Add callback mechanism to TransientReactiveTransport

[ma-sadeghi]

Closes #2207.

Here's a working example:

import numpy as np
import openpnm as op
import matplotlib.pyplot as plt

Nx = 101
shape = [Nx, 1, 1]
spacing = 1/Nx * 5
net = op.network.Cubic(shape=shape, spacing=spacing)
air = op.phases.Air(network=net)
air["throat.diffusive_conductance"] = spacing * np.ones(net.Nt)
net["pore.volume"] = spacing**3

# Set up transient Fickian diffusion algorithm
tfd = op.algorithms.TransientFickianDiffusion(network=net, phase=air)
tfd.set_value_BC(net.pores("left"), 0)
tfd.set_value_BC(net.pores("right"), 0)

# Define a pulse signal
def pulse(t, y):
    if 0 <= t <= 0.05:
        y[net.Np//2] = 1.0

# Add the pulse signal to the algorithm as a callback
tfd.set_callback(pulse)

# Solve the transient algorithm
c0 = np.zeros(tfd.Np)
tspan = [0, 0.4]
sol = tfd.run(x0=c0, tspan=tspan)

# Plot c vs. time
tout = np.linspace(tspan[0], tspan[1], 10)
fig, ax = plt.subplots()
for i, t in enumerate(tout):
    ax.plot(sol(t), label=f"{t:.2f} (s)")
ax.legend()
ax.set_title("Dissipation of a pulse signal , c(x=0,L) = 0")
ax.set_xlabel("distance (m)")
ax.set_ylabel("concentration (mol/m$^3$)")

[codecov]

Codecov Report

Merging #2254 (f5264f5) into dev (31f6b26) will decrease coverage by 0.0%.
The diff coverage is 88.8%.

Additional details and impacted files

@@           Coverage Diff           @@
##             dev   #2254     +/-   ##
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- Coverage   89.8%   89.8%   -0.1%     
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  Files        145     145             
  Lines       8405    8414      +9     
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+ Hits        7555    7563      +8     
- Misses       850     851      +1