def create_complex_bulk_reaction(self, is_kinetic=True, k_fwd_min=1):
# Reactions
# 0: NH4+(aq) <=> NH3(aq) + H+(aq)
# 1: Lys2+(aq) <=> Lys+(aq) + H+(aq)
# 2: Lys+(aq) <=> Lys(aq) + H+(aq)
# 3: Lys(aq) <=> Lys-(aq) + H+(aq)
# 4: Arg2+ <=> Arg+ + H+
# 5: Arg+ <=> Arg + H+
# 6: Arg <=> Arg- + H+
component_system = ComponentSystem()
component_system.add_component('H+', charges=[1])
component_system.add_component(
'Ammonia', species=['NH4+', 'NH3'], charges=[1,0]
)
component_system.add_component(
'Lysine',
species=['Lys2+', 'Lys+', 'Lys', 'Lys-'],
charges=[2,1,0,-1]
)
component_system.add_component(
'Arginine',
species=['Arg2+', 'Arg+', 'Arg', 'Arg-'],
charges=[2,1,0,-1]
)
reaction_model = MassActionLaw(component_system, 'complex')
reaction_model.add_reaction(
[1, 2, 0], [-1, 1, 1], 10**(-9.2)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[3, 4, 0], [-1, 1, 1], 10**(-2.20)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[4, 5, 0], [-1, 1, 1], 10**(-8.90)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[5, 6, 0], [-1, 1, 1], 10**(-10.28)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[7, 8, 0], [-1, 1, 1], 10**(-2.18)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[8, 9, 0], [-1, 1, 1], 10**(-9.09)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
reaction_model.add_reaction(
[9, 10, 0], [-1, 1, 1], 10**(-13.2)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
return reaction_model
def setUp(self):
component_system = ComponentSystem()
component_system.add_component('A')
component_system.add_component('B')
binding_model = Langmuir(component_system, name='test')
binding_model.adsorption_rate = [0.02, 0.03]
binding_model.desorption_rate = [1, 1]
binding_model.saturation_capacity = [100, 100]
self.binding_model = binding_model
def create_simple_bulk_reaction(self, is_kinetic=True, k_fwd_min=100):
# 0: NH4+(aq) <=> NH3(aq) + H+(aq)
component_system = ComponentSystem()
component_system.add_component('H+', charges=[1])
component_system.add_component(
'Ammonia', species=['NH4+', 'NH3'], charges=[1,0]
)
reaction_model = MassActionLaw(component_system, 'simple')
reaction_model.add_reaction(
[1, 2, 0], [-1, 1, 1], 10**(-9.2)*1e3,
is_kinetic=is_kinetic, k_fwd_min=k_fwd_min
)
return reaction_model
def setUp(self):
component_system = ComponentSystem()
component_system.add_component('A')
component_system.add_component('B')
self.single_0 = MassActionLaw(component_system, name='simple')
self.single_0.add_reaction([0, 1], [-1, 1], 2, k_bwd=2)
self.single_1 = MassActionLaw(component_system, name='simple')
self.single_1.add_reaction([0, 1], [-1, 1], 1, k_bwd=1)
component_system = ComponentSystem()
component_system.add_component('A')
component_system.add_component('B')
component_system.add_component('C')
self.single_2 = MassActionLaw(n_comp=3, name='simple')
self.single_2.add_reaction([0, 1], [-1, 1], 1, k_bwd=1)
self.multi = MassActionLaw(n_comp=3, name='simple')
self.multi.add_reaction([0, 1], [-1, 1], 1, k_bwd=1)
self.multi.add_reaction([1, 2], [-1, 1], 1, k_bwd=1)
self.multi = MassActionLaw(n_comp=3, name='simple')
self.multi.add_reaction([0, 1], [-1, 1], 1, k_bwd=1)
self.multi.add_reaction([1, 2], [-1, 1], 1, k_bwd=1)
self.lysine = MassActionLaw(n_comp=5, name='Lysine')
self.lysine.add_reaction([0, 1, -1], [-1, 1, 1],
10**(-2.20) * 1e3,
is_kinetic=False)
self.lysine.add_reaction([1, 2, -1], [-1, 1, 1],
10**(-8.90) * 1e3,
is_kinetic=False)
self.lysine.add_reaction([2, 3, -1], [-1, 1, 1],
10**(-10.28) * 1e3,
is_kinetic=False)
def setUp(self):
self.component_system = ComponentSystem()
self.component_system.add_component(
'Ammonia',
species=['NH4+', 'NH3'],
charges=[1,0]
)
self.component_system.add_component(
'Lysine',
['Lys2+', 'Lys+', 'Lys', 'Lys'],
[2,1,0,-1]
)
self.component_system.add_component(
'H+',
charges=[1]
)
self.component_system.add_component()
tags:
steric mass action law
lwe
single column
gradient
"""
from CADETProcess.processModel import ComponentSystem
from CADETProcess.processModel import StericMassAction
from CADETProcess.processModel import Source, GeneralRateModel, Sink
from CADETProcess.processModel import FlowSheet
from CADETProcess.processModel import Process
# Component System
component_system = ComponentSystem()
component_system.add_component('A')
component_system.add_component('B')
# Binding Model
binding_model = StericMassAction(component_system, name='SMA')
binding_model.is_kinetic = True
binding_model.adsorption_rate = [0.0, 0.3]
binding_model.desorption_rate = [0.0, 1.5]
binding_model.characteristic_charge = [0.0, 7.0]
binding_model.steric_factor = [0.0, 50.0]
binding_model.capacity = 225.0
# Unit Operations
feed = Source(component_system, name='feed')
feed.c = [180.0, 0.1]
def create_cross_phase_reaction(self):
component_system = ComponentSystem()
component_system.add_component(
'Ammonia', species=['NH4+', 'NH3'], charges=[1,0]
)
component_system.add_component(
'Lysine',
species=['Lys2+', 'Lys+', 'Lys', 'Lys-'],
charges=[2,1,0,-1]
)
component_system.add_component('H+', charges=[1])
reaction_model = MassActionLawParticle(component_system, 'complex')
# Pore Liquid
# 0: NH4+(aq) <=> NH3(aq) + H+(aq)
# 1: Lys2+(aq) <=> Lys+(aq) + H+(aq)
# 2: Lys+(aq) <=> Lys(aq) + H+(aq)
# 3: Lys(aq) <=> Lys-(aq) + H+(aq)
reaction_model.add_liquid_reaction(
[1, 2, 0], [-1, 1, 1], 10**(-9.2)*1e3, is_kinetic=False
)
reaction_model.add_liquid_reaction(
[3, 4, 0], [-1, 1, 1], 10**(-2.20)*1e3, is_kinetic=False
)
reaction_model.add_liquid_reaction(
[4, 5, 0], [-1, 1, 1], 10**(-8.90)*1e3, is_kinetic=False
)
reaction_model.add_liquid_reaction(
[5, 6, 0], [-1, 1, 1], 10**(-10.28)*1e3, is_kinetic=False
)
# Adsorption
k_fwd_min_ads = 100
# 0: NH4+(aq) + H+(s) <=> NH4+(s) + H+(aq)
# 1: NH4+(s) <=> NH3(aq) + H+(s)
reaction_model.add_cross_phase_reaction(
[1, 0, 1, 0], [-1, -1, 1, 1], [0, 1, 1, 0], 1/1.5,
k_fwd_min=k_fwd_min_ads
)
reaction_model.add_cross_phase_reaction(
[1, 2, 0], [-1, 1, 1], [1, 0, 1], 1.5, k_fwd_min=k_fwd_min_ads
)
# 2: Lys2+(aq) + 2H+(s) <=> Lys2+(s) + 2H+(aq)
# 3: Lys2+(s) <=> Lys+(aq) + H+(s)
reaction_model.add_cross_phase_reaction(
[3, 0, 3, 0], [-1, -2, 1, 2], [0, 1, 1, 0], 1/5,
k_fwd_min=k_fwd_min_ads
)
reaction_model.add_cross_phase_reaction(
[3, 2, 0], [-1, 1, 1], [1, 0, 1], 5,
k_fwd_min=k_fwd_min_ads
)
# 4: Lys+(aq) + H+(s) <=> Lys+(s) + H+(aq)
# 5: Lys+(s) <=> Lys(aq) + H+(s)
reaction_model.add_cross_phase_reaction(
[4, 0, 4, 0], [-1, -1, 1, 1], [0, 1, 1, 0], 1/0.75,
k_fwd_min=k_fwd_min_ads
)
reaction_model.add_cross_phase_reaction(
[4, 5, 0], [-1, 1, 1], [1, 0, 1], 0.75,
k_fwd_min=k_fwd_min_ads
)
return reaction_model
def setUp(self):
self.component_system = ComponentSystem()
self.component_system.add_component('A')
self.component_system.add_component('B')