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Merge pull request #109 from QSD-Group/beta
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Changes to allow customized properties and impact item creation
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@yalinli2
yalinli2 authored Oct 13, 2023
2 parents 946bf48 + dece5c5 commit 411e65c
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Showing 10 changed files with 920 additions and 38 deletions.
23 changes: 13 additions & 10 deletions qsdsan/_component.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,10 @@ def __new__(cls, ID, search_ID=None, formula=None, phase=None, measured_as=None,
self._chem_MW = molecular_weight(self.atoms)
if phase: lock_phase(self, phase)

self._particle_size = particle_size
self._degradability = degradability
self._organic = organic
self.description = description
self._measured_as = measured_as
self.i_mass = i_mass
self.i_C = i_C
Expand All @@ -245,10 +249,7 @@ def __new__(cls, ID, search_ID=None, formula=None, phase=None, measured_as=None,
self.f_BOD5_COD = f_BOD5_COD
self.f_uBOD_COD = f_uBOD_COD
self.f_Vmass_Totmass = f_Vmass_Totmass
self._particle_size = particle_size
self._degradability = degradability
self._organic = organic
self.description = description

if not self.MW and not self.formula: self.MW = 1.
self.i_COD = i_COD
self.i_NOD = i_NOD
Expand Down Expand Up @@ -340,7 +341,8 @@ def i_mass(self, i):
chem_charge = charge_from_formula(self.formula)
Cr2O7 = - cod_test_stoichiometry(self.atoms, chem_charge)['Cr2O7-2']
cod = Cr2O7 * 1.5 * molecular_weight({'O':2})
i = self.chem_MW/cod
try: i = self.chem_MW/cod
except: breakpoint()
elif self.measured_as:
raise AttributeError(f'Must specify i_mass for component {self.ID} '
f'measured as {self.measured_as}.')
Expand Down Expand Up @@ -532,7 +534,7 @@ def i_COD(self):
def i_COD(self, i):
if i is not None: self._i_COD = check_return_property('i_COD', i)
else:
if self.organic or self.formula in ('H2', 'O2', 'N2', 'NO2-', 'NO3-'):
if self.organic or self.formula in ('H2', 'O2', 'N2', 'NO2-', 'NO3-', 'H2S', 'S'):
if self.measured_as == 'COD': self._i_COD = 1.
elif not self.atoms:
raise AttributeError(f"Must specify `i_COD` for organic component {self.ID}, "
Expand Down Expand Up @@ -792,6 +794,10 @@ def from_chemical(cls, ID, chemical=None, formula=None, phase=None, measured_as=
new.Tm, new.Tb, new.eos, new.phase_ref, new.S0)
TDependentProperty.RAISE_PROPERTY_CALCULATION_ERROR = True

new.description = description
new._particle_size = particle_size
new._degradability = degradability
new._organic = organic
new._measured_as = measured_as
new.i_mass = i_mass
new.i_C = i_C
Expand All @@ -804,10 +810,7 @@ def from_chemical(cls, ID, chemical=None, formula=None, phase=None, measured_as=
new.f_BOD5_COD = f_BOD5_COD
new.f_uBOD_COD = f_uBOD_COD
new.f_Vmass_Totmass = f_Vmass_Totmass
new.description = description
new._particle_size = particle_size
new._degradability = degradability
new._organic = organic

new.i_COD = i_COD
new.i_NOD = i_NOD
return new
11 changes: 8 additions & 3 deletions qsdsan/_impact_item.py
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Original file line number Diff line number Diff line change
Expand Up @@ -383,8 +383,12 @@ def get_item(cls, ID):
@classmethod
def _load_from_df(cls, name, df):
if name.lower() == 'info':
if 'kind' not in df.columns: df['kind'] = 'ImpactItem'
for num in df.index:
new = cls.__new__(cls)
kind = df.iloc[num].kind.lower()
if kind == 'streamimpactitem':
new = StreamImpactItem.__new__(StreamImpactItem)
else: new = cls.__new__(cls)
new.__init__(ID=df.iloc[num].ID,
functional_unit=df.iloc[num].functional_unit)
else:
Expand All @@ -409,8 +413,9 @@ def load_from_file(cls, path_or_dict, index_col=None):
This Excel should have multiple sheets:
- The "info" sheet should have two columns: "ID" (e.g., Cement) \
and "functional_unit" (e.g., kg) of different impact items.
- The "info" sheet should have three columns: "ID" (e.g., Cement) \
"functional_unit" (e.g., kg), and "kind" ("ImpactItem" or "StreamImpactItem")
of different impact items.
- The remaining sheets should contain characterization factors of \
impact indicators.
Expand Down
5 changes: 3 additions & 2 deletions qsdsan/_process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -706,8 +706,9 @@ def _normalize_stoichiometry(self, new_ref):
self._stoichiometry = [v/factor for v in stoich]

def _normalize_rate_eq(self, new_ref):
factor = abs(self._stoichiometry[self._components.index(str(new_ref))])
self._rate_equation *= factor
if self._rate_equation:
factor = abs(self._stoichiometry[self._components.index(str(new_ref))])
self._rate_equation *= factor

def show(self):
info = f"Process: {self.ID}"
Expand Down
35 changes: 26 additions & 9 deletions qsdsan/_waste_stream.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,12 +40,13 @@
_defined_composite_vars = ('COD', 'BOD5', 'BOD', 'uBOD', 'NOD', 'ThOD', 'cnBOD',
'C', 'N', 'P', 'K', 'Mg', 'Ca', 'solids', 'charge')

_common_composite_vars = ('_COD', '_BOD', '_uBOD', '_TC', '_TOC', '_TN',
_common_composite_vars = ('_COD', '_BOD', '_uBOD', '_ThOD', '_cnBOD',
'_TC', '_TOC', '_TN',
'_TKN', '_TP', '_TK', '_TMg', '_TCa',
'_dry_mass', '_charge', '_ThOD', '_cnBOD')
'_dry_mass', '_charge',)

_ws_specific_slots = (*_common_composite_vars,
'_pH', '_SAlk', '_ratios',
'_pH', '_SAlk', '_ratios', 'additional_properties',
# '_stream_impact_item', (pls keep this here, might be useful in debugging)
'_state', '_dstate', '_scope')

Expand Down Expand Up @@ -249,7 +250,9 @@ class WasteStream(SanStream):
TO BE IMPLEMENTED
stream_impact_item : :class:`StreamImpactItem`
The :class:`StreamImpactItem` this stream is linked to.
component_flows : kwargs
additional_properties : dict
Additional properties (e.g., turbidity).
component_flows : dict
Component flow data.
Expand All @@ -271,20 +274,28 @@ def __init__(self, ID='', flow=(), phase='l', T=298.15, P=101325.,
pH=7., SAlk=2.5, COD=None, BOD=None, uBOD=None,
ThOD=None, cnBOD=None,
TC=None, TOC=None, TN=None, TKN=None, TP=None, TK=None,
TMg=None, TCa=None, dry_mass=None, charge=None, ratios=None,
stream_impact_item=None, **component_flows):
TMg=None, TCa=None,
dry_mass=None, charge=None, ratios=None,
stream_impact_item=None, additional_properties={},
**component_flows):
SanStream.__init__(self=self, ID=ID, flow=flow, phase=phase, T=T, P=P,
units=units, price=price, thermo=thermo,
stream_impact_item=stream_impact_item, **component_flows)

self._init_ws(pH, SAlk, COD, BOD, uBOD, TC, TOC, TN, TKN,
TP, TK, TMg, TCa, ThOD, cnBOD, dry_mass, charge, ratios)
self._init_ws(pH=pH, SAlk=SAlk, COD=COD, BOD=BOD, uBOD=uBOD,
ThOD=ThOD, cnBOD=cnBOD,
TC=TC, TOC=TOC, TN=TN, TKN=TKN,
TP=TP, TK=TK, TMg=TMg, TCa=TCa,
dry_mass=dry_mass, charge=charge, ratios=ratios,
additional_properties=additional_properties,
)

def _init_ws(self, pH=7., SAlk=None, COD=None, BOD=None,
uBOD=None, ThOD=None, cnBOD=None,
TC=None, TOC=None, TN=None, TKN=None,
TP=None, TK=None, TMg=None, TCa=None,
dry_mass=None, charge=None, ratios=None):
dry_mass=None, charge=None, ratios=None,
additional_properties={}):

self._pH = pH
self._SAlk = SAlk
Expand All @@ -306,6 +317,7 @@ def _init_ws(self, pH=7., SAlk=None, COD=None, BOD=None,
self._ratios = ratios
self._state = None
self._dstate = None
self.additional_properties = {}

@staticmethod
def from_stream(stream, ID='', **kwargs):
Expand Down Expand Up @@ -2241,6 +2253,11 @@ def dry_mass(self):
def density(self):
'''[float] Density of the stream, in mg/L (kg/m3).'''
return 0.

@property
def additional_property(self):
'''[dict] Additional properties (e.g., turbidity).'''
return {}

#!!! Keep this up-to-date with WasteStream
# @property
Expand Down
47 changes: 47 additions & 0 deletions qsdsan/data/process_data/_madm1.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
S_su S_aa S_fa S_va S_bu S_pro S_ac S_h2 S_ch4 S_IC S_IN S_IP S_I X_ch X_pr X_li X_su X_aa X_fa X_c4 X_pro X_ac X_h2 X_I X_PHA X_PP X_PAO S_K S_Mg S_SO4 S_IS X_hSRB X_aSRB X_pSRB X_c4SRB S_S0 S_Fe3 S_Fe2 X_HFO_H X_HFO_L X_HFO_old X_HFO_HP X_HFO_LP X_HFO_HP_old X_HFO_LP_old
hydrolysis_carbs 1 ? ? ? -1
hydrolysis_proteins 1 ? ? ? -1
hydrolysis_lipids 1-f_fa_li f_fa_li ? ? ? -1
uptake_sugars -1 (1-Y_su)*f_bu_su (1-Y_su)*f_pro_su (1-Y_su)*f_ac_su (1-Y_su)*f_h2_su ? ? ? Y_su
uptake_amino_acids -1 (1-Y_aa)*f_va_aa (1-Y_aa)*f_bu_aa (1-Y_aa)*f_pro_aa (1-Y_aa)*f_ac_aa (1-Y_aa)*f_h2_aa ? ? ? Y_aa
uptake_LCFA -1 (1-Y_fa)*f_ac_fa (1-Y_fa)*f_h2_fa ? ? ? Y_fa
uptake_valerate -1 (1-Y_c4)*f_pro_va (1-Y_c4)*f_ac_va (1-Y_c4)*f_h2_va ? ? ? Y_c4
uptake_butyrate -1 (1-Y_c4)*f_ac_bu (1-Y_c4)*f_h2_bu ? ? ? Y_c4
uptake_propionate -1 (1-Y_pro)*f_ac_pro (1-Y_pro)*f_h2_pro ? ? ? Y_pro
uptake_acetate -1 1-Y_ac ? ? ? Y_ac
uptake_h2 -1 1-Y_h2 ? ? ? Y_h2
decay_Xsu ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xaa ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xfa ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xc4 ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xpro ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xac ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
decay_Xh2 ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb -1 f_xI_xb
storage_PHA_valerate -1 ? ? ? 1 -Y_PO4 Y_PO4*K_XPP Y_PO4*Mg_XPP
storage_PHA_butyrate -1 ? ? ? 1 -Y_PO4 Y_PO4*K_XPP Y_PO4*Mg_XPP
storage_PHA_propionate -1 ? ? ? 1 -Y_PO4 Y_PO4*K_XPP Y_PO4*Mg_XPP
storage_PHA_actate -1 ? ? ? 1 -Y_PO4 Y_PO4*K_XPP Y_PO4*Mg_XPP
lysis_XPAO ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb f_xI_xb -1
lysis_XPP ? ? ? -1 K_XPP Mg_XPP
lysis_XPHA f_va_pha f_bu_pha f_pro_pha f_ac_pha ? ? ? -1
growth_SRB_h2 -1 ? ? ? -1*(1-Y_hSRB)*i_mass_IS*(MW_S0/MW_IS) 1-Y_hSRB Y_hSRB
decay_XhSRB ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb f_xI_xb -1
growth_SRB_acetate -1 ? ? ? -1*(1-Y_aSRB)*i_mass_IS*(MW_S0/MW_IS) 1-Y_aSRB Y_aSRB
decay_XaSRB ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb f_xI_xb -1
growth_SRB_propionate -1 (1-Y_pSRB)*f_ac_pro ? ? ? -1*(1-Y_pSRB)*f_is_pro*i_mass_IS*(MW_S0/MW_IS) (1-Y_pSRB)*f_is_pro Y_pSRB
decay_XpSRB ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb f_xI_xb -1
growth_SRB_butyrate -1 (1-Y_c4SRB)*f_ac_bu ? ? ? -1*(1-Y_c4SRB)*f_is_bu*i_mass_IS*(MW_S0/MW_IS) (1-Y_c4SRB)*f_is_bu Y_c4SRB
growth_SRB_valerate -1 (1-Y_c4SRB)*f_pro_va (1-Y_c4SRB)*f_ac_va ? ? ? -1*(1-Y_c4SRB)*f_is_va*i_mass_IS*(MW_S0/MW_IS) (1-Y_c4SRB)*f_is_va Y_c4SRB
decay_Xc4SRB ? ? ? f_sI_xb f_ch_xb f_pr_xb f_li_xb f_xI_xb -1
reduction_HFO_H_h2 -1 1 -1*i_mass_Fe2
reduction_HFO_L_h2 -1 1 -1*i_mass_Fe2
reduction_HFO_H_IS -1 (MW_S0/i_mass_S0)/(MW_IS/i_mass_IS) 1-(MW_S0/i_mass_S0)/(MW_IS/i_mass_IS) i_mass_Fe2*((MW_S0/i_mass_S0)/(MW_IS/i_mass_IS)-1)
reduction_HFO_L_IS -1 (MW_S0/i_mass_S0)/(MW_IS/i_mass_IS) 1-(MW_S0/i_mass_S0)/(MW_IS/i_mass_IS) i_mass_Fe2*((MW_S0/i_mass_S0)/(MW_IS/i_mass_IS)-1)
aging_HFO_H -1 1
aging_HFO_L -1 1
fast_P_binding ? -1 1
slow_P_sorption ? -1 1
aging_HFO_HP -1 1
aging_HFO_LP -1 1
dissolution_HFO_HP ? 1 -1
dissolution_HFO_LP ? 1 -1
3 changes: 3 additions & 0 deletions qsdsan/processes/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
from ._asm1 import *
from ._asm2d import *
from ._adm1 import *
from ._madm1 import *
from ._decay import *
from ._kinetic_reaction import *
from ._pm2 import *
Expand All @@ -26,6 +27,7 @@
_asm1,
_asm2d,
_adm1,
_madm1,
_decay,
_kinetic_reaction,
)
Expand All @@ -35,6 +37,7 @@
*_asm1.__all__,
*_asm2d.__all__,
*_adm1.__all__,
*_madm1.__all__,
*_decay.__all__,
*_kinetic_reaction.__all__,
*_pm2.__all__,
Expand Down
27 changes: 22 additions & 5 deletions qsdsan/processes/_adm1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,6 +190,9 @@ def mass2mol_conversion(cmps):
# return np.exp(theta * (T2-T1))

def T_correction_factor(T1, T2, delta_H):
"""compute temperature correction factor for equilibrium constants based on
the Van't Holf equation."""
if T1 == T2: return 1
return np.exp(delta_H/(R*100) * (1/T1 - 1/T2)) # R converted to SI

# def calc_Kas(pKas, T_base, T_op, theta):
Expand Down Expand Up @@ -267,10 +270,24 @@ def rhos_adm1(state_arr, params):
weak_acids = cmps_in_M[[24, 25, 10, 9, 6, 5, 4, 3]]

T_op = state_arr[-1]
if T_op == T_base:
Ka = Kab
KH = KHb / unit_conversion[7:10]
else:
T_temp = params.pop('T_op', None)
if T_op == T_temp:
params['T_op'] = T_op
Ka = params['Ka']
KH = params['KH']
else:
params['T_op'] = T_op
Ka = params['Ka'] = Kab * T_correction_factor(T_base, T_op, Ka_dH)
KH = params['KH'] = KHb * T_correction_factor(T_base, T_op, KH_dH) / unit_conversion[7:10]

biogas_S = state_arr[7:10].copy()
biogas_p = R * T_op * state_arr[27:30]
Kas = Kab * T_correction_factor(T_base, T_op, Ka_dH)
KH = KHb * T_correction_factor(T_base, T_op, KH_dH) / unit_conversion[7:10]
# Kas = Kab * T_correction_factor(T_base, T_op, Ka_dH)
# KH = KHb * T_correction_factor(T_base, T_op, KH_dH) / unit_conversion[7:10]

rhos[:-3] = ks * Cs
Monod = substr_inhibit(substrates, Ks)
Expand All @@ -279,12 +296,12 @@ def rhos_adm1(state_arr, params):
if S_bu > 0: rhos[8] *= 1/(1+S_va/S_bu)

h = brenth(acid_base_rxn, 1e-14, 1.0,
args=(weak_acids, Kas),
args=(weak_acids, Ka),
xtol=1e-12, maxiter=100)
# h = 10**(-7.46)

nh3 = Kas[1] * weak_acids[2] / (Kas[1] + h)
co2 = weak_acids[3] - Kas[2] * weak_acids[3] / (Kas[2] + h)
nh3 = Ka[1] * weak_acids[2] / (Ka[1] + h)
co2 = weak_acids[3] - Ka[2] * weak_acids[3] / (Ka[2] + h)
biogas_S[-1] = co2 / unit_conversion[9]

Iph = Hill_inhibit(h, pH_ULs, pH_LLs)
Expand Down
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