i+1, if_resistant=False, titer_range=titer_range) SHF_reg_b = save_data_clear() SHF_reg_b.to_excel(f'SHF_reg_batch{i + 1}.xlsx')

print('\n---------- SHF Regular Strain Continuous ----------') run_TRY(yield_range=yield_range, kind='SHF', mode='continuous', feed_freq=1, if_resistant=False, titer_range=titer_range) SHF_reg_c = save_data_clear() SHF_reg_c.to_excel('SHF_reg_continuous.xlsx')

print('\n---------- SSCF Regular Strain Batch Mode ----------') run_TRY(yield_range=yield_range, kind='SSCF', mode='batch', feed_freq=1, if_resistant=True, titer_range=titer_range) SSCF_reg_b = save_data_clear() SSCF_reg_b.to_excel('SSCF_reg_batch.xlsx')

for i in (1,): print(f'\n---------- SHF Regular Strain Batch Feed {i} Times ----------') run_TRY(yield_range=yield_range, kind='SHF', mode='batch', feed_freq=i, if_resistant=True, titer_range=titer_range) SHF_reg_b = save_data_clear() SHF_reg_b.to_excel(f'SHF_reg_batch{i + 1}.xlsx')

print('\n---------- SHF Regular Strain Continuous ----------') run_TRY(yield_range=yield_range, kind='SHF', mode='continuous', feed_freq=1, if_resistant=True, titer_range=titer_range) SHF_reg_c = save_data_clear() SHF_reg_c.to_excel('SHF_reg_continuous.xlsx')

I'm getting the following errors (I have used Pycharm):-

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C:\Users\oshet\pythonProject\Scripts\python.exe C:\Users\oshet\AppData\Roaming\JetBrains\PyCharmCE2023.2\scratches\Fermentation.py Traceback (most recent call last): File "C:\Users\oshet\AppData\Roaming\JetBrains\PyCharmCE2023.2\scratches\Fermentation.py", line 10, in _load_system('SSCF') File "C:\Users\oshet\AppData\Local\Programs\Python\Python311\Lib\site-packages\biorefineries\lactic__init.py", line 76, in _load_system bst.settings.set_thermo(_chemicals) File "C:\Users\oshet\AppData\Local\Programs\Python\Python311\Lib\site-packages\thermosteam_settings.py", line 137, in set_thermo thermo = tmo.Thermo(thermo, mixture=mixture, cache=cache, skip_checks=skip_checks, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\oshet\AppData\Local\Programs\Python\Python311\Lib\site-packages\thermosteam_thermo.py", line 139, in init if not isinstance(chemicals, Chemicals): chemicals = Chemicals(chemicals, cache) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\oshet\AppData\Local\Programs\Python\Python311\Lib\site-packages\thermosteam_chemicals.py", line 123, in new__ chemicals = [i if isa(i, Chemical) else Chemical(i, cache=cache) for i in chemicals] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'module' object is not iterable

---

Unable to debug these errors.

[yoelcortes]

@om11kar, I will let @yalinli2 take the first look at this issue (whenever she gets a chance... she may be busy). In the mean while, could you please update your issue with the following guidelines?

1. Start code block with ```python and end with ``` (https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/creating-and-highlighting-code-blocks)
2. Clearly show return value of the code (the code must print this if I run it). You did do this by posting the full trace back, good job!
3. Clearly show expected result (what should have been printed).
4. Remove lines that do not affect the issue/result. Remove everything after line 10 load_system('SSCF')
5. Note your Python, biosteam, thermosteam, and biorefineries version. This is critical!

Thanks

[yalinli2]

Hi @om11kar , yes following Yoel's suggestions would make it much easier for us to debug. But by looking at your script, it seems that you were trying to run the old analysis codes, the module has been updated updated, the easiest way to create a model would be:

from biorefineries import lactic as la
model = la.create_model()
sys = model.system # accessing the system
flowsheet = sys.flowsheet