Expected behavior.
Hello! Flynn shared with me his version of cadet core that was allowing him to run a two component simulation with the ACT isotherm. Since Im using cadet-process and hes using a more advanced version (6.x.x) that is nor supported by cadet-process, there are incompatibilities that dont allow the code to run and there are a lot of errors that I dont know how to fix. Im not super familiar with all the proper terminology, so Im sorry if this sounds confusing. But I would really appreciate if someone could help me and let me know what more information I need to share in order to get help. Here is the initial thread An example to use ACT isotherm for protein A affinity chromatography - #56 by Flynn
Thanks a lot in advance 
I share below the code I would like to run and the new environment I created with the changes Flynn shared with me.
Actual behavior
Error message: CADETProcessError: CADET Error: Simulation failed with IO ERROR: Group ‘/input/model/unit_001/particle_type_000’ doesn’t exist in file
How to produce bug (including a minimal reproducible example)
import numpy as np
from CADETProcess.processModel import (
ComponentSystem, Inlet, GeneralRateModel, Outlet, FlowSheet, Process,
AffinityComplexTitration
)
from CADETProcess.simulator import Cadet
cs = ComponentSystem()
cs.add_component("pH")
cs.add_component("Main Peak")
cs.add_component("Far BV")
act = AffinityComplexTitration(cs, name="ACT")
act.is_kinetic = 0
act.bound_states = [0, 1, 1]
protein_MW = 100 #kDa
act.adsorption_rate = [1.0, (80 * protein_MW) * (1-0.945), (80 * protein_MW) * (1-0.945)] # ka [m^3/mol/s] (fit later)
act.desorption_rate = [1.0, 1, 1 ] # kd [1/s] (fit later; pH=1.0 to avoid zero issues)
act.capacity = [1e-10, (50 / protein_MW) / (1-0.945), (50 / protein_MW) / (1-0.945)] # qmax [mol/m^3 solid] (kept fixed in fitting if desired)
act.eta_a = [0.0, 1.16, 1]
act.pka_a = [0.0, 5.25, 4.5]
act.eta_g = [0.0, 0.88, 0.9]
act.pka_g = [0.0, 4.14, 3.5]
print("ACT param check:", act.check_required_parameters())
inlet = Inlet(cs, name="inlet")
inlet.flow_rate = 2.3e-8 # m^3/s
col = GeneralRateModel(cs, name="column")
col.binding_model = act
col.length = 0.204 # m
col.diameter = 0.0066 # m
col.bed_porosity = 0.44
col.particle_radius = 5e-5
col.particle_porosity = 0.902
col.axial_dispersion = 1.4e-08 #m2/s
col.film_diffusion = [1, 1.4e-05, 1.4e-05] # m/s
col.pore_diffusion = [1, 2e-11, 2e-11 ] #m2/s
col.surface_diffusion = [0, 0]
# initial concentrations
col.c = [7.0, 0.0, 0.0]
col.cp = [7.0, 0.0, 0.0]
outlet = Outlet(cs, name="outlet")
# ===================== Flow sheet ============================================
fs = FlowSheet(cs)
fs.add_unit(inlet); fs.add_unit(col); fs.add_unit(outlet, product_outlet=True)
fs.add_connection(inlet, col)
fs.add_connection(col, outlet)
# ===================== Process & Events (load → wash → pH gradient) ===========
process = Process(fs, 'mp_act_sim')
process.cycle_time = 260.0 * 60.0 # total [s]
load_duration = 42 * 60 # [s]
t_gradient_start = 100 * 60 # [s]
gradient_duration = process.cycle_time - t_gradient_start
t_strip = 120 *60
MP_load = (3.6 * 0.35 / 100615.0) * 1e3
fBV_load = (3.6 * 0.30 / 100615.0) * 1e3
c_load = np.array([7.00, MP_load, fBV_load])
c_wash = np.array([5.6, 0.0, 0.0])
c_elute = np.array([3.34, 0.0, 0.0])
gradient_slope = (c_elute - c_wash) / gradient_duration
c_gradient_poly = np.array(list(zip(c_wash, gradient_slope))) # shape (2,2)
process.add_event('load', 'flow_sheet.inlet.c', c_load)
process.add_event('wash', 'flow_sheet.inlet.c', c_wash, load_duration)
process.add_event('grad_start', 'flow_sheet.inlet.c', c_gradient_poly, t_gradient_start)
from CADETProcess.simulator import Cadet
# === Run ACT simulation (using the process you built above) ===
if __name__ == '__main__':
from CADETProcess.simulator import Cadet
process_simulator = Cadet()
process_simulator.install_path = r"C:\Users\InesSilva\anaconda3\envs\cadet_"
simulation_results = process_simulator.simulate(process)
from CADETProcess.plotting import SecondaryAxis
sec = SecondaryAxis()
sec.components = ['pH']
sec.y_label = '$c_{pH}$'
simulation_results.solution.column.outlet.plot(secondary_axis=sec)
File produced by conda env export > environment.yml
cadet_.yml (7.34 KB)