# 1D_packbed.ipynb (Source)

Data files used in this example: Ammonia-Ru-Ba-YSZ.yaml# One-dimensional packed-bed, catalytic-membrane reactor model without streamwise diffusion¶

The present model simulates heterogeneous catalytic processes inside packed-bed, catalytic membrane reactors. The gas-phase and surface-phase species conservation equations are derived and the system of differential-algebraic equations (DAE) is solved using the scikits.odes.dae IDA solver.

```
# Import Cantera and scikits
import numpy as np
from scikits.odes import dae
import cantera as ct
import matplotlib.pyplot as plt
%matplotlib inline
%config InlineBackend.figure_formats = ["svg"]
print("Runnning Cantera version: " + ct.__version__)
```

## Methodology¶

One-dimensional, steady-state catalytic-membrane reactor model with surface chemistry is developed to analyze species profiles along the length of a packed-bed, catalytic membrane reactor. The same model can further be simplified to simulate a simple packed-bed reactor by excluding the membrane. The example here demonstrates the one-dimensional reactor model explained by G. Kogekar, et al., "Efficient and robust computational models of heterogeneous catalysis in catalytic membrane reactors," (2022), In preparation [1].

### Governing equations¶

Assuming steady-state, one-dimensional flow within the packed bed, total-mass, species mass and energy conservation may be stated as [2]

$$ \frac{d(\rho u)}{dz} = \sum_{k=1}^{K_{\mathrm{g}}} \dot {s}_k W_k A_{\mathrm{s}} + \frac{P_{\mathrm b}}{A_{\mathrm b}} j_{k_{\mathrm M}}, \\ \rho u \frac{dY_k}{dz} + A_{\mathrm{s}} Y_k \sum_{k=1}^{K_{\mathrm{g}}} \dot {s}_k W_k = A_{\mathrm s} \dot {s}_k W_k + \delta_{k, k_{\mathrm M}} \frac{P_{\mathrm b}}{A_{\mathrm b}} j_{k_{\mathrm M}}, \\ \rho u c_{\mathrm p} \frac{dT}{dz} + \sum_{k=1}^{K_{\mathrm g}} h_k (\phi_{\mathrm g} \dot {\omega}_k + A_{\mathrm s} \dot {s}_k) W_k = \hat h \frac{P_{\mathrm b}}{A_{\mathrm b}}(T_{\mathrm w} - T) + \delta_{k, k_{\mathrm M}} \frac{P_{\mathrm b}}{A_{\mathrm b}} h_{k_{\rm M}} j_{k_{\mathrm M}}. $$The fractional coverages of the $K_{\rm s}$ surface adsorbates $\theta_k$ must satisfy $$ \dot {s}_k = 0, {\ \ \ \ \ \ } (k = 1,\ldots, K_{\mathrm s}), $$ which, at steady state, requires no net production/consumption of surface species by the heterogeneous reactions [3].

The pressure within the bed is calculated as $$ \frac{dp}{dz} = - \left( \frac{\phi_{\mathrm{g}} \mu}{\beta_{\mathrm{g}}} \right) u, $$ where $\mu$ is the gas-phase mixture viscosity. The packed-bed permeability $\beta_{\rm g}$ is evaluated using the Kozeny-Carman relationship as $$ \beta_{\mathrm g} = \frac{\phi_{\mathrm{g}}^3 D_{\mathrm p}^2}{72 \tau_{\mathrm{g}}(1 - \phi_{\mathrm{g}})^2}, $$ where $\phi_{\mathrm{g}}$, $\tau_{\mathrm{g}}$, and $D_{\mathrm {p}}$ are the bed porosity, tortuosity, and particle diameter, respectively.

The independent variable in these conservation equations is the position $z$ along the reactor length. The dependent variables include total mass flux $\rho u$, pressure $p$, temperature $T$, gas-phase mass fractions $Y_k$, and surfaces coverages $\theta_k$. Gas-phase fluxes through the membrane are represented as $j_{k, {\mathrm M}}$. Geometric parameters $A_{\mathrm s}$, $P_{\mathrm b}$, and $A_{\mathrm b}$ represent the catalyst specific surface area (dimensions of surface area per unit volume), reactor perimeter, and reactor cross-sectional flow area, respectively. Other parameters include bed porosity $\phi_{\mathrm g}$ and gas-phase species molecular weights $W_k$. The gas density $\rho$ is evaluated using the equation of state (ideal Eos, RK or PR EoS).

If a perm-selective membrane is present, then $j_{k_{\mathrm M}}$ represents the gas-phase flux through the membrane and ${k_{\mathrm M}}$ is the gas-phase species that permeates through the membrane. The Kronecker delta, $\delta_{k, k_{\mathrm M}} = 1$ for the membrane-permeable species and $\delta_{k, k_{\mathrm M}} = 0$ otherwise. The membrane flux is calculated using Sievert's law as $$ {j_{k_{\mathrm M}}}^{\text{Mem}} = \frac{B_{k_{\mathrm M}}}{t} \left ( p_{k_{\mathrm M} {\text{, mem}}}^\alpha - p_{k_{\mathrm M} \text{, sweep}}^\alpha \right ) W_{k_{\rm M}} $$ where $B_{k_{\mathrm M}}$ is the membrane permeability, $t$ is the membrane thickness. $p_{k_{\mathrm M} \text{, mem}}$ and $p_{k_{\mathrm M} \text{, sweep}}$ represent perm-selective species partial pressures within the packed-bed and the exterior sweep channel. The present model takes the pressure exponent $\alpha$ to be unity. The membrane flux for all other species ($ k \neq k_{\mathrm M}$) is zero.

### Chemistry mechanism¶

This example uses a detailed 12-step elementary micro-kinetic reaction mechanism that describes ammonia formation and decomposition kinetics over the Ru/Ba-YSZ catalyst. The reaction mechanism is developed and validated using measured performance in a laboratory-scale packed-bed reactor [4]. This example also incorporates a Pd-based H_{2} perm-selective membrane.

### Solver¶

Above governing equations represent a complete solution for a steady-state packed-bed, catalytic membrane reactor model. The dependent variables are the mass-flux $\rho u$, species mass-fractions $Y_k$, pressure $p$, temperature $T$, and surface coverages $\theta_k$. The equation of state is used to obtain the mass density, $\rho$.

The governing equations form an initial value problem (IVP) in a differential-algebraic (DAE) form as follows:
$$
f(z,{\bf{y}}, \bf {y'}, c) = 0,
$$
where $\bf{y}$ and $\bf{y'}$ represent the solution vector and its derivative vector, respectively. All other constants such as reference temperature, chemical constants, etc. are incorporated in vector $c$ (Refer to [5] for more details). This type of DAE system in this example is solved using the `scikits.odes.dae`

IDA solver.

- G. Kogekar, H. Zhu, R.J. Kee, 'Efficient and robust computational models of heterogeneous catalysis in catalytic membrane reactors', (2022), In preparation
- B. Kee, C. Karakaya, H. Zhu, S. DeCaluwe, and R.J. Kee, 'The Influence of Hydrogen-Permeable Membranes and Pressure on Methane Dehydroaromatization in Packed-Bed Catalytic Reactors', Industrial & Engineering Chemistry Research (2017) 56, 13:3551 - 3559
- R.J. Kee, M.E. Coltrin, P. Glarborg, and H. Zhu, 'Chemically Reacting Flow: Theory, Modeling and Simulation', Wiley (2018)
- Z. Zhang, C. Karakaya, R.J. Kee, J. Douglas Way, C. Wolden,, 'Barium-Promoted Ruthenium Catalysts on Yittria-Stabilized Zirconia Supports for Ammonia Synthesis', ACS Sustainable Chemistry & Engineering (2019) 7:18038 - 18047
- G. Kogekar, 'Computationally efficient and robust models of non-ideal thermodynamics, gas-phase kinetics and heterogeneous catalysis in chemical reactors' (2021), Doctoral dissertation.

### Define gas-phase and surface-phase species¶

```
# Import the reaction mechanism for Ammonia synthesis/decomposition on Ru-Ba/YSZ catalyst
mechfile = "data/Ammonia-Ru-Ba-YSZ.yaml"
# Import the models for gas-phase
gas = ct.Solution(mechfile, "gas")
# Import the model for surface-phase
surf = ct.Interface(mechfile, "Ru_surface", [gas])
# Other parameters
n_gas = gas.n_species # number of gas species
n_surf = surf.n_species # number of surface species
n_gas_reactions = gas.n_reactions # number of gas-phase reactions
# Set offsets of dependent variables in the solution vector
offset_rhou = 0
offset_p = 1
offset_T = 2
offset_Y = 3
offset_Z = offset_Y + n_gas
n_var = offset_Z + n_surf # total number of variables (rhou, P, T, Yk and Zk)
print("Number of gas-phase species = ", n_gas)
print("Number of surface-phase species = ", n_surf)
print("Number of variables = ", n_var)
```

### Define reactor geometry and operating conditions¶

```
# Reactor geometry
L = 5e-2 # length of the reactor (m)
R = 5e-3 # radius of the reactor channel (m)
phi = 0.5 # porosity of the bed (-)
tau = 2.0 # tortuosity of the bed (-)
dp = 3.37e-4 # particle diameter (m)
As = 3.5e6 # specific surface area (1/m)
# Energy (adiabatic or isothermal)
solve_energy = True # True: Adiabatic, False: isothermal
# Membrane (True: membrane, False: no membrane)
membrane_present = True
membrane_perm = 1e-15 # membrane permeability (kmol*m3/s/Pa)
thickness = 3e-6 # membrane thickness (m)
membrane_sp_name = "H2" # membrane-permeable species name
p_sweep = 1e5 # partial pressure of permeable species in the sweep channel (Pa)
permeance = membrane_perm / thickness # permeance of the membrane (kmol*m2/s/Pa)
if membrane_present:
print("Modeling packed-bed, catalytic-membrane reactor...")
print(membrane_sp_name, "permeable membrane is present.")
# Get required properties based on the geometry and mechanism
W_g = gas.molecular_weights # vector of molecular weight of gas species
vol_ratio = phi / (1 - phi)
eff_factor = phi / tau # effective factor for permeability calculation
# permeability based on Kozeny-Carman equation
B_g = B_g = vol_ratio**2 * dp**2 * eff_factor / 72
area2vol = 2 / R # area to volume ratio assuming a cylindrical reactor
D_h = 2 * R # hydraulic diameter
membrane_sp_ind = gas.species_index(membrane_sp_name)
# Inlet operating conditions
T_in = 673 # inlet temperature [K]
p_in = 5e5 # inlet pressure [Pa]
v_in = 0.001 # inlet velocity [m/s]
T_wall = 723 # wall temperature [K]
h_coeff = 1e2 # heat transfer coefficient [W/m2/K]
# Set gas and surface states
gas.TPX = T_in, p_in, "NH3:0.99, AR:0.01" # inlet composition
surf.TP = T_in, p_in
Yk_0 = gas.Y
rhou0 = gas.density * v_in
# Initial surface coverages
# advancing coverages over a long period of time to get the steady state.
surf.advance_coverages(1e10)
Zk_0 = surf.coverages
```

### Define residual function required for IDA solver¶

```
def residual(z, y, yPrime, res):
"""Solution vector for the model
y = [rho*u, p, T, Yk, Zk]
yPrime = [d(rho*u)dz, dpdz, dTdz, dYkdz, dZkdz]
"""
# Get current thermodynamic state from solution vector and save it to local variables.
rhou = y[offset_rhou] # mass flux (density * velocity)
Y = y[offset_Y : offset_Y + n_gas] # vector of mass fractions
Z = y[offset_Z : offset_Z + n_surf] # vector of site fractions
p = y[offset_p] # pressure
T = y[offset_T] # temperature
# Get derivatives of dependent variables
drhoudz = yPrime[offset_rhou]
dYdz = yPrime[offset_Y : offset_Y + n_gas]
dZdz = yPrime[offset_Z : offset_Z + n_surf]
dpdz = yPrime[offset_p]
dTdz = yPrime[offset_T]
# Set current thermodynamic state for the gas and surface phases
# Note: use unnormalized mass fractions and site fractions to avoid over-constraining the system
gas.set_unnormalized_mass_fractions(Y)
gas.TP = T, p
surf.set_unnormalized_coverages(Z)
surf.TP = T, p
# Calculate required variables based on the current state
coverages = surf.coverages # surface site coverages
# heterogeneous production rate of gas species
sdot_g = surf.get_net_production_rates("gas")
# heterogeneous production rate of surface species
sdot_s = surf.get_net_production_rates("Ru_surface")
wdot_g = np.zeros(n_gas)
# specific heat of the mixture
cp = gas.cp_mass
# partial enthalpies of gas species
hk_g = gas.partial_molar_enthalpies
if n_gas_reactions > 0:
# homogeneous production rate of gas species
wdot_g = gas.net_production_rates
mu = gas.viscosity # viscosity of the gas-phase
# Calculate density using equation of state
rho = gas.density
# Calculate flux term through the membrane
# partial pressure of membrane-permeable species
memsp_pres = (p * gas.X[membrane_sp_ind])
# negative sign indicates the flux going out
membrane_flux = (-permeance * (memsp_pres - p_sweep) / W_g[membrane_sp_ind])
# Conservation of total-mass
# temporary variable
sum_continuity = As * np.sum(sdot_g * W_g) + phi * np.sum(wdot_g * W_g)
res[offset_rhou] = (drhoudz - sum_continuity - area2vol * membrane_flux * membrane_present)
# Conservation of gas-phase species
res[offset_Y:offset_Y+ n_gas] = (dYdz + (Y * sum_continuity - phi * np.multiply(wdot_g,W_g)
- As * np.multiply(sdot_g,W_g)) / rhou)
res[offset_Y + membrane_sp_ind] -= area2vol * membrane_flux * membrane_present
# Conservation of site fractions (algebraic contraints in this example)
res[offset_Z : offset_Z + n_surf] = sdot_s
# For the species with largest site coverage (k_large), solve the constraint equation: sum(Zk) = 1
# The residual function for 'k_large' would be 'res[k_large] = 1 - sum(Zk)'
# Note that here sum(Zk) will be the sum of coverages for all surface species, including the 'k_large' species.
ind_large = np.argmax(coverages)
res[offset_Z + ind_large] = 1 - np.sum(coverages)
# Conservation of momentum
u = rhou / rho
res[offset_p] = dpdz + phi * mu * u / B_g
# Conservation of energy
res[offset_T] = dTdz - 0 # isothermal condition
# Note: One can just not solve the energy equation by keeping temperature constant.
# But since 'T' is used as the dependent variable, the residual is res[T] = dTdz - 0
# One can also write res[T] = 0 directly, but that leads to a solver failure due to singular jacobian
if solve_energy:
conv_term = (4 / D_h) * h_coeff * (T_wall - T) * (2 * np.pi * R)
chem_term = np.sum(hk_g * (phi * wdot_g + As * sdot_g))
res[offset_T] -= (conv_term - chem_term) / (rhou * cp)
```

### Calculate the spatial derivatives at the inlet that will be used as the initial conditions for the IDA solver¶

```
# Initialize yPrime to 0 and call residual to get initial derivatives
y0 = np.hstack((rhou0, p_in, T_in, Yk_0, Zk_0))
yprime0 = np.zeros(n_var)
res = np.zeros(n_var)
residual(0, y0, yprime0, res)
yprime0 = -res
```

### Solve the system of DAEs using ida solver¶

```
solver = dae(
"ida",
residual,
first_step_size=1e-15,
atol=1e-14, # absolute tolerance for solution
rtol=1e-06, # relative tolerance for solution
algebraic_vars_idx=[np.arange(offset_Y + n_gas, offset_Z + n_surf, 1)],
max_steps=8000,
one_step_compute=True,
old_api=False, # forces use of new api (namedtuple)
)
distance = []
solution = []
state = solver.init_step(0.0, y0, yprime0)
# Note that here the variable t is an internal varible used in scikits. In this example, it represents
# the natural variable z, which corresponds to the axial distance inside the reactor.
while state.values.t < L:
distance.append(state.values.t)
solution.append(state.values.y)
state = solver.step(L)
distance = np.array(distance)
solution = np.array(solution)
print(state)
```

### Plot results¶

```
plt.rcParams["font.size"] = 14
f, ax = plt.subplots(3, 2, figsize=(12, 12), dpi=96)
# Plot gas pressure profile along the flow direction
ax[0, 0].plot(distance, solution[:, offset_p], color="C0")
ax[0, 0].set_xlabel("Distance (m)")
ax[0, 0].set_ylabel("Pressure (Pa)")
# Plot gas temperature profile along the flow direction
ax[0, 1].plot(distance, solution[:, offset_T], color="C1")
ax[0, 1].set_xlabel("Distance (m)")
ax[0, 1].set_ylabel("Temperature (K)")
# Plot major and minor gas species separately
minor_idx = []
major_idx = []
for j, name in enumerate(gas.species_names):
mean = np.mean(solution[:, offset_Y + j])
if mean <= 0.1:
minor_idx.append(j)
else:
major_idx.append(j)
# Plot mass fractions of the gas-phase species along the flow direction
# Major gas-phase species
for j in major_idx:
ax[1, 0].plot(distance, solution[:, offset_Y + j], label=gas.species_names[j])
ax[1, 0].legend(fontsize=12, loc="best")
ax[1, 0].set_xlabel("Distance (m)")
ax[1, 0].set_ylabel("Mass Fraction")
# Minor gas-phase species
for j in minor_idx:
ax[1, 1].plot(distance, solution[:, offset_Y + j], label=gas.species_names[j])
ax[1, 1].legend(fontsize=12, loc="best")
ax[1, 1].set_xlabel("Distance (m)")
ax[1, 1].set_ylabel("Mass Fraction")
# Plot major and minor surface species separately
minor_idx = []
major_idx = []
for j, name in enumerate(surf.species_names):
mean = np.mean(solution[:, offset_Z + j])
if mean <= 0.1:
minor_idx.append(j)
else:
major_idx.append(j)
# Plot the site fraction of the surface-phase species along the flow direction
# Major surf-phase species
for j in major_idx:
ax[2, 0].plot(distance, solution[:, offset_Z + j], label=surf.species_names[j])
ax[2, 0].legend(fontsize=12, loc="best")
ax[2, 0].set_xlabel("Distance (m)")
ax[2, 0].set_ylabel("Site Fraction")
# Minor surf-phase species
for j in minor_idx:
ax[2, 1].plot(distance, solution[:, offset_Z + j], label=surf.species_names[j])
ax[2, 1].legend(fontsize=12, loc="best")
ax[2, 1].set_xlabel("Distance (m)")
ax[2, 1].set_ylabel("Site Fraction")
f.tight_layout()
```

```
```