## Solute Diffusion

This benchmark is available as a Jupyter notebook: TH2M/H2/diffusion/diffusion.ipynb.

# 1D Linear Diffusion

## Analytical Solution

The solution of the diffusion equation for a point x in time t reads:

$$c(x,t) = \left(c_0-c_i\right)\operatorname{erfc}\left(\frac{x}{\sqrt{4Dt}}\right)+c_i$$

where $$c$$ is the concentration of a solute in mol$$\cdot$$m$$^{-3}$$, $$c_i$$ and $$c_b$$ are initial and boundary concentrations; $$D$$ is the diffusion coefficient of the solute in water, x and t are location and time of solution.

import numpy as np
from scipy.special import erfc

# Analytical solution of the diffusion equation
def Diffusion(x,t):
if type(t) != int and type(t) != np.float64 and type(t) != float:
# In order to avoid a division by zero, the time field is increased
# by a small time unit at the start time (t=0). This should have no
# effect on the result.
tiny = np.finfo(np.float64).tiny
t[t < tiny] = tiny

d = np.sqrt(4*D*t)
e = (c_b - c_i)*erfc(x/d)+c_i
return e

# Utility-function transforming mass fraction into conctration
def concentration(xm_WL):
xm_CL = 1. - xm_WL
return xm_CL / beta_c

### Material properties and problem specification

# Henry-coefficient and compressibility of solution
H = 7.65e-6
beta_c = 2.e-6

# Diffusion coefficient
D = 1.0e-9

# Boundary and initial gas pressures
pGR_b = 9e5
pGR_i = 1e5

# Boundary and initial concentration
c_b = concentration(1. - (beta_c*H*pGR_b))
c_i = concentration(1. - (beta_c*H*pGR_i))

## Numerical Solution

import os

out_dir = os.environ.get('OGS_TESTRUNNER_OUT_DIR', '_out')
if not os.path.exists(out_dir):
os.makedirs(out_dir)
from ogs6py.ogs import OGS

model=OGS(INPUT_FILE="diffusion.prj", PROJECT_FILE=f"{out_dir}/modified.prj")
model.replace_text(1e7, xpath="./time_loop/processes/process/time_stepping/t_end")
model.replace_text(5e4, xpath="./time_loop/processes/process/time_stepping/timesteps/pair/delta_t")
# Write every timestep
model.replace_text(1, xpath="./time_loop/output/timesteps/pair/each_steps")
model.write_input()

# Run OGS
model.run_model(logfile=f"{out_dir}/out.txt", args=f"-o {out_dir} -m .")
OGS finished with project file /var/lib/gitlab-runner/builds/vZ6vnZiU/0/ogs/build/release-all/Tests/Data/TH2M/H/diffusion/diffusion/modified.prj.
Execution took 72.88334250450134 s

 #Colors
cls1 = ['#4a001e', '#731331', '#9f2945', '#cc415a', '#e06e85', '#ed9ab0']
cls2 = ['#0b194c', '#163670', '#265191', '#2f74b3', '#5d94cb', '#92b2de']
import vtuIO

pvdfile = vtuIO.PVDIO(f"{out_dir}/result_diffusion.pvd", dim=2)

# Get all written timesteps
time = pvdfile.timesteps

# Select individual timesteps for c vs. x plots for plotting
time_steps = [1e6, 2e6, 4e6, 6e6, 8e6, 1e7]

# 'Continuous' space axis for c vs. x plots for plotting
length = np.linspace(0,1.0,101)

# Draws a line through the domain for sampling results
x_axis=[(i,0,0) for i in length]

# Discrete locations for c vs. t plots
location = [0.01,0.05,0.1,0.2,0.5,1.0]
WARNING: Default interpolation backend changed to VTK. This might result in
slight changes of interpolated values if defaults are/were used.

 # The sample locations have to be converted into a 'dict' for vtuIO
observation_points = dict(('x='+str(x),(x,0.0,0.0)) for x in location)
# Samples concentration field at the observation points for all timesteps

c_over_t_at_x = pvdfile.read_time_series('xmWL', observation_points)
for key in c_over_t_at_x:
x = c_over_t_at_x[key];
c_over_t_at_x[key] = concentration(x)

# Samples concentration field along the domain at certain timesteps
c_over_x_at_t = []
for t in range(0,len(time_steps)):
c_over_x_at_t.append(concentration(pvdfile.read_set_data(time_steps[t], "xmWL", pointsetarray=x_axis)))
import matplotlib.pyplot as plt
plt.rcParams['figure.figsize'] = (14, 4)

# Plot of concentration vs. time at different locations
fig1, (ax1, ax2) = plt.subplots(1, 2)

ax1.set_xlabel("$t$ / s", fontsize=12)
ax1.set_ylabel("$c$ / mol m$^{-3}$", fontsize=12)

ax2.set_xlabel("$t$ / s", fontsize=12)
ax2.set_ylabel("$\epsilon_\mathrm{abs}$ / mol m$^{-3}$", fontsize=12)

label_x = []
for key, c in c_over_t_at_x.items():
x = observation_points[key][0]
label_x.append(key+r" m")
# numerical solution
ax1.plot(time, c_over_t_at_x[key], color=cls1[location.index(x)], linewidth=3,
linestyle="--")
# analytical solution
ax1.plot(time, Diffusion(x,time), color=cls1[location.index(x)], linewidth=2,
linestyle="-")
# absolute error
err_abs = Diffusion(x,time) - c_over_t_at_x[key]
ax2.plot(time, err_abs, color=cls1[location.index(x)], linewidth=1, linestyle="-", label=key+r" m")

# Hack to force a custom legend:
from matplotlib.lines import Line2D
custom_lines = []

for i in range(0,6):
custom_lines.append(Line2D([0], [0], color=cls1[i], lw=4))

custom_lines.append(Line2D([0], [0], color='black', lw=3, linestyle="--"))
custom_lines.append(Line2D([0], [0], color='black', lw=2, linestyle="-"))
label_x.append('OGS-TH2M')
label_x.append('analytical')

ax1.legend(custom_lines, label_x, loc='right')
ax2.legend()
fig1.savefig(f"{out_dir}/diffusion_c_vs_t.pdf")

# Plot of concentration vs. location at different times
fig1, (ax1, ax2) = plt.subplots(1, 2)

ax1.set_xlabel("$x$ / m", fontsize=12)
ax1.set_ylabel("$c$ / mol m$^{-3}$", fontsize=12)
ax1.set_xlim(0,0.4)

ax2.set_xlabel("$x$ / m", fontsize=12)
ax2.set_ylabel("$\epsilon$ / mol $m^{-3}$", fontsize=12)
ax2.set_xlim(0,0.4)

# Plot concentration over domain at five moments
label_t = []
for t in range(0,len(time_steps)):
s = r"$t=$"+str(time_steps[t]/1e6)+"$\,$Ms"
label_t.append(s)
# numerical solution
ax1.plot(length, c_over_x_at_t[t], color=cls2[t], linewidth=3, linestyle="--")
# analytical solution
ax1.plot(length, Diffusion(length,time_steps[t]),color=cls2[t], linewidth=2, \
linestyle="-")
# absolute error
err_abs = Diffusion(length,time_steps[t]) - c_over_x_at_t[t]
ax2.plot(length, err_abs, color=cls2[t], linewidth=1, linestyle="-", label=s)

custom_lines = []

for i in range(0,6):
custom_lines.append(Line2D([0], [0], color=cls2[i], lw=4))

custom_lines.append(Line2D([0], [0], color='black', lw=3, linestyle="--"))
custom_lines.append(Line2D([0], [0], color='black', lw=2, linestyle="-"))
label_t.append('OGS-TH2M')
label_t.append('analytical')

ax1.legend(custom_lines, label_t, loc='right')
ax2.legend()

fig1.savefig(f"{out_dir}/diffusion_c_vs_x.pdf")

The numerical approximation approaches the exact solution quite well. Deviations can be reduced if the resolution of the temporal discretisation is increased.

This article was written by Norbert Grunwald. If you are missing something or you find an error please let us know.
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