Hello everyone, I have a question about correctly setting section and connections which are consistent to settings for concentration dynamic.
The situation is: 4 steps are involved in the simulation.
(1) Protein loading for 32 s. (Protein concentration 0.0115 mM in 20 mM salt)
(2) Step wash starts after and for 365s. (Salt buffer 25 mM)
(3) Gradient wash starts after 954 s from 20 mM salt to 1020 mM salt
(4)A high salt push step starts after 1247 s with 1020 mM salt.
In my following code support by my previous post, it seems like in this setting, the protein is continuously injected, however, this is not what I want. But if I used my previous setting, the simulation always fails. Can anyone please help on how should I correctly define the sections and switches and connections?
wash_start = 32 # s
grad_start = wash_start + 365 # s
HighSalt_start = grad_start + 954 # s
t_end = HighSalt_start + 1247 # s
# Volumetric flow rate
vol_flow_rate = 1.6e-8 # m3/s
# Salt inlet concentration
salt_initial_concentration = 20 # mM
salt_final_concentration = 1020 # mM
# Lysozyme feed concentration
protein_initial_concentration = 0.0115 # mM
# Column dimensions (in meters)
column_dia = 0.007 # m
bed_height = 0.025 # m
lwe_model = get_cadet_template(n_units=5)
# Sections and Switches
lwe_model.root.input.solver.sections.nsec = 4
lwe_model.root.input.solver.sections.section_times = [0.0, wash_start, grad_start, HighSalt_start, t_end]
lwe_model.root.input.model.unit_000.sec_000.const_coeff = [salt_initial_concentration, 0]
lwe_model.root.input.model.unit_000.sec_001.const_coeff = [salt_initial_concentration, 0]
lwe_model.root.input.model.unit_000.sec_002.const_coeff = [salt_initial_concentration, 0.0]
lwe_model.root.input.model.unit_000.sec_002.lin_coeff = [1.05,0.0]
lwe_model.root.input.model.unit_000.sec_003.const_coeff = [salt_final_concentration,0]
lwe_model.root.input.model.unit_001.sec_000.const_coeff = [salt_initial_concentration, protein_initial_concentration]
# Set the times that the simulator writes out data for
lwe_model.root.input.solver.user_solution_times = np.linspace(0, t_end, int(t_end) + 1)
# System of Unit Operations
n_comp = 2
#Feed
lwe_model.root.input.model.unit_000.unit_type = 'INLET'
lwe_model.root.input.model.unit_000.ncomp = 1
lwe_model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
#Inlet
lwe_model.root.input.model.unit_001.unit_type = 'INLET'
lwe_model.root.input.model.unit_001.ncomp = n_comp
lwe_model.root.input.model.unit_001.inlet_type = 'PIECEWISE_CUBIC_POLY'
#Mixer
lwe_model.root.input.model.unit_002.unit_type = 'CSTR'
lwe_model.root.input.model.unit_002.ncomp = n_comp
lwe_model.root.input.model.unit_002.init_volume = 5e-7
lwe_model.root.input.model.unit_002.init_c = n_comp*[0]
#Column Chromatogaphy Model
lwe_model.root.input.model.unit_003.unit_type = 'GENERAL_RATE_MODEL'
lwe_model.root.input.model.unit_003.ncomp = n_comp
# Column parameters
lwe_model.root.input.model.unit_003.col_length = bed_height
lwe_model.root.input.model.unit_003.cross_section_area = 3.142*((column_dia/2)**2)
lwe_model.root.input.model.unit_003.col_porosity = 0.268
lwe_model.root.input.model.unit_003.par_porosity = 0.827
lwe_model.root.input.model.unit_003.par_radius = 4.5e-5
lwe_model.root.input.model.unit_003.col_dispersion = 3.73e-7
lwe_model.root.input.model.unit_003.film_diffusion = [1.0E-5, 1.0E-5]
lwe_model.root.input.model.unit_003.par_diffusion = [6e-11, 8e-12]
lwe_model.root.input.model.unit_003.par_surfdiffusion = [0.0, 1e-10]
## OUTLET
lwe_model.root.input.model.unit_004.unit_type = 'OUTLET'
lwe_model.root.input.model.unit_004.ncomp = n_comp
## Discretization
set_discretization(lwe_model, n_bound=[0,1])
# Connections
lwe_model.root.input.model.connections.nswitches = 2
lwe_model.root.input.model.connections.switch_000.section = 0
lwe_model.root.input.model.connections.switch_000.connections = [0, 2, 0, 0, vol_flow_rate,
2, 3, -1, -1, vol_flow_rate,
3, 4, -1, -1, vol_flow_rate]
lwe_model.root.input.model.connections.switch_001.section = 1
lwe_model.root.input.model.connections.switch_001.connections = [1, 2, -1, -1, vol_flow_rate,
2, 3, -1, -1, vol_flow_rate,
3, 4, -1, -1, vol_flow_rate]
adsorption_model = "MULTI_COMPONENT_COLLOIDAL"
adsorption_parameters = Dict()
# Vijesh's model parameters for Bpp
adsorption_parameters.col_bpp_ph_exp = [0.0, 0.0]
adsorption_parameters.col_bpp_salt_expargmult = [0.0, 0.0]
adsorption_parameters.col_bpp_salt_expfact = [0.0, 0.2625]
adsorption_parameters.col_bpp_salt_powexp = [0.0, -2.252]
adsorption_parameters.col_bpp_salt_powfact = [0.0, 37220.0]
adsorption_parameters.col_cordnum = 6.0 # hexagonal packing
adsorption_parameters.col_kappa_const = 2.5 # nm
adsorption_parameters.col_kappa_exp = 0.0
adsorption_parameters.col_kappa_fact = 0.0
adsorption_parameters.col_kkin = [1.0e10, 1.0e10] # e6 to e12 for instant equilibration; 0.1-0.9 for kinetic effects -- doesn't work though
adsorption_parameters.col_linear_threshold = 1.0e-7
# Vijesh's model parameters for Keq
adsorption_parameters.col_logkeq_ph_exp = [0.0, 0.0]
adsorption_parameters.col_logkeq_salt_expargmult = [0.0, 0.0]
adsorption_parameters.col_logkeq_salt_expfact = [0.0, -3.929]
adsorption_parameters.col_logkeq_salt_powexp = [0.0, 1.715]
adsorption_parameters.col_logkeq_salt_powfact = [0.0, 53430.0]
adsorption_parameters.col_phi = 4.923e7 # m2 / m3
adsorption_parameters.col_radius = [1.59e-9, 4.5e-9] # make nonzero
adsorption_parameters.col_use_ph = False
adsorption_parameters.is_kinetic = True
lwe_model.root.input.model.unit_003.adsorption_model = adsorption_model
lwe_model.root.input.model.unit_003.adsorption = adsorption_parameters
lwe_model.root.input.model.unit_003.init_c = [salt_initial_concentration, 0]
lwe_model.root.input.model.unit_003.init_q = [0, 0.0]
run_simulation(lwe_model)