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Paper_settings.py
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# -*- coding: utf-8 -*-
"""
Created March 2023
This script defines model settings considered in
"Spatial discontinuous Galerkin spectral element method in CADET"
published in computers and chemical engineering, 2023.
@author: Jan Michael Breuer
"""
import convergence
from cadet import Cadet
import numpy as np
from matplotlib import pyplot as plt
# =============================================================================
# All simulations should be saved for the evaluation!
#
# Naming of files follows the logic: prefix + "_" + transport model + "_" +
# binding model + "_" + nComp + "_" + siscretization
# Example: heyho_GRMsurfDiff_reqLinear_1Comp_DG_P3Z5parP4Z1.h5
# =============================================================================
def GRMlinear1Comp_VerificationSetting(
method_=0, colCells_=5,
parMethod_=0, parCells_=1,
isKinetic_=True, surfDiff=False,
tolerance=1e-12,
plot_=False, run_=True,
save_path="C:/Users/jmbr/JupyterNotebooks/",
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe"
):
Cadet.cadet_path = cadet_path
# =========================================================================
# PARAMETERS
# =========================================================================
velocity = 5.75E-4 # m / s
film_diffusion = 6.9e-6 # m / s
length = 0.014 # m
adsorption = 3.55 # m^3 / (mol * s) (mobile phase)
desorption = 0.1 # 1 / s (desorption)
isKinetic = isKinetic_
D_ax = 5.75e-8 # m^2 / s (interstitial volume)
par_diffusion = 6.07E-11
if(surfDiff):
par_surfdiffusion = 1.0E-11
else:
par_surfdiffusion = 0.0
porosity = 0.37
par_porosity = 0.75
par_radius = 4.5e-5 # m
inlet = 1.0 # mol / m^3 = (1/1000) mol / liter
t_end = 1500 # s
solution_times_factor = 4
idas_tolerance = tolerance
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 3
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
# [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
0, 1, -1, -1, 60/1e6,
1, 2, -1, -1, 60/1e6]
model.root.input.solver.sections.nsec = 2
model.root.input.solver.sections.section_times = [0.0, 10, t_end]
model.root.input.solver.sections.section_continuity = [0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
model.root.input.solver.nthreads = 1
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = idas_tolerance
model.root.input.solver.time_integrator.algtol = idas_tolerance*100
model.root.input.solver.time_integrator.reltol = idas_tolerance*100
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 1000000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_000.unit_type = 'INLET'
model.root.input.model.unit_000.ncomp = 1
model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
model.root.input.model.unit_000.sec_000.const_coeff = [
inlet,] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_000.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.cube_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.const_coeff = [
0.0,] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_001.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.cube_coeff = [0.0,]
# UNIT OPERATIONS - MODEL
if(method_ == 0):
model.root.input.model.unit_001.unit_type = 'GENERAL_RATE_MODEL'
else:
model.root.input.model.unit_001.unit_type = 'GENERAL_RATE_MODEL_DG'
model.root.input.model.unit_001.ncomp = 1
model.root.input.model.unit_001.adsorption_model = 'LINEAR'
model.root.input.model.unit_001.adsorption_model_multiplex = 1
# NO REACTIONS
model.root.input.model.unit_001.adsorption.is_kinetic = isKinetic
model.root.input.model.unit_001.adsorption.lin_ka = [
adsorption,] # m^3 / (mol * s) (mobile phase)
model.root.input.model.unit_001.adsorption.lin_kd = [
desorption,] # 1 / s (desorption)
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_c = [0.0,]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_cp = [0.0,]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_q = [0.0,]
model.root.input.model.unit_001.col_dispersion = D_ax
model.root.input.model.unit_001.col_length = length
model.root.input.model.unit_001.col_porosity = porosity
model.root.input.model.unit_001.film_diffusion = film_diffusion
model.root.input.model.unit_001.film_diffusion_multiplex = 0
model.root.input.model.unit_001.par_porosity = par_porosity
model.root.input.model.unit_001.par_radius = par_radius
model.root.input.model.unit_001.par_coreradius = 0.0
model.root.input.model.unit_001.par_diffusion = par_diffusion
model.root.input.model.unit_001.PAR_SURFDIFFUSION = par_surfdiffusion
model.root.input.model.unit_001.velocity = velocity
model.root.input.model.unit_001.par_type_volfrac = 1
# Discretization
model.root.input.model.unit_001.discretization.ncol = colCells_
model.root.input.model.unit_001.discretization.npartype = 1
if(method_ == 0):
model.root.input.model.unit_001.discretization.npar = parCells_
else:
model.root.input.model.unit_001.discretization.polyDeg = abs(
int(method_)) # polynomial degree
model.root.input.model.unit_001.discretization.exact_integration = 0 if method_ > 0 else 1
model.root.input.model.unit_001.discretization.parPolyDeg = abs(
int(parMethod_)) # polynomial degree
model.root.input.model.unit_001.discretization.nparcell = parCells_
model.root.input.model.unit_001.discretization.par_exact_integration = 1 if parMethod_ > 0 else 0
model.root.input.model.unit_001.discretization.nbound = [1]
model.root.input.model.unit_001.discretization.par_geom = [
"SPHERE"] # particle geometry (sphere, cylinder, slab)
model.root.input.model.unit_001.discretization.par_disc_type = [
"EQUIDISTANT_PAR"] # EQUIDISTANT_PAR, EQUIVOLUME_PAR, USER_DEFINED_PAR
model.root.input.model.unit_001.discretization.par_boundary_order = 2
model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
model.root.input.model.unit_001.discretization.gs_type = 0
model.root.input.model.unit_001.discretization.max_krylov = 10
model.root.input.model.unit_001.discretization.max_restarts = 100
model.root.input.model.unit_001.discretization.schur_safety = 0.1
model.root.input.model.unit_001.discretization.weno.boundary_model = 0
model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10
model.root.input.model.unit_001.discretization.weno.weno_order = 3
# UNIT OPERATIONS - OUTLET
model.root.input.model.unit_002.unit_type = 'OUTLET'
model.root.input.model.unit_002.ncomp = 1
# RETURN DATA
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].unit_000.write_solution_bulk = 0
model.root.input['return'].unit_000.write_solution_inlet = 0
model.root.input['return'].unit_000.write_solution_outlet = 0
model.root.input['return'].unit_001.write_solution_bulk = 0
model.root.input['return'].unit_001.write_solution_inlet = 0
model.root.input['return'].unit_001.write_solution_particle = 0
model.root.input['return'].unit_001.write_solution_outlet = 1
model.root.input['return'].unit_001.WRITE_COORDINATES = 0
# Copy inlet return settings to the outlet unit operation
model.root.input['return'].unit_002 = model.root.input['return'].unit_000
# Solution times
model.root.input.solver.user_solution_times = np.linspace(
0, t_end, t_end*solution_times_factor + 1)
prefix = save_path+"GRM"
if surfDiff:
prefix += "sd"
prefix += "_dynLin" if isKinetic else "_reqLin"
prefix += "_1comp"
model.filename = convergence.generate_GRM_name(
prefix, method_, colCells_, parMethod_, parCells_, '.h5')
model.save()
# RUN
if(run_):
data = model.run()
if data.returncode == 0:
print(model.filename + " simulation completed successfully")
model.load()
else:
print(data)
raise Exception(model.filename + " simulation failed")
# PLOT
if(plot_):
solution_times = model.root.output.solution.solution_times
c_outlet = model.root.output.solution.unit_001.solution_outlet
plt.plot()
plt.plot(solution_times, c_outlet)
plt.xlabel('$time~/~min$')
plt.ylabel('$Outlet~concentration~/~mol \cdot m^{-3} $')
plt.show()
def LRMlinear1Comp_VerificationSetting(
method_=0, colCells_=5,
isKinetic_=True,
tolerance=1e-12, plot_=False, run_=True,
save_path="C:\\Users\\jmbr\\JupyterNotebooks\\",
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe"
):
Cadet.cadet_path = cadet_path
# =========================================================================
# PARAMETERS
# =========================================================================
velocity = 2.0/60.0 # m / s = 6000 cm / min
length = 1.0 # m
adsorption = 1.0 # m^3 / (mol * s) (mobile phase)
desorption = 1.0 # 1 / s (desorption)
D_ax = 1e-4 # m^2 / s (interstitial volume)
porosity = 0.6
inlet = 1.0 # mol / m^3 = (1/1000) mol / liter
nCells = colCells_
t_end = 130
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 3
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
# [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
0, 1, -1, -1, 60/1e6,
1, 2, -1, -1, 60/1e6]
model.root.input.solver.sections.nsec = 2
model.root.input.solver.sections.section_times = [0.0, 60, t_end] # s
model.root.input.solver.sections.section_continuity = [0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
model.root.input.solver.nthreads = 1
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = tolerance
model.root.input.solver.time_integrator.algtol = tolerance*100
model.root.input.solver.time_integrator.reltol = tolerance*100
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 1000000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_000.unit_type = 'INLET'
model.root.input.model.unit_000.ncomp = 1
model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
model.root.input.model.unit_000.sec_000.const_coeff = [
inlet,] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_000.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.cube_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.const_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.cube_coeff = [0.0,]
# UNIT OPERATIONS - MODEL
if method_ == 0:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES'
else:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES_DG'
model.root.input.model.unit_001.ncomp = 1
model.root.input.model.unit_001.adsorption_model = 'LINEAR'
model.root.input.model.unit_001.adsorption.is_kinetic = int(
isKinetic_) # Kinetic binding
model.root.input.model.unit_001.adsorption.lin_ka = [adsorption,]
model.root.input.model.unit_001.adsorption.lin_kd = [desorption,]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_c = [0.0,]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_q = [0.0,]
model.root.input.model.unit_001.col_dispersion = D_ax
model.root.input.model.unit_001.col_length = length
model.root.input.model.unit_001.total_porosity = porosity
# m / s = 6000 cm / min
model.root.input.model.unit_001.velocity = velocity
# Discretization
model.root.input.model.unit_001.discretization.ncol = nCells
if method_ != 0:
model.root.input.model.unit_001.discretization.polydeg = int(
abs(method_))
model.root.input.model.unit_001.discretization.exact_integration = 0 if method_ > 0 else 1
model.root.input.model.unit_001.discretization.nbound = [1] # Bound states
model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
model.root.input.model.unit_001.discretization.weno.boundary_model = 0
model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10
model.root.input.model.unit_001.discretization.weno.weno_order = 3
# UNIT OPERATIONS - OUTLET
model.root.input.model.unit_002.unit_type = 'OUTLET'
model.root.input.model.unit_002.ncomp = 1
# RETURN DATA
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].unit_000.write_solution_bulk = 0
model.root.input['return'].unit_000.write_solution_inlet = 0
model.root.input['return'].unit_000.write_solution_outlet = 0
model.root.input['return'].unit_001.write_solution_bulk = 0
model.root.input['return'].unit_001.write_solution_inlet = 0
model.root.input['return'].unit_001.write_solution_outlet = 1
model.root.input['return'].unit_001.WRITE_COORDINATES = 0
# Copy inlet return settings to the outlet unit operation
model.root.input['return'].unit_002 = model.root.input['return'].unit_000
# Solution times
model.root.input.solver.user_solution_times = np.linspace(
0, t_end, t_end + 1)
prefix = save_path + 'LRM'
if isKinetic_:
prefix += '_dyn'
else:
prefix += '_req'
prefix += '_1comp'
model.filename = convergence.generate_1D_name(prefix, method_, nCells)
model.save()
# RUN
if run_:
data = model.run()
if data.returncode == 0:
print("method " + str(int(method_)) + "Z" +
str(int(nCells)) + " simulation completed successfully")
model.load()
else:
print(data)
raise Exception("method " + str(int(method_)) +
"Z" + str(int(nCells)) + " simulation failed")
if plot_:
solution_times = model.root.output.solution.solution_times
c_outlet = model.root.output.solution.unit_001.solution_outlet
plt.plot()
plt.plot(solution_times, c_outlet)
plt.xlabel('$time~/~min$')
plt.ylabel('$Outlet~concentration~/~mol \cdot m^{-3} $')
plt.show()
def LRMPlinear1Comp_VerificationSetting(
method_=0, colCells_=5,
isKinetic_=True,
tolerance=1e-12, plot_=False, run_=True,
save_path="C:\\Users\\jmbr\\JupyterNotebooks\\",
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe"
):
Cadet.cadet_path = cadet_path
## PARAMETERS ###########
velocity = 2.0/60.0 # m / s
film_diffusion = [velocity / 10] # m / s
length = 1.0 # m
# m^3 / (mol * s) (mobile phase)
adsorption = [1.0]
desorption = [1.0] # 1 / s (desorption)
D_ax = [1e-4] # m^2 / s (interstitial volume)
porosity = 0.6
par_porosity = 0.2
par_radius = 0.0001 # m
inlet = 1.0 # mol / m^3 = (1/1000) mol / liter
nCells = colCells_
t_end = 130
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 3
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
# [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
0, 1, -1, -1, 60/1e6,
1, 2, -1, -1, 60/1e6]
model.root.input.solver.sections.nsec = 2
model.root.input.solver.sections.section_times = [0.0, 60, t_end] # s
model.root.input.solver.sections.section_continuity = [0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
model.root.input.solver.nthreads = 1
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = 1e-12
model.root.input.solver.time_integrator.algtol = 1e-10
model.root.input.solver.time_integrator.reltol = 1e-10
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 1000000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_000.unit_type = 'INLET'
model.root.input.model.unit_000.ncomp = 1
model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
model.root.input.model.unit_000.sec_000.const_coeff = [
inlet, inlet] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_000.lin_coeff = [0.0]
model.root.input.model.unit_000.sec_000.quad_coeff = [0.0]
model.root.input.model.unit_000.sec_000.cube_coeff = [0.0]
model.root.input.model.unit_000.sec_001.const_coeff = [
0.0] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_001.lin_coeff = [0.0]
model.root.input.model.unit_000.sec_001.quad_coeff = [0.0]
model.root.input.model.unit_000.sec_001.cube_coeff = [0.0]
# UNIT OPERATIONS - MODEL
if method_ == 0:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITH_PORES'
else:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITH_PORES_DG'
model.root.input.model.unit_001.ncomp = 1
model.root.input.model.unit_001.adsorption_model = 'LINEAR'
model.root.input.model.unit_001.adsorption_model_multiplex = 1
model.root.input.model.unit_001.adsorption.is_kinetic = int(
isKinetic_) # Kinetic binding
# m^3 / (mol * s) (mobile phase)
model.root.input.model.unit_001.adsorption.lin_ka = adsorption
# 1 / s (desorption)
model.root.input.model.unit_001.adsorption.lin_kd = desorption
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_c = [0.0]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_cp = [0.0]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_q = [0.0]
model.root.input.model.unit_001.col_dispersion = D_ax
model.root.input.model.unit_001.col_length = length
model.root.input.model.unit_001.col_porosity = porosity
model.root.input.model.unit_001.film_diffusion = film_diffusion
model.root.input.model.unit_001.film_diffusion_multiplex = 1
model.root.input.model.unit_001.par_porosity = par_porosity
model.root.input.model.unit_001.par_radius = par_radius
model.root.input.model.unit_001.velocity = velocity
model.root.input.model.unit_001.par_type_volfrac = 1
# Discretization
if method_ != 0:
model.root.input.model.unit_001.discretization.exact_integration = 0 if method_ > 0 else 1 # cells
model.root.input.model.unit_001.discretization.polydeg = int(
abs(method_)) # cells
model.root.input.model.unit_001.discretization.ncol = nCells
model.root.input.model.unit_001.discretization.npartype = 1
model.root.input.model.unit_001.discretization.nbound = [1]
model.root.input.model.unit_001.discretization.par_geom = [
"SPHERE"] # particle geometry (sphere, cylinder, slab)
model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
model.root.input.model.unit_001.discretization.gs_type = 0
model.root.input.model.unit_001.discretization.max_krylov = 10
model.root.input.model.unit_001.discretization.max_restarts = 100
model.root.input.model.unit_001.discretization.schur_safety = 0.1
model.root.input.model.unit_001.discretization.weno.boundary_model = 0
model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10
model.root.input.model.unit_001.discretization.weno.weno_order = 3
# UNIT OPERATIONS - OUTLET
model.root.input.model.unit_002.unit_type = 'OUTLET'
model.root.input.model.unit_002.ncomp = 1
# RETURN DATA
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].unit_000.write_solution_bulk = 0
model.root.input['return'].unit_000.write_solution_inlet = 0
model.root.input['return'].unit_000.write_solution_outlet = 0
model.root.input['return'].unit_001.write_solution_bulk = 1
model.root.input['return'].unit_001.write_solution_inlet = 1
model.root.input['return'].unit_001.write_solution_outlet = 1
model.root.input['return'].unit_001.WRITE_COORDINATES = 1
# Copy inlet return settings to the outlet unit operation
model.root.input['return'].unit_002 = model.root.input['return'].unit_000
# Solution times
model.root.input.solver.user_solution_times = np.linspace(
0, t_end, t_end + 1)
prefix = save_path + 'LRMP'
if isKinetic_:
prefix += '_dyn'
else:
prefix += '_req'
prefix += '_1comp'
model.filename = convergence.generate_1D_name(prefix, method_, nCells)
model.save()
# RUN
if(run_):
data = model.run()
if data.returncode == 0:
print("method " + str(int(method_)) + "Z" +
str(int(nCells)) + " simulation completed successfully")
model.load()
else:
print(data)
raise Exception("method " + str(int(method_)) +
"Z" + str(int(nCells)) + " simulation failed")
if(plot_):
solution_times = model.root.output.solution.solution_times
c_outlet = model.root.output.solution.unit_001.solution_outlet
plt.plot()
plt.plot(solution_times, c_outlet)
plt.xlabel('$time~/~min$')
plt.ylabel('$Outlet~concentration~/~mol \cdot m^{-3} $')
plt.show()
def LRMlinear1Comp_noBind(
method_=0, colCells_=5,
tolerance=1e-12,
plot_=False, run_=True,
save_path="C:\\Users\\jmbr\\JupyterNotebooks\\",
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe"
):
Cadet.cadet_path = cadet_path
## PARAMETERS ###########
velocity = 2.0/60.0 # m / s = 6000 cm / min
length = 1.0 # m
D_ax = 5e-4 # m^2 / s (interstitial volume)
porosity = 0.6
inlet = 1.0 # mol / m^3 = (1/1000) mol / liter
nCells = colCells_
t_end = 130
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 3
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
# [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
0, 1, -1, -1, 60/1e6,
1, 2, -1, -1, 60/1e6]
model.root.input.solver.sections.nsec = 2
model.root.input.solver.sections.section_times = [0.0, 60, t_end] # s
model.root.input.solver.sections.section_continuity = [0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
model.root.input.solver.nthreads = 1
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = tolerance
model.root.input.solver.time_integrator.algtol = tolerance*100
model.root.input.solver.time_integrator.reltol = tolerance*100
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 1000000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_000.unit_type = 'INLET'
model.root.input.model.unit_000.ncomp = 1
model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
model.root.input.model.unit_000.sec_000.const_coeff = [
inlet,] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_000.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_000.cube_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.const_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.lin_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.quad_coeff = [0.0,]
model.root.input.model.unit_000.sec_001.cube_coeff = [0.0,]
# UNIT OPERATIONS - MODEL
if method_ == 0:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES'
else:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES_DG'
model.root.input.model.unit_001.ncomp = 1
model.root.input.model.unit_001.adsorption_model = 'NONE'
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_c = [0.0,]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_q = [0.0,]
model.root.input.model.unit_001.col_dispersion = D_ax
model.root.input.model.unit_001.col_length = length
model.root.input.model.unit_001.total_porosity = porosity
model.root.input.model.unit_001.velocity = velocity
# Discretization
model.root.input.model.unit_001.discretization.ncol = nCells
if method_ != 0:
model.root.input.model.unit_001.discretization.polydeg = int(
abs(method_))
model.root.input.model.unit_001.discretization.exact_integration = 0 if method_ > 0 else 1
model.root.input.model.unit_001.discretization.nbound = [1] # Bound states
model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
model.root.input.model.unit_001.discretization.weno.boundary_model = 0
model.root.input.model.unit_001.discretization.weno.weno_eps = 1e-10
model.root.input.model.unit_001.discretization.weno.weno_order = 3
# UNIT OPERATIONS - OUTLET
model.root.input.model.unit_002.unit_type = 'OUTLET'
model.root.input.model.unit_002.ncomp = 1
# RETURN DATA
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].unit_000.write_solution_bulk = 0
model.root.input['return'].unit_000.write_solution_inlet = 0
model.root.input['return'].unit_000.write_solution_outlet = 0
model.root.input['return'].unit_001.write_solution_bulk = 0
model.root.input['return'].unit_001.write_solution_inlet = 0
model.root.input['return'].unit_001.write_solution_outlet = 1
model.root.input['return'].unit_001.WRITE_COORDINATES = 0
# Copy inlet return settings to the outlet unit operation
model.root.input['return'].unit_002 = model.root.input['return'].unit_000
# Solution times
model.root.input.solver.user_solution_times = np.linspace(
0, t_end, t_end + 1)
prefix = save_path + 'LRM_noBind'
prefix += '_1comp'
model.filename = convergence.generate_1D_name(prefix, method_, nCells)
model.save()
# RUN
if(run_):
data = model.run()
if data.returncode == 0:
print("method " + str(int(method_)) + "Z" +
str(int(nCells)) + " simulation completed successfully")
model.load()
else:
print(data)
raise Exception("method " + str(int(method_)) +
"Z" + str(int(nCells)) + " simulation failed")
if(plot_):
solution_times = model.root.output.solution.solution_times
c_outlet = model.root.output.solution.unit_001.solution_outlet
plt.plot()
plt.plot(solution_times, c_outlet)
plt.xlabel('$time~/~min$')
plt.ylabel('$Outlet~concentration~/~mol \cdot m^{-3} $')
plt.show()
def LWE_setting(
method, nCells,
par_method, nParCells,
save_path,
transport_model='GENERAL_RATE_MODEL',
is_kinetic=0,
idas_tolerance=1E-8,
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe",
rad_method=0, nRadCells=3,
run_sim=False,
n_threads=1):
Cadet.cadet_path = cadet_path
# =========================================================================
# PARAMETERS
# =========================================================================
polyDeg = int(abs(method))
parPolyDeg = int(abs(par_method))
velocity = 5.75e-4 # m / s
length = 0.014 # m
D_ax = 5.75e-8 # m^2 / s (interstitial volume)
col_porosity = 0.37
par_porosity = 0.75
total_porosity = 0.8425
film_diffusion = [6.9E-6, 6.9E-6, 6.9E-6, 6.9E-6]
par_radius = 4.5E-5
par_diffusion = [70.0E-11, 6.07E-11, 6.07E-11, 6.07E-11]
surface_diffusion = [0.0, 0.0, 0.0, 0.0]
binding = "STERIC_MASS_ACTION"
adsorption = [0.0, 35.5, 1.59, 7.7] # m^2 / s
desorption = [0.0, 1000.0, 1000.0, 1000.0] # 1 / s
charge = [0.0, 4.7, 5.29, 3.7]
steric_factor = [0.0, 11.83, 10.6, 10.0]
n_binding_sites = 1200.0
init_cb_cp = [50, 0.0, 0.0, 0.0]
init_cs = [1200, 0.0, 0.0, 0.0]
inlet1 = [50.0, 1.0, 1.0, 1.0] # mol / m^3 = (1/1000) mol / liter
inlet2 = [50.0, 0.0, 0.0, 0.0]
inlet3 = [100.0, 0.0, 0.0, 0.0]
inlet3_lin = [0.2, 0.0, 0.0, 0.0]
nComp = 4
time_sections = [0, 12, 40]
solution_resolution = 1.0
section_times = [0.0, 10.0, 90.0, 1500.0]
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 2
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.CONNECTIONS_INCLUDE_PORTS = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
1.0, 0.0, -1.0, -1.0, -1.0, -1.0, 1.0
] # [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
model.root.input.solver.sections.nsec = 3
model.root.input.solver.sections.section_times = section_times # s
model.root.input.solver.sections.section_continuity = [0, 0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
# Number of cores for parallel simulation
model.root.input.solver.nthreads = n_threads
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = idas_tolerance
model.root.input.solver.time_integrator.algtol = idas_tolerance*100
model.root.input.solver.time_integrator.reltol = idas_tolerance*100
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 10000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_001.unit_type = 'INLET'
model.root.input.model.unit_001.ncomp = nComp
model.root.input.model.unit_001.inlet_type = 'PIECEWISE_CUBIC_POLY'
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.sec_000.const_coeff = inlet1
model.root.input.model.unit_001.sec_000.lin_coeff = [0.0, 0.0, 0.0, 0.0]
model.root.input.model.unit_001.sec_000.quad_coeff = [0.0, 0.0, 0.0, 0.0]
model.root.input.model.unit_001.sec_000.cube_coeff = [0.0, 0.0, 0.0, 0.0]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.sec_001.const_coeff = inlet2
model.root.input.model.unit_001.sec_001.lin_coeff = [0.0, 0.0, 0.0, 0.0]
model.root.input.model.unit_001.sec_001.quad_coeff = [0.0, 0.0, 0.0, 0.0]
model.root.input.model.unit_001.sec_001.cube_coeff = [0.0, 0.0, 0.0, 0.0]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.sec_002.const_coeff = inlet3
model.root.input.model.unit_001.sec_002.lin_coeff = inlet3_lin
model.root.input.model.unit_001.sec_002.quad_coeff = [0.0, 0.0, 0.0, 0.0]
model.root.input.model.unit_001.sec_002.cube_coeff = [0.0, 0.0, 0.0, 0.0]
# UNIT OPERATIONS - MODEL
if method == 0:
model.root.input.model.unit_000.unit_type = transport_model
else:
model.root.input.model.unit_000.unit_type = transport_model + '_DG'
model.root.input.model.unit_000.ncomp = nComp
model.root.input.model.unit_000.adsorption_model = binding
model.root.input.model.unit_000.adsorption.is_kinetic = is_kinetic
# m^3 / (mol * s) (mobile phase)
model.root.input.model.unit_000.adsorption.SMA_KA = adsorption
# 1 / s (desorption)
model.root.input.model.unit_000.adsorption.SMA_KD = desorption
model.root.input.model.unit_000.adsorption.SMA_LAMBDA = n_binding_sites
model.root.input.model.unit_000.adsorption.SMA_NU = charge
model.root.input.model.unit_000.adsorption.SMA_SIGMA = steric_factor
model.root.input.model.unit_000.par_radius = par_radius
model.root.input.model.unit_000.par_coreradius = 0.0
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.init_c = init_cb_cp
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.init_q = init_cs
# m / s = 6000 cm / min
model.root.input.model.unit_000.velocity = velocity
model.root.input.model.unit_000.col_dispersion = D_ax
model.root.input.model.unit_000.par_diffusion = par_diffusion
model.root.input.model.unit_000.par_surfdiffusion = surface_diffusion
model.root.input.model.unit_000.film_diffusion = film_diffusion
model.root.input.model.unit_000.col_dispersion_radial = 1.0E-6
model.root.input.model.unit_000.col_length = length
model.root.input.model.unit_000.col_radius = 0.01
model.root.input.model.unit_000.col_porosity = col_porosity
model.root.input.model.unit_000.par_porosity = par_porosity
model.root.input.model.unit_000.total_porosity = total_porosity
# Discretization
model.root.input.model.unit_000.discretization.ncol = nCells
model.root.input.model.unit_000.discretization.nrad = nRadCells
if method != 0:
model.root.input.model.unit_000.discretization.polydeg = polyDeg
model.root.input.model.unit_000.discretization.exact_integration = 1 if method < 0 else 0
model.root.input.model.unit_000.discretization.par_exact_integration = 0 if par_method < 0 else 1
model.root.input.model.unit_000.discretization.nparcell = nParCells
model.root.input.model.unit_000.discretization.parpolydeg = parPolyDeg
else:
model.root.input.model.unit_000.discretization.npar = nParCells
model.root.input.model.unit_000.discretization.nbound = [1, 1, 1, 1]
# model.root.input.model.unit_000.discretization.par_geom = [
# "SPHERE"] # particle geometry (sphere, cylinder, slab)
model.root.input.model.unit_000.discretization.par_disc_type = [
"EQUIDISTANT_PAR"] # EQUIDISTANT_PAR, EQUIVOLUME_PAR, USER_DEFINED_PAR
model.root.input.model.unit_000.discretization.radial_disc_type = [
"EQUIDISTANT"] # EQUIDISTANT_PAR, EQUIVOLUME_PAR, USER_DEFINED_PAR
model.root.input.model.unit_000.discretization.use_analytic_jacobian = 1
# model.root.input.model.unit_000.discretization.reconstruction = 'WENO'
model.root.input.model.unit_000.discretization.gs_type = 1
model.root.input.model.unit_000.discretization.max_krylov = 0
model.root.input.model.unit_000.discretization.max_restarts = 10
model.root.input.model.unit_000.discretization.schur_safety = 1E-8
model.root.input.model.unit_000.discretization.weno.boundary_model = 0
model.root.input.model.unit_000.discretization.weno.weno_eps = 1e-10
model.root.input.model.unit_000.discretization.weno.weno_order = 3
# RETURN DATA
model.root.input['return'].split_components_data = 0
model.root.input['return'].split_ports_data = 0
model.root.input['return'].write_solution_times = 1
model.root.input['return'].unit_000.WRITE_SENS_BULK = 0
model.root.input['return'].unit_000.WRITE_SOLUTION_SOLID = 0
model.root.input['return'].unit_000.WRITE_COORDINATES = 0
model.root.input['return'].unit_000.WRITE_SOLUTION_BULK = 0
model.root.input['return'].unit_000.WRITE_SOLUTION_PARTICLE = 0
model.root.input['return'].unit_000.WRITE_SOLUTION_INLET = 0
model.root.input['return'].unit_000.WRITE_SOLUTION_OUTLET = 1
model.root.input['return'].unit_000.WRITE_SOLUTION_FLUX = 0
model.root.input['return'].unit_000.WRITE_SENS_OUTLET = 1
model.root.input['return'].unit_000.WRITE_SENS_FLUX = 0
model.root.input['return'].unit_000.WRITE_SENS_PARTICLE = 0
model.root.input['return'].unit_000.WRITE_SENS_INLET = 0
# Solution times
model.root.input.solver.user_solution_times = np.linspace(
section_times[0],
section_times[3],
int(section_times[3] * solution_resolution) + 1)
name = save_path
if n_threads != 1:
name += str(n_threads) + 'thread'
if transport_model == 'GENERAL_RATE_MODEL':
model.filename = convergence.generate_GRM_name(
name+'GRM_SMA_4comp',
method, nCells, par_method, nParCells, '.h5')
elif transport_model == 'LUMPED_RATE_MODEL_WITH_PORES':
model.filename = convergence.generate_1D_name(
name+'LRMP_SMA_4comp', method, nCells, '.h5')
elif transport_model == 'LUMPED_RATE_MODEL_WITHOUT_PORES':
model.filename = convergence.generate_1D_name(
name+'LRM_SMA_4comp', method, nCells, '.h5')
model.save()
# RUN
if run_sim:
data = model.run()
if data.returncode == 0:
print(model.filename + " simulation completed successfully")
model.load()
else:
print(data)
raise Exception(model.filename + " simulation failed")
def LRM_langmuir_oscillations(
method, ncells,
save_path,
D_ax=1e-4,
is_kinetic=False,
cadet_path="C:/Users/jmbr/Cadet/code/out/install/MS_MKL_RELEASE/bin/cadet-cli.exe",
run_=True):
Cadet.cadet_path = cadet_path
## PARAMETERS ###########
polyDeg = int(abs(method))
nCells = ncells
velocity = 0.1 # m / s = 6000 cm / min
length = 1.0 # m
adsorption = [0.1, 0.05]
desorption = [1.0, 1.0]
qmax = [10.0, 10.0]
binding = "MULTI_COMPONENT_LANGMUIR"
D_ax = D_ax # 1e-4 # m^2 / s (interstitial volume)
porosity = 0.4
inlet1 = 10.0 # mol / m^3 = (1/1000) mol / liter
inlet2 = 10.0 # mol / m^3 = (1/1000) mol / liter
nComp = 2
time_sections = [0, 12, 40]
solution_resolution = 10
time_sections = [0, 12, 40]
#########################
model = Cadet()
# SYSTEM
model.root.input.model.nunits = 3
model.root.input.model.connections.nswitches = 1
model.root.input.model.connections.switch_000.section = 0
model.root.input.model.connections.switch_000.connections = [
# [unit_000, unit_001, all components, all components, Q/ m^3*s^-1
0, 1, -1, -1, 60/1e6,
1, 2, -1, -1, 60/1e6] # [unit_001, unit_002, all components, all components, Q/ m^3*s^-1
model.root.input.solver.sections.nsec = 2
model.root.input.solver.sections.section_times = time_sections # s
model.root.input.solver.sections.section_continuity = [0]
# SOLVER
model.root.input.model.solver.gs_type = 1
model.root.input.model.solver.max_krylov = 0
model.root.input.model.solver.max_restarts = 10
model.root.input.model.solver.schur_safety = 1e-8
model.root.input.solver.nthreads = 1
# Tolerances for the time integrator
model.root.input.solver.time_integrator.abstol = 1e-10
model.root.input.solver.time_integrator.algtol = 1e-8
model.root.input.solver.time_integrator.reltol = 1e-8
model.root.input.solver.time_integrator.init_step_size = 1e-10
model.root.input.solver.time_integrator.max_steps = 1000000
# UNIT OPERATIONS - INLET
model.root.input.model.unit_000.unit_type = 'INLET'
model.root.input.model.unit_000.ncomp = nComp
model.root.input.model.unit_000.inlet_type = 'PIECEWISE_CUBIC_POLY'
model.root.input.model.unit_000.sec_000.const_coeff = [
inlet1, inlet2] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_000.lin_coeff = [0.0, 0.0]
model.root.input.model.unit_000.sec_000.quad_coeff = [0.0, 0.0]
model.root.input.model.unit_000.sec_000.cube_coeff = [0.0, 0.0]
model.root.input.model.unit_000.sec_001.const_coeff = [
0.0, 0.0] # mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_000.sec_001.lin_coeff = [0.0, 0.0]
model.root.input.model.unit_000.sec_001.quad_coeff = [0.0, 0.0]
model.root.input.model.unit_000.sec_001.cube_coeff = [0.0, 0.0]
# UNIT OPERATIONS - MODEL
if method == 0:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES'
else:
model.root.input.model.unit_001.unit_type = 'LUMPED_RATE_MODEL_WITHOUT_PORES_DG'
model.root.input.model.unit_001.ncomp = nComp
model.root.input.model.unit_001.adsorption_model = binding
model.root.input.model.unit_001.adsorption.is_kinetic = is_kinetic
# m^3 / (mol * s) (mobile phase)
model.root.input.model.unit_001.adsorption.MCL_KA = adsorption
# 1 / s (desorption)
model.root.input.model.unit_001.adsorption.MCL_KD = desorption
model.root.input.model.unit_001.adsorption.MCL_QMAX = qmax
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_c = [0.0, 0.0]
# mol / m^3 = (1/1000) mol / liter
model.root.input.model.unit_001.init_q = [0.0, 0.0]
model.root.input.model.unit_001.col_dispersion = D_ax
model.root.input.model.unit_001.col_length = length
model.root.input.model.unit_001.total_porosity = porosity
# m / s = 6000 cm / min
model.root.input.model.unit_001.velocity = velocity
# Discretization
model.root.input.model.unit_001.discretization.ncol = nCells
if method != 0:
model.root.input.model.unit_001.discretization.polydeg = polyDeg
model.root.input.model.unit_001.discretization.exact_integration = 1 if method < 0 else 0
model.root.input.model.unit_001.discretization.nbound = [1, 1]
model.root.input.model.unit_001.discretization.use_analytic_jacobian = 1
# @todo: needed in convDispOp FV
model.root.input.model.unit_001.discretization.reconstruction = 'WENO'
model.root.input.model.unit_001.discretization.weno.boundary_model = 0