r.test() # sanity checks
nodes = r.get_nodes()
cci = picker(nodes[0, 0], nodes[0, 1], nodes[0, 2]) # collar cell index
""" Numerical solution """
start_time = timeit.default_timer()
x_, y_ = [], []
sx = s.getSolutionHead() # inital condition, solverbase.py
N = round(sim_time / dt)
t = 0.
for i in range(0, N):
rx = r.solve(rs_age + t, -trans * sinusoidal(t), sx[cci], sx, True,
wilting_point) # xylem_flux.py
x_.append(t)
y_.append(float(r.collar_flux(rs_age + t, rx, sx)))
fluxes = r.soilFluxes(rs_age + t, rx, sx, False)
s.setSource(fluxes) # richards.py
s.solve(dt)
sx = s.getSolutionHead() # richards.py
min_sx, min_rx, max_sx, max_rx = np.min(sx), np.min(rx), np.max(
sx), np.max(rx)
n = round(float(i) / float(N) * 100.)
print("[" + ''.join(["*"]) * n + ''.join([" "]) * (100 - n) +
"], [{:g}, {:g}] cm soil [{:g}, {:g}] cm root at {:g} days {:g}".
format(min_sx, max_sx, min_rx, max_rx, s.simTime, rx[0]))
t += dt
print("Coupled benchmark solved in ",
simtime = 14 # [day] for task b
""" root system """
rs = pb.MappedRootSystem()
path = "../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010" # Zea_mays_1_Leitner_2010
rs.readParameters(path + name + ".xml")
rs.initialize()
rs.simulate(simtime, False)
""" root problem """
r = XylemFluxPython(rs)
r.setKr([kr])
r.setKx([kz])
nodes = r.get_nodes()
soil_index = lambda x, y, z: 0
r.rs.setSoilGrid(soil_index)
""" Numerical solution """
rx = r.solve_dirichlet(0., p0, p_s, [p_s], True)
fluxes = r.segFluxes(simtime, rx, -200 * np.ones(rx.shape), False) # cm3/day
print("Transpiration", r.collar_flux(simtime, rx, [p_s]), "cm3/day")
""" plot results """
plt.plot(rx, nodes[:, 2], "r*")
plt.xlabel("Xylem pressure (cm)")
plt.ylabel("Depth (m)")
plt.title("Xylem matric potential (cm)")
plt.show()
""" Additional vtk plot """
ana = pb.SegmentAnalyser(r.rs)
ana.addData("rx", rx)
ana.addData("fluxes", np.maximum(fluxes, -1.e-3)) # cut off for vizualisation
vp.plot_roots(ana, "rx", "Xylem matric potential (cm)") # "fluxes"
cci = picker(nodes[0, 0], nodes[0, 1], nodes[0, 2]) # collar cell index
""" Numerical solution """
start_time = timeit.default_timer()
x_, y_ = [], []
sx = s.getSolutionHead() # inital condition, solverbase.py
N = round(sim_time / dt)
t = 0.
for i in range(0, N):
rs.simulate(dt)
rx = r.solve(rs_age + t, -trans * sinusoidal(t), sx[cci], sx, True,
wilting_point) # xylem_flux.py
x_.append(t)
y_.append(float(r.collar_flux(rs_age + t, rx,
sx))) # exact root collar flux
fluxes = r.soilFluxes(rs_age + t, rx, sx, False)
s.setSource(fluxes) # richards.py
s.solve(dt)
sx = s.getSolutionHead() # richards.py
min_sx, min_rx, max_sx, max_rx = np.min(sx), np.min(rx), np.max(
sx), np.max(rx)
n = round(float(i) / float(N) * 100.)
print("[" + ''.join(["*"]) * n + ''.join([" "]) * (100 - n) +
"], [{:g}, {:g}] cm soil [{:g}, {:g}] cm root at {:g} days {:g}".
format(min_sx, max_sx, min_rx, max_rx, s.simTime, rx[0]))
t += dt
print("Coupled benchmark solved in ",
soil_index = lambda x, y, z: int(-10 * z
) # maps to p_s (hydrostatic equilibirum)
rs.setSoilGrid(soil_index)
path = "../../../modelparameter/rootsystem/"
name = "Anagallis_femina_Leitner_2010" # Zea_mays_1_Leitner_2010
rs.setSeed(1)
rs.readParameters(path + name + ".xml")
rs.initialize()
rs.simulate(simtime, False)
p_s = np.linspace(-200, -400, 2001) # 2 meter down, resolution in mm
""" set up xylem parameters """
r = XylemFluxPython(rs)
r.setKr([kr]) # or use setKrTables, see XylemFlux.h
r.setKx([kz])
""" numerical solution of transpiration -1 cm3/day"""
rx = r.solve_neumann(
simtime, -1, p_s,
True) # True: matric potential given per cell (not per segment)
print("solved")
fluxes = r.segFluxes(simtime, rx, p_s, False,
True) # cm3/day (double simTime, rx, sx, approx, cells
print("Transpiration", r.collar_flux(simtime, rx, p_s), np.sum(fluxes),
"cm3/day")
suf = np.array(fluxes) / -1. # [1]
""" Additional vtk plot """
ana = pb.SegmentAnalyser(r.rs)
ana.addData("SUF", np.minimum(suf, 1.e-2)) # cut off for vizualisation
vp.plot_roots(ana, "SUF", "Soil uptake fraction (cm3 day)") # "fluxes"
rs.getRootSystemParameter().seedPos.z = -0.1
rs.initialize()
rs.simulate(simtime, False)
""" set up xylem parameters """
r = XylemFluxPython(rs)
r.setKr([kr]) # or use setKrTables, see XylemFlux.h
r.setKx([kz])
""" numerical solution of transpiration -10000 cm3/day - very high to avoid numerical errors"""
rx = r.solve_neumann(
simtime, -10000, p_s,
True) # True: matric potential given per cell (not per segment)
print("solved")
fluxes = r.segFluxes(simtime, rx, p_s, False,
True) # cm3/day (double simTime, rx, sx, approx, cells
print("Transpiration", r.collar_flux(simtime, rx, p_s), np.sum(fluxes),
"cm3/day")
suf = np.array(fluxes) / -10000. # [1]
# # """ vtk plot """
# ana = pb.SegmentAnalyser(r.rs)
# ana.addData("SUF", suf) # cut off for vizualisation np.minimum(suf, 1.e-4)
# vp.plot_roots(ana, "SUF", "Soil uptake fraction (cm3 day)") # "fluxes"
print("Sum of suf", np.sum(suf), "from", np.min(suf), "to", np.max(suf))
""" 2. Equivalent soil water potential """
#nodes = r.get_nodes()
p_s = np.linspace(-14000, -10000, 3001)
p_s[0:10] = -300
# 3 meter down, resolution in mm, dry with moist top
soil_index = lambda x, y, z: int(-10 * z)